I: pbuilder: network access will be disabled during build
I: Current time: Fri Mar  7 02:55:38 -12 2025
I: pbuilder-time-stamp: 1741359338
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [libgoby-java_3.3.1+dfsg2-11.dsc]
I: copying [./libgoby-java_3.3.1+dfsg2.orig.tar.xz]
I: copying [./libgoby-java_3.3.1+dfsg2-11.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./libgoby-java_3.3.1+dfsg2-11.dsc: unsupported subcommand
dpkg-source: info: extracting libgoby-java in libgoby-java-3.3.1+dfsg2
dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2.orig.tar.xz
dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying protoc.patch
dpkg-source: info: applying adding_dependencies.patch
dpkg-source: info: applying using_jbzip2.patch
dpkg-source: info: applying adapting_to_old_fastutil.patch
dpkg-source: info: applying using_GeneratedMessageV3.patch
dpkg-source: info: applying using_commons-cli.patch
dpkg-source: info: applying using_correct_SamReader_api.patch
dpkg-source: info: applying inclusions_in_SplitTranscriptsMode.patch
dpkg-source: info: applying catch_IOException_LineIterator.patch
dpkg-source: info: applying computing_fisher_pvalue_hypergeom.patch
dpkg-source: info: applying exclude_not_runnable_tests.patch
dpkg-source: info: applying goby_script.patch
dpkg-source: info: applying path_of_goby_jar_for_Debian.patch
dpkg-source: info: applying jaxb_dependency.patch
dpkg-source: info: applying using_pcre2.patch
dpkg-source: info: applying omit_test_failing_randomly.patch
dpkg-source: info: applying adding_opens_arg_for_tests.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1194656/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='arm64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
  DISTRIBUTION='unstable'
  HOME='/root'
  HOST_ARCH='arm64'
  IFS=' 	
  '
  INVOCATION_ID='ff3aeadc58e54db5859688d733a88694'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='1194656'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.iiiaJM7S/pbuilderrc_yUNh --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iiiaJM7S/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc'
  SUDO_GID='109'
  SUDO_UID='104'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://192.168.101.4:3128'
I: uname -a
  Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Mar  4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1194656/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), maven-debian-helper, javahelper, default-jdk, ant, ant-contrib, libjbzip2-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-exec-java, libcommons-io-java, libcommons-lang-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libdistlib-java, liblog4j1.2-java, libexec-maven-plugin-java, libjaxb-api-java, libmaven-assembly-plugin-java, libmaven-antrun-plugin-java, libbuild-helper-maven-plugin-java, libmaven-dependency-plugin-java, libmaven-source-plugin-java, libmaven-javadoc-plugin-java, libprotobuf-java, libhtsjdk-java, libfastutil-java, protobuf-compiler, libjsap-java, libdsiutils-java, libicb-utils-java, libreflections-java, libpj-java, libprotobuf-dev, pkgconf, r-cran-rjava, libeasymock-java, junit4, testng, libpicard-java
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19897 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on maven-debian-helper; however:
  Package maven-debian-helper is not installed.
 pbuilder-satisfydepends-dummy depends on javahelper; however:
  Package javahelper is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk; however:
  Package default-jdk is not installed.
 pbuilder-satisfydepends-dummy depends on ant; however:
  Package ant is not installed.
 pbuilder-satisfydepends-dummy depends on ant-contrib; however:
  Package ant-contrib is not installed.
 pbuilder-satisfydepends-dummy depends on libjbzip2-java; however:
  Package libjbzip2-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-collections3-java; however:
  Package libcommons-collections3-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-configuration-java; however:
  Package libcommons-configuration-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-exec-java; however:
  Package libcommons-exec-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-io-java; however:
  Package libcommons-io-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-lang-java; however:
  Package libcommons-lang-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however:
  Package libcommons-logging-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-math-java; however:
  Package libcommons-math-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-cli-java; however:
  Package libcommons-cli-java is not installed.
 pbuilder-satisfydepends-dummy depends on libdistlib-java; however:
  Package libdistlib-java is not installed.
 pbuilder-satisfydepends-dummy depends on liblog4j1.2-java; however:
  Package liblog4j1.2-java is not installed.
 pbuilder-satisfydepends-dummy depends on libexec-maven-plugin-java; however:
  Package libexec-maven-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however:
  Package libjaxb-api-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-assembly-plugin-java; however:
  Package libmaven-assembly-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-antrun-plugin-java; however:
  Package libmaven-antrun-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libbuild-helper-maven-plugin-java; however:
  Package libbuild-helper-maven-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-dependency-plugin-java; however:
  Package libmaven-dependency-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-source-plugin-java; however:
  Package libmaven-source-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-javadoc-plugin-java; however:
  Package libmaven-javadoc-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libprotobuf-java; however:
  Package libprotobuf-java is not installed.
 pbuilder-satisfydepends-dummy depends on libhtsjdk-java; however:
  Package libhtsjdk-java is not installed.
 pbuilder-satisfydepends-dummy depends on libfastutil-java; however:
  Package libfastutil-java is not installed.
 pbuilder-satisfydepends-dummy depends on protobuf-compiler; however:
  Package protobuf-compiler is not installed.
 pbuilder-satisfydepends-dummy depends on libjsap-java; however:
  Package libjsap-java is not installed.
 pbuilder-satisfydepends-dummy depends on libdsiutils-java; however:
  Package libdsiutils-java is not installed.
 pbuilder-satisfydepends-dummy depends on libicb-utils-java; however:
  Package libicb-utils-java is not installed.
 pbuilder-satisfydepends-dummy depends on libreflections-java; however:
  Package libreflections-java is not installed.
 pbuilder-satisfydepends-dummy depends on libpj-java; however:
  Package libpj-java is not installed.
 pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however:
  Package libprotobuf-dev is not installed.
 pbuilder-satisfydepends-dummy depends on pkgconf; however:
  Package pkgconf is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-rjava; however:
  Package r-cran-rjava is not installed.
 pbuilder-satisfydepends-dummy depends on libeasymock-java; however:
  Package libeasymock-java is not installed.
 pbuilder-satisfydepends-dummy depends on junit4; however:
  Package junit4 is not installed.
 pbuilder-satisfydepends-dummy depends on testng; however:
  Package testng is not installed.
 pbuilder-satisfydepends-dummy depends on libpicard-java; however:
  Package libpicard-java is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  adwaita-icon-theme{a} ant{a} ant-contrib{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} gpgv{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbarclay-java{a} libblas3{a} libbrotli1{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcolord2{a} libcolt-free-java{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdsiutils-java{a} libdynaloader-functions-perl{a} libeasymock-java{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastutil-java{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgbm1{a} libgcrypt20{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicb-utils-java{a} libice6{a} libicu4j-java{a} libicu72{a} libidn2-0{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libjansi-java{a} libjavassist-java{a} libjaxb-api-java{a} libjaxen-java{a} libjbig0{a} libjboss-logging-java{a} libjboss-vfs-java{a} libjbzip2-java{a} libjcommander-java{a} libjetty9-java{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjsap-java{a} libjson-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblightcouch-java{a} libllvm19{a} liblog4j1.2-java{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven-source-plugin-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libpcsclite1{a} libpicard-java{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libpj-java{a} libpkgconf3{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} libreflections-java{a} librhino-java{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1t64{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} liburi-perl{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxom-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxss1{a} libxstream-java{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} mesa-libgallium{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sopv-gpgv{a} systemd{a} systemd-sysv{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg-utils gpg-wks-client krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpg-error-l10n libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjline3-java libjson-perl libkmod2 libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl libnss-systemd librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian linux-sysctl-defaults lynx lzip mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc publicsuffix python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended strace systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 
0 packages upgraded, 465 newly installed, 0 to remove and 0 not upgraded.
Need to get 374 MB of archives. After unpacking 1015 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 257.4-1 [1909 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 libapparmor1 arm64 4.1.0~beta5-3 [42.6 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 systemd arm64 257.4-1 [2922 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 systemd-sysv arm64 257.4-1 [61.8 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-1 [169 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 dbus-bin arm64 1.16.2-1 [78.2 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 dbus-session-bus-common all 1.16.2-1 [51.6 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 dbus-daemon arm64 1.16.2-1 [151 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 dbus-system-bus-common all 1.16.2-1 [52.7 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 dbus arm64 1.16.2-1 [70.1 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 media-types all 12.0.0 [28.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB]
Get: 22 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB]
Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB]
Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-1 [745 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.2-2 [28.1 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB]
Get: 32 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB]
Get: 33 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 34 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 35 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 36 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 37 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 38 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 39 http://deb.debian.org/debian unstable/main arm64 libpam-systemd arm64 257.4-1 [272 kB]
Get: 40 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB]
Get: 41 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 42 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B]
Get: 43 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 44 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0050 [42.7 kB]
Get: 45 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB]
Get: 46 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.83.5-1 [1422 kB]
Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB]
Get: 49 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b2 [756 kB]
Get: 50 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB]
Get: 51 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1 [274 kB]
Get: 52 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB]
Get: 53 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB]
Get: 55 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB]
Get: 56 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB]
Get: 57 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get: 58 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [131 kB]
Get: 59 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 4.17.5+ds-3 [51.1 kB]
Get: 60 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-2 [11.8 kB]
Get: 61 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 48~beta-3 [504 kB]
Get: 62 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB]
Get: 63 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B]
Get: 64 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get: 65 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.36-1 [102 kB]
Get: 66 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.109-1 [1291 kB]
Get: 67 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.1-1 [55.3 kB]
Get: 68 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.6+7-1 [40.6 MB]
Get: 69 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B]
Get: 70 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB]
Get: 71 http://deb.debian.org/debian unstable/main arm64 ant-contrib all 1.0~b3+svn177-12 [262 kB]
Get: 72 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.55.2-1 [170 kB]
Get: 73 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB]
Get: 74 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 75 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 76 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB]
Get: 77 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 78 http://deb.debian.org/debian unstable/main arm64 dbus-user-session arm64 1.16.2-1 [51.5 kB]
Get: 79 http://deb.debian.org/debian unstable/main arm64 libdconf1 arm64 0.40.0-5 [40.4 kB]
Get: 80 http://deb.debian.org/debian unstable/main arm64 dconf-service arm64 0.40.0-5 [30.9 kB]
Get: 81 http://deb.debian.org/debian unstable/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [27.3 kB]
Get: 82 http://deb.debian.org/debian unstable/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB]
Get: 83 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 84 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB]
Get: 85 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 86 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 87 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 88 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 89 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 90 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 91 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 92 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 93 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 94 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 95 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 96 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.55.2-1 [50.1 kB]
Get: 97 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get: 98 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB]
Get: 99 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get: 100 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 101 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB]
Get: 102 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB]
Get: 103 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB]
Get: 104 http://deb.debian.org/debian unstable/main arm64 libatspi2.0-0t64 arm64 2.55.2-1 [73.1 kB]
Get: 105 http://deb.debian.org/debian unstable/main arm64 libatk-bridge2.0-0t64 arm64 2.55.2-1 [64.5 kB]
Get: 106 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB]
Get: 107 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get: 108 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 109 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 110 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB]
Get: 111 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB]
Get: 112 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB]
Get: 113 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB]
Get: 114 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB]
Get: 115 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB]
Get: 116 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get: 117 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB]
Get: 118 http://deb.debian.org/debian unstable/main arm64 libcloudproviders0 arm64 0.3.6-1+b1 [27.7 kB]
Get: 119 http://deb.debian.org/debian unstable/main arm64 libcolord2 arm64 1.4.7-3 [130 kB]
Get: 120 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-16 [112 kB]
Get: 121 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-16 [43.3 kB]
Get: 122 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-16 [46.7 kB]
Get: 123 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB]
Get: 124 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB]
Get: 125 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB]
Get: 126 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB]
Get: 127 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB]
Get: 128 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get: 129 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB]
Get: 130 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
Get: 131 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB]
Get: 132 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB]
Get: 133 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB]
Get: 134 http://deb.debian.org/debian unstable/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB]
Get: 135 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB]
Get: 136 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get: 137 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB]
Get: 138 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2 [462 kB]
Get: 139 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB]
Get: 140 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB]
Get: 141 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB]
Get: 142 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB]
Get: 143 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB]
Get: 144 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB]
Get: 145 http://deb.debian.org/debian unstable/main arm64 libwayland-client0 arm64 1.23.1-3 [26.1 kB]
Get: 146 http://deb.debian.org/debian unstable/main arm64 libwayland-cursor0 arm64 1.23.1-3 [11.7 kB]
Get: 147 http://deb.debian.org/debian unstable/main arm64 libwayland-egl1 arm64 1.23.1-3 [5952 B]
Get: 148 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB]
Get: 149 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b4 [20.5 kB]
Get: 150 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.3-1 [39.3 kB]
Get: 151 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB]
Get: 152 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b3 [16.1 kB]
Get: 153 http://deb.debian.org/debian unstable/main arm64 xkb-data all 2.42-1 [790 kB]
Get: 154 http://deb.debian.org/debian unstable/main arm64 libxkbcommon0 arm64 1.7.0-2 [106 kB]
Get: 155 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1+b3 [35.9 kB]
Get: 156 http://deb.debian.org/debian unstable/main arm64 libgtk-3-common all 3.24.48-4 [4873 kB]
Get: 157 http://deb.debian.org/debian unstable/main arm64 libgtk-3-0t64 arm64 3.24.48-4 [2562 kB]
Get: 158 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB]
Get: 159 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.124-1 [8180 B]
Get: 160 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.124-1 [38.2 kB]
Get: 161 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [241 kB]
Get: 162 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB]
Get: 163 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB]
Get: 164 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB]
Get: 165 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB]
Get: 166 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b4 [19.2 kB]
Get: 167 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.124-1 [21.8 kB]
Get: 168 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB]
Get: 169 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB]
Get: 170 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-1+b1 [23.3 MB]
Get: 171 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get: 172 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.0-10+b1 [34.3 kB]
Get: 173 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB]
Get: 174 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB]
Get: 175 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3-1+b3 [9104 B]
Get: 176 http://deb.debian.org/debian unstable/main arm64 mesa-libgallium arm64 25.0.1-1 [8022 kB]
Get: 177 http://deb.debian.org/debian unstable/main arm64 libwayland-server0 arm64 1.23.1-3 [33.7 kB]
Get: 178 http://deb.debian.org/debian unstable/main arm64 libgbm1 arm64 25.0.1-1 [43.4 kB]
Get: 179 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.4.304.0-1 [126 kB]
Get: 180 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 25.0.1-1 [45.1 kB]
Get: 181 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 25.0.1-1 [142 kB]
Get: 182 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB]
Get: 183 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB]
Get: 184 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.13-1 [21.1 kB]
Get: 185 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.13-1+b1 [338 kB]
Get: 186 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB]
Get: 187 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB]
Get: 188 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.5-1 [25.7 kB]
Get: 189 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre arm64 21.0.6+7-1 [193 kB]
Get: 190 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.21-76 [1068 B]
Get: 191 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk-headless arm64 21.0.6+7-1 [81.9 MB]
Get: 192 http://deb.debian.org/debian unstable/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B]
Get: 193 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk arm64 21.0.6+7-1 [3438 kB]
Get: 194 http://deb.debian.org/debian unstable/main arm64 default-jdk arm64 2:1.21-76 [1076 B]
Get: 195 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB]
Get: 196 http://deb.debian.org/debian unstable/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB]
Get: 197 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB]
Get: 198 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.2.46-3 [114 kB]
Get: 199 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB]
Get: 200 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB]
Get: 201 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB]
Get: 202 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB]
Get: 203 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-2 [22.8 kB]
Get: 204 http://deb.debian.org/debian unstable/main arm64 dirmngr arm64 2.2.46-3 [345 kB]
Get: 205 http://deb.debian.org/debian unstable/main arm64 gnupg-l10n all 2.2.46-3 [703 kB]
Get: 206 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.2.46-3 [483 kB]
Get: 207 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.3.1-2 [83.5 kB]
Get: 208 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.2.46-3 [232 kB]
Get: 209 http://deb.debian.org/debian unstable/main arm64 gpgsm arm64 2.2.46-3 [232 kB]
Get: 210 http://deb.debian.org/debian unstable/main arm64 gnupg all 2.2.46-3 [376 kB]
Get: 211 http://deb.debian.org/debian unstable/main arm64 gpgv arm64 2.2.46-3 [201 kB]
Get: 212 http://deb.debian.org/debian unstable/main arm64 sopv-gpgv all 0.1.1-1 [10.7 kB]
Get: 213 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 214 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 215 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 216 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B]
Get: 217 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB]
Get: 218 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 219 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get: 220 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB]
Get: 221 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB]
Get: 222 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get: 223 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB]
Get: 224 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB]
Get: 225 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 226 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 227 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 228 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 229 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 230 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 231 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 232 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get: 233 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get: 234 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get: 235 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB]
Get: 236 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB]
Get: 237 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 238 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB]
Get: 239 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 240 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 241 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get: 242 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get: 243 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 244 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B]
Get: 245 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB]
Get: 246 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB]
Get: 247 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB]
Get: 248 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get: 249 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get: 250 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 251 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.78-1 [183 kB]
Get: 252 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB]
Get: 253 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-7 [121 kB]
Get: 254 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.25.5 [1058 kB]
Get: 255 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB]
Get: 256 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.80 [9692 B]
Get: 257 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.80 [80.4 kB]
Get: 258 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB]
Get: 259 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-5 [350 kB]
Get: 260 http://deb.debian.org/debian unstable/main arm64 libapiguardian-java all 1.1.2-1 [4656 B]
Get: 261 http://deb.debian.org/debian unstable/main arm64 libopentest4j-java all 1.2.0-4 [9516 B]
Get: 262 http://deb.debian.org/debian unstable/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get: 263 http://deb.debian.org/debian unstable/main arm64 libpicocli-java all 4.6.2-2 [390 kB]
Get: 264 http://deb.debian.org/debian unstable/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get: 265 http://deb.debian.org/debian unstable/main arm64 junit5 all 5.10.3-1 [2459 kB]
Get: 266 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 267 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B]
Get: 268 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B]
Get: 269 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.7.1-1 [391 kB]
Get: 270 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B]
Get: 271 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 272 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB]
Get: 273 http://deb.debian.org/debian unstable/main arm64 libfreemarker-java all 2.3.32-2 [1546 kB]
Get: 274 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get: 275 http://deb.debian.org/debian unstable/main arm64 libjoptsimple-java all 5.0.4-7 [73.7 kB]
Get: 276 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.18.0-1 [304 kB]
Get: 277 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 278 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 279 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 280 http://deb.debian.org/debian unstable/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB]
Get: 281 http://deb.debian.org/debian unstable/main arm64 libmongodb-java all 3.6.3-2 [1901 kB]
Get: 282 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 283 http://deb.debian.org/debian unstable/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB]
Get: 284 http://deb.debian.org/debian unstable/main arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB]
Get: 285 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB]
Get: 286 http://deb.debian.org/debian unstable/main arm64 libbsh-java all 2.0b4-20 [291 kB]
Get: 287 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.18.0-1 [509 kB]
Get: 288 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB]
Get: 289 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get: 290 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 291 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 292 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-12 [26.6 kB]
Get: 293 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB]
Get: 294 http://deb.debian.org/debian unstable/main arm64 libguice-java all 5.1.0-1 [932 kB]
Get: 295 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 43-2 [6252 B]
Get: 296 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 297 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 298 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB]
Get: 299 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 300 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 301 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 302 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB]
Get: 303 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 304 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B]
Get: 305 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-4 [55.3 kB]
Get: 306 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB]
Get: 307 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB]
Get: 308 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB]
Get: 309 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 310 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-2 [35.1 kB]
Get: 311 http://deb.debian.org/debian unstable/main arm64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB]
Get: 312 http://deb.debian.org/debian unstable/main arm64 libbyte-buddy-java all 1.14.19-1 [4756 kB]
Get: 313 http://deb.debian.org/debian unstable/main arm64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB]
Get: 314 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get: 315 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB]
Get: 316 http://deb.debian.org/debian unstable/main arm64 libcommons-collections4-java all 4.4-2 [682 kB]
Get: 317 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB]
Get: 318 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 319 http://deb.debian.org/debian unstable/main arm64 libcommons-configuration-java all 1.10-7 [348 kB]
Get: 320 http://deb.debian.org/debian unstable/main arm64 libcommons-digester-java all 1.8.1-7 [138 kB]
Get: 321 http://deb.debian.org/debian unstable/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get: 322 http://deb.debian.org/debian unstable/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 323 http://deb.debian.org/debian unstable/main arm64 libcommons-math-java all 2.2-9 [933 kB]
Get: 324 http://deb.debian.org/debian unstable/main arm64 libcommons-math3-java all 3.6.1-4 [2040 kB]
Get: 325 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 326 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.1-1+b1 [28.7 kB]
Get: 327 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.7-1 [6476 B]
Get: 328 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.7-1 [87.6 kB]
Get: 329 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB]
Get: 330 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 331 http://deb.debian.org/debian unstable/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB]
Get: 332 http://deb.debian.org/debian unstable/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get: 333 http://deb.debian.org/debian unstable/main arm64 libcommons-text-java all 1.13.0-1 [228 kB]
Get: 334 http://deb.debian.org/debian unstable/main arm64 libcommons-validator-java all 1:1.9.0-1 [191 kB]
Get: 335 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB]
Get: 336 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB]
Get: 337 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB]
Get: 338 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB]
Get: 339 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB]
Get: 340 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-3 [339 kB]
Get: 341 http://deb.debian.org/debian unstable/main arm64 libdistlib-java all 1.0-5 [72.5 kB]
Get: 342 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-5 [214 kB]
Get: 343 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB]
Get: 344 http://deb.debian.org/debian unstable/main arm64 libdoxia-core-java all 2.0.0-1 [149 kB]
Get: 345 http://deb.debian.org/debian unstable/main arm64 libplexus-xml-java all 3.0.1-2 [93.7 kB]
Get: 346 http://deb.debian.org/debian unstable/main arm64 libdoxia-java all 2.0.0-1 [113 kB]
Get: 347 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-api-java all 4.0.0-1 [6724 B]
Get: 348 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-9 [132 kB]
Get: 349 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 350 http://deb.debian.org/debian unstable/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB]
Get: 351 http://deb.debian.org/debian unstable/main arm64 velocity all 1.7-7 [431 kB]
Get: 352 http://deb.debian.org/debian unstable/main arm64 libplexus-velocity-java all 1.2-4 [9676 B]
Get: 353 http://deb.debian.org/debian unstable/main arm64 liboro-java all 2.0.8a-14 [70.5 kB]
Get: 354 http://deb.debian.org/debian unstable/main arm64 libvelocity-tools-java all 2.0-9 [311 kB]
Get: 355 http://deb.debian.org/debian unstable/main arm64 libdoxia-sitetools-java all 2.0.0-1 [176 kB]
Get: 356 http://deb.debian.org/debian unstable/main arm64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB]
Get: 357 http://deb.debian.org/debian unstable/main arm64 libxpp3-java all 1.1.4c-4 [294 kB]
Get: 358 http://deb.debian.org/debian unstable/main arm64 libxstream-java all 1.4.21-1 [567 kB]
Get: 359 http://deb.debian.org/debian unstable/main arm64 libjsap-java all 2.1-5 [102 kB]
Get: 360 http://deb.debian.org/debian unstable/main arm64 liblogback-java all 1:1.2.11-6 [701 kB]
Get: 361 http://deb.debian.org/debian unstable/main arm64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB]
Get: 362 http://deb.debian.org/debian unstable/main arm64 libobjenesis-java all 3.4-2 [41.3 kB]
Get: 363 http://deb.debian.org/debian unstable/main arm64 libeasymock-java all 5.5.0-1 [134 kB]
Get: 364 http://deb.debian.org/debian unstable/main arm64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 365 http://deb.debian.org/debian unstable/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB]
Get: 366 http://deb.debian.org/debian unstable/main arm64 libezmorph-java all 1.0.6-4 [75.9 kB]
Get: 367 http://deb.debian.org/debian unstable/main arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B]
Get: 368 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-17 [361 kB]
Get: 369 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get: 370 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 371 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 372 http://deb.debian.org/debian unstable/main arm64 libxom-java all 1.3.9-1 [174 kB]
Get: 373 http://deb.debian.org/debian unstable/main arm64 libjson-java all 3.1.0+dfsg-2 [142 kB]
Get: 374 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto16 arm64 3.6.2-3 [341 kB]
Get: 375 http://deb.debian.org/debian unstable/main arm64 libmbedx509-7 arm64 3.6.2-3 [146 kB]
Get: 376 http://deb.debian.org/debian unstable/main arm64 libmbedtls21 arm64 3.6.2-3 [222 kB]
Get: 377 http://deb.debian.org/debian unstable/main arm64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB]
Get: 378 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.0.9+dfsg-2 [1110 kB]
Get: 379 http://deb.debian.org/debian unstable/main arm64 libncbi-ngs3 arm64 3.0.9+dfsg-7+b2 [143 kB]
Get: 380 http://deb.debian.org/debian unstable/main arm64 libngs-jni arm64 3.0.9+dfsg-7+b2 [25.9 kB]
Get: 381 http://deb.debian.org/debian unstable/main arm64 libngs-java arm64 3.0.9+dfsg-7+b2 [112 kB]
Get: 382 http://deb.debian.org/debian unstable/main arm64 librhino-java all 1.7.15-1 [1382 kB]
Get: 383 http://deb.debian.org/debian unstable/main arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB]
Get: 384 http://deb.debian.org/debian unstable/main arm64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB]
Get: 385 http://deb.debian.org/debian unstable/main arm64 libicu4j-java all 73.2-1 [16.4 MB]
Get: 386 http://deb.debian.org/debian unstable/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB]
Get: 387 http://deb.debian.org/debian unstable/main arm64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB]
Get: 388 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB]
Get: 389 http://deb.debian.org/debian unstable/main arm64 libjansi-java all 2.4.1-2 [100 kB]
Get: 390 http://deb.debian.org/debian unstable/main arm64 libjavassist-java all 1:3.27.0-1 [731 kB]
Get: 391 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 392 http://deb.debian.org/debian unstable/main arm64 libjboss-logging-java all 3.5.3-1 [56.2 kB]
Get: 393 http://deb.debian.org/debian unstable/main arm64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB]
Get: 394 http://deb.debian.org/debian unstable/main arm64 libjbzip2-java all 0.9.1-8 [42.7 kB]
Get: 395 http://deb.debian.org/debian unstable/main arm64 libjcommander-java all 1.71-4 [73.0 kB]
Get: 396 http://deb.debian.org/debian unstable/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 397 http://deb.debian.org/debian unstable/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 398 http://deb.debian.org/debian unstable/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 399 http://deb.debian.org/debian unstable/main arm64 libjetty9-java all 9.4.57-1 [2965 kB]
Get: 400 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 401 http://deb.debian.org/debian unstable/main arm64 libjtidy-java all 7+svn20110807-6 [251 kB]
Get: 402 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB]
Get: 403 http://deb.debian.org/debian unstable/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB]
Get: 404 http://deb.debian.org/debian unstable/main arm64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB]
Get: 405 http://deb.debian.org/debian unstable/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB]
Get: 406 http://deb.debian.org/debian unstable/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB]
Get: 407 http://deb.debian.org/debian unstable/main arm64 libmaven-filtering-java all 3.4.0-1 [51.4 kB]
Get: 408 http://deb.debian.org/debian unstable/main arm64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB]
Get: 409 http://deb.debian.org/debian unstable/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB]
Get: 410 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B]
Get: 411 http://deb.debian.org/debian unstable/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB]
Get: 412 http://deb.debian.org/debian unstable/main arm64 libqdox2-java all 2.0.3-1 [296 kB]
Get: 413 http://deb.debian.org/debian unstable/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
Get: 414 http://deb.debian.org/debian unstable/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB]
Get: 415 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-analyzer-java all 1.15.1-1 [38.5 kB]
Get: 416 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-tree-java all 3.3.0-1 [35.0 kB]
Get: 417 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-impl-java all 4.0.0-1 [17.6 kB]
Get: 418 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-plugin-java all 3.8.1-1 [191 kB]
Get: 419 http://deb.debian.org/debian unstable/main arm64 libmaven-invoker-java all 3.3.0-1 [29.1 kB]
Get: 420 http://deb.debian.org/debian unstable/main arm64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB]
Get: 421 http://deb.debian.org/debian unstable/main arm64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB]
Get: 422 http://deb.debian.org/debian unstable/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB]
Get: 423 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B]
Get: 424 http://deb.debian.org/debian unstable/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B]
Get: 425 http://deb.debian.org/debian unstable/main arm64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB]
Get: 426 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB]
Get: 427 http://deb.debian.org/debian unstable/main arm64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB]
Get: 428 http://deb.debian.org/debian unstable/main arm64 libmaven-site-plugin-java all 3.21.0-1 [106 kB]
Get: 429 http://deb.debian.org/debian unstable/main arm64 libmaven-source-plugin-java all 3.3.1-1 [27.7 kB]
Get: 430 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b1 [16.6 kB]
Get: 431 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b1 [16.3 kB]
Get: 432 http://deb.debian.org/debian unstable/main arm64 libpicard-java all 3.3.0+dfsg-2 [1778 kB]
Get: 433 http://deb.debian.org/debian unstable/main arm64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB]
Get: 434 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get: 435 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 436 http://deb.debian.org/debian unstable/main arm64 libprotobuf32t64 arm64 3.21.12-10+b6 [859 kB]
Get: 437 http://deb.debian.org/debian unstable/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b6 [250 kB]
Get: 438 http://deb.debian.org/debian unstable/main arm64 libprotobuf-dev arm64 3.21.12-10+b6 [1263 kB]
Get: 439 http://deb.debian.org/debian unstable/main arm64 libprotobuf-java all 3.21.12-10 [1268 kB]
Get: 440 http://deb.debian.org/debian unstable/main arm64 libprotoc32t64 arm64 3.21.12-10+b6 [790 kB]
Get: 441 http://deb.debian.org/debian unstable/main arm64 libreflections-java all 0.10.2+dfsg-2 [125 kB]
Get: 442 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB]
Get: 443 http://deb.debian.org/debian unstable/main arm64 libsurefire-java all 2.22.3-3 [1284 kB]
Get: 444 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB]
Get: 445 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 446 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get: 447 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB]
Get: 448 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB]
Get: 449 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB]
Get: 450 http://deb.debian.org/debian unstable/main arm64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 451 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get: 452 http://deb.debian.org/debian unstable/main arm64 libxml2-utils arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [97.8 kB]
Get: 453 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB]
Get: 454 http://deb.debian.org/debian unstable/main arm64 maven all 3.9.9-1 [19.7 kB]
Get: 455 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB]
Get: 456 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB]
Get: 457 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.7 [108 kB]
Get: 458 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get: 459 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get: 460 http://deb.debian.org/debian unstable/main arm64 protobuf-compiler arm64 3.21.12-10+b6 [84.9 kB]
Get: 461 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-14+b1 [227 kB]
Get: 462 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 463 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.3-1 [28.1 MB]
Get: 464 http://deb.debian.org/debian unstable/main arm64 r-cran-rjava arm64 1.0-11-1+b1 [709 kB]
Get: 465 http://deb.debian.org/debian unstable/main arm64 testng all 6.9.12-4 [795 kB]
Fetched 374 MB in 2s (152 MB/s)
Preconfiguring packages ...
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Setting up libsystemd-shared:arm64 (257.4-1) ...
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Unpacking systemd (257.4-1) ...
Setting up libapparmor1:arm64 (4.1.0~beta5-3) ...
Setting up systemd (257.4-1) ...
Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'.

Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'.

Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'.

Initializing machine ID from random generator.

Creating group 'systemd-journal' with GID 999.

Creating group 'systemd-network' with GID 998.

Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998.

/usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring.

Selecting previously unselected package systemd-sysv.
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Unpacking systemd-sysv (257.4-1) ...
Selecting previously unselected package libdbus-1-3:arm64.
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Unpacking dbus-bin (1.16.2-1) ...
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Unpacking dbus-session-bus-common (1.16.2-1) ...
Selecting previously unselected package libexpat1:arm64.
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Unpacking libexpat1:arm64 (2.6.4-1) ...
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Unpacking dbus-daemon (1.16.2-1) ...
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Unpacking dbus (1.16.2-1) ...
Selecting previously unselected package libpipeline1:arm64.
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Unpacking libpipeline1:arm64 (1.5.8-1) ...
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Selecting previously unselected package libpython3.13-minimal:arm64.
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Unpacking python3.13-minimal (3.13.2-1) ...
Setting up libpython3.13-minimal:arm64 (3.13.2-1) ...
Setting up libexpat1:arm64 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.2-1) ...
Selecting previously unselected package python3-minimal.
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Selecting previously unselected package readline-common.
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Selecting previously unselected package libreadline8t64:arm64.
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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:arm64 (8.2-6) ...
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Setting up python3-minimal (3.13.2-2) ...
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Selecting previously unselected package openssl.
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Unpacking openssl (3.4.1-1) ...
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Unpacking ca-certificates (20241223) ...
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
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Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
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Unpacking file (1:5.45-3+b1) ...
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Unpacking gettext-base (0.23.1-1) ...
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Selecting previously unselected package groff-base.
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Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package libpam-systemd:arm64.
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Unpacking libpam-systemd:arm64 (257.4-1) ...
Selecting previously unselected package bsdextrautils.
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Unpacking man-db (2.13.0-1) ...
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Moving old data out of the way
Unpacking ucf (3.0050) ...
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Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ...
Selecting previously unselected package libglib2.0-0t64:arm64.
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invoke-rc.d: policy-rc.d denied execution of start.
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Setting up libservlet-api-java (4.0.1-2) ...
Setting up libplexus-xml-java (3.0.1-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libopentest4j-java (1.2.0-4) ...
Setting up libtasn1-6:arm64 (4.20.0-2) ...
Setting up libx11-6:arm64 (2:1.8.10-2) ...
Setting up ncbi-vdb-data (3.0.9+dfsg-2) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...
Setting up libcommons-math3-java (3.6.1-4) ...
Setting up sgml-base (1.31) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libclass-xsaccessor-perl (1.19-4+b5) ...
Setting up libkrb5-3:arm64 (1.21.3-4) ...
Setting up libwayland-egl1:arm64 (1.23.1-3) ...
Setting up libmbedcrypto16:arm64 (3.6.2-3) ...
Setting up libpaper2:arm64 (2.2.5-0.3+b1) ...
Setting up libssh2-1t64:arm64 (1.11.1-1) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libjoptsimple-java (5.0.4-7) ...
Setting up libprotoc32t64:arm64 (3.21.12-10+b6) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up libfile-dirlist-perl (0.05-3) ...
Setting up dbus-system-bus-common (1.16.2-1) ...
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
Setting up libfile-homedir-perl (1.006-2) ...
Setting up libpj-java (0.0~20150107+dfsg-5) ...
Setting up openssl (3.4.1-1) ...
Setting up libdrm-common (2.4.124-1) ...
Setting up libcdi-api-java (1.2-4) ...
Setting up libsnappy-jni (1.1.10.7-1) ...
Setting up libezmorph-java (1.0.6-4) ...
Setting up libxcomposite1:arm64 (1:0.4.6-1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up xdg-utils (1.2.1-2) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libldap2:arm64 (2.6.9+dfsg-1) ...
Setting up liburi-perl (5.30-1) ...
Setting up dbus-bin (1.16.2-1) ...
Setting up libfile-touch-perl (0.12-2) ...
Setting up dctrl-tools (2.24-3+b1) ...
Setting up libxkbcommon0:arm64 (1.7.0-2) ...
Setting up libwayland-client0:arm64 (1.23.1-3) ...
Setting up libnet-ssleay-perl:arm64 (1.94-3) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libksba8:arm64 (1.6.7-2+b1) ...
Setting up pinentry-curses (1.3.1-2) ...
Setting up libdom4j-java (2.1.4-1) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libllvm19:arm64 (1:19.1.7-1+b1) ...
Setting up libwayland-server0:arm64 (1.23.1-3) ...
Setting up libx11-xcb1:arm64 (2:1.8.10-2) ...
Setting up libice6:arm64 (2:1.1.1-1) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up libxstream-java (1.4.21-1) ...
Setting up liblapack3:arm64 (3.12.1-2) ...
update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
Setting up gettext (0.23.1-1) ...
Setting up libjetty9-java (9.4.57-1) ...
Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libplexus-languages-java (1.1.1-2) ...
Setting up protobuf-compiler (3.21.12-10+b6) ...
Setting up libjboss-vfs-java (3.2.15.Final-3) ...
Setting up libxrender1:arm64 (1:0.9.10-1.1+b4) ...
Setting up jarwrapper (0.80) ...
Setting up libtool (2.5.4-4) ...
Setting up fontconfig-config (2.15.0-2) ...
Setting up libmaven-parent-java (43-2) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:arm64 (0.8-16) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:arm64 (2:1.3.4-1+b3) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libsisu-inject-java (0.3.5-1) ...
Setting up libidn2-0:arm64 (2.3.7-2+b1) ...
Setting up libnss3:arm64 (2:3.109-1) ...
Setting up dbus-daemon (1.16.2-1) ...
Setting up libpaper-utils (2.2.5-0.3+b1) ...
Setting up libxom-java (1.3.9-1) ...
Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libmaven-dependency-analyzer-java (1.15.1-1) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up pkgconf:arm64 (1.8.1-4) ...
Setting up libxxf86vm1:arm64 (1:1.1.4-1+b4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libprotobuf-dev:arm64 (3.21.12-10+b6) ...
Setting up dh-autoreconf (20) ...
Setting up patchutils (0.4.2-1+b1) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:arm64 (0.1.29-2+b1) ...
Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.5-1) ...
Setting up libglib2.0-0t64:arm64 (2.83.5-1) ...
Setting up libmbedx509-7:arm64 (3.6.2-3) ...
Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ...
Setting up libxfixes3:arm64 (1:6.0.0-2+b4) ...
Setting up testng (6.9.12-4) ...
Setting up dbus (1.16.2-1) ...
Running in chroot, ignoring request.

invoke-rc.d: policy-rc.d denied execution of start.
Setting up shared-mime-info (2.4-5+b2) ...
Setting up libp11-kit0:arm64 (0.25.5-3) ...
Setting up libxinerama1:arm64 (2:1.1.4-3+b3) ...
Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ...
Setting up libxrandr2:arm64 (2:1.5.4-1+b3) ...
Setting up libcommons-collections4-java (4.4-2) ...
Setting up ucf (3.0050) ...
Setting up libcommons-lang3-java (3.17.0-1) ...
Setting up libmbedtls21:arm64 (3.6.2-3) ...
Setting up libreadline8t64:arm64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libdrm2:arm64 (2.4.124-1) ...
Setting up groff-base (1.23.0-7) ...
Setting up libwayland-cursor0:arm64 (1.23.1-3) ...
Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ...
Setting up gpgconf (2.2.46-3) ...
Setting up libpam-systemd:arm64 (257.4-1) ...
Setting up libcommons-beanutils-java (1.9.4-2) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ...
Setting up libsnappy-java (1.1.10.7-1) ...
Setting up libxss1:arm64 (1:1.2.3-1+b3) ...
Setting up libfontconfig1:arm64 (2.15.0-2) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libcommons-configuration-java (1.10-7) ...
Setting up libwagon-file-java (3.5.3-1) ...
Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up libcommons-codec-java (1.18.0-1) ...
Setting up libsm6:arm64 (2:1.2.4-1) ...
Setting up libreflections-java (0.10.2+dfsg-2) ...
Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ...
Setting up libavahi-client3:arm64 (0.8-16) ...
Setting up libio-socket-ssl-perl (2.089-1) ...
Setting up gpg (2.2.46-3) ...
Setting up libpython3-stdlib:arm64 (3.13.2-2) ...
Setting up libhttp-message-perl (7.00-2) ...
Setting up libdrm-amdgpu1:arm64 (2.4.124-1) ...
Setting up libgnutls30t64:arm64 (3.8.9-2) ...
Setting up gtk-update-icon-cache (4.17.5+ds-3) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up mesa-libgallium:arm64 (25.0.1-1) ...
Setting up velocity (1.7-7) ...
Setting up fontconfig (2.15.0-2) ...
Regenerating fonts cache... done.
Setting up libxft2:arm64 (2.3.6-1+b4) ...
Setting up gpg-agent (2.2.46-3) ...
Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'.

Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'.

Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'.

Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'.

Setting up libatk1.0-0t64:arm64 (2.55.2-1) ...
Setting up openjdk-21-jre-headless:arm64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxi6:arm64 (2:1.8.2-1) ...
Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ...
Setting up libgbm1:arm64 (25.0.1-1) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up python3.13 (3.13.2-1) ...
Setting up libcommons-io-java (2.18.0-1) ...
Setting up libcommons-digester-java (1.8.1-7) ...
Setting up libxtst6:arm64 (2:1.2.5-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libtk8.6:arm64 (8.6.16-1) ...
Setting up libdistlib-java (1.0-5) ...
Setting up libxcursor1:arm64 (1:1.2.3-1) ...
Setting up libparams-classify-perl:arm64 (0.015-2+b4) ...
Setting up gpgsm (2.2.46-3) ...
Setting up libpango-1.0-0:arm64 (1.56.1-1) ...
Setting up libgl1-mesa-dri:arm64 (25.0.1-1) ...
Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ...
Setting up libncbi-vdb3:arm64 (3.0.9+dfsg-2) ...
Setting up libcloudproviders0:arm64 (0.3.6-1+b1) ...
Setting up python3 (3.13.2-2) ...
Setting up sopv-gpgv (0.1.1-1) ...
update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'.

Setting up libcairo2:arm64 (1.18.2-2) ...
Setting up libcolord2:arm64 (1.4.7-3) ...
Setting up libdconf1:arm64 (0.40.0-5) ...
Setting up dirmngr (2.2.46-3) ...
Created symlink '/etc/systemd/user/sockets.target.wants/dirmngr.socket' -> '/usr/lib/systemd/user/dirmngr.socket'.

Setting up libmaven-filtering-java (3.4.0-1) ...
Setting up dbus-user-session (1.16.2-1) ...
Setting up libmaven-resolver-java (1.9.22-1) ...
Setting up adwaita-icon-theme (48~beta-3) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libatspi2.0-0t64:arm64 (2.55.2-1) ...
Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libmaven-common-artifact-filters-java (3.4.0-1) ...
Setting up libmaven-dependency-tree-java (3.3.0-1) ...
Setting up gnupg (2.2.46-3) ...
Setting up liblightcouch-java (0.2.0-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libcairo-gobject2:arm64 (1.18.2-2) ...
Setting up libmaven-shared-utils-java (3.4.2-1) ...
Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ...
Setting up libmaven-resources-plugin-java (3.3.1-1) ...
Setting up libcups2t64:arm64 (2.4.10-2+b1) ...
Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ...
Setting up libncbi-ngs3:arm64 (3.0.9+dfsg-7+b2) ...
Setting up libatk-bridge2.0-0t64:arm64 (2.55.2-1) ...
Setting up libngs-jni:arm64 (3.0.9+dfsg-7+b2) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libglx-mesa0:arm64 (25.0.1-1) ...
Setting up libglx0:arm64 (1.7.0-1+b2) ...
Setting up libcommons-compress-java (1.27.1-2) ...
Setting up libcurl4t64:arm64 (8.12.1-3) ...
Setting up libcommons-validator-java (1:1.9.0-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up liblog4j2-java (2.19.0-2) ...
Setting up libmaven-invoker-java (3.3.0-1) ...
Setting up debhelper (13.24.1) ...
Setting up dconf-service (0.40.0-5) ...
Setting up libgl1:arm64 (1.7.0-1+b2) ...
Setting up r-base-core (4.4.3-1) ...
Creating config file /etc/R/Renviron with new version
Setting up libmaven-clean-plugin-java (3.2.0-2) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libngs-java:arm64 (3.0.9+dfsg-7+b2) ...
Setting up libbarclay-java (5.0.0+dfsg-1) ...
Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ...
Setting up libmaven-archiver-java (3.6.2-1) ...
Setting up libmaven-source-plugin-java (3.3.1-1) ...
Setting up libgtk-3-common (3.24.48-4) ...
Setting up libgtk-3-0t64:arm64 (3.24.48-4) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libwww-perl (6.78-1) ...
Setting up devscripts (2.25.5) ...
Setting up libguava-java (32.0.1-1) ...
Setting up javahelper (0.80) ...
Setting up libprotobuf-java (3.21.12-10) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Setting up libguice-java (5.1.0-1) ...
Setting up libplexus-i18n-java (1.0-beta-10-6) ...
Setting up libplexus-container-default1.5-java (2.1.1-1) ...
Setting up libplexus-velocity-java (1.2-4) ...
Setting up libmaven3-core-java (3.9.9-1) ...
Setting up libmaven-shared-incremental-java (1.1-6) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ...
Setting up libplexus-compiler-java (2.13.0-1) ...
Setting up libmaven-compiler-plugin-java (3.13.0-1) ...
Setting up libmaven-artifact-transfer-java (0.13.1-2) ...
Setting up libmaven-file-management-java (3.0.0-2) ...
Setting up libbyte-buddy-java (1.14.19-1) ...
Setting up libbuild-helper-maven-plugin-java (3.3.0-1) ...
Setting up libeasymock-java (5.5.0-1) ...
Setting up libmaven-jar-plugin-java (3.3.0-2) ...
Setting up libmaven-assembly-plugin-java (3.4.2-2) ...
Setting up libcommons-text-java (1.13.0-1) ...
Setting up libdoxia-core-java (2.0.0-1) ...
Setting up libdoxia-java (2.0.0-1) ...
Setting up libmaven-reporting-api-java (4.0.0-1) ...
Setting up libmaven-reporting-exec-java (2.0.0-1) ...
Processing triggers for libc-bin (2.41-3) ...
Processing triggers for systemd (257.4-1) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureSign_Root_CA12.pem
Adding debian:SecureSign_Root_CA14.pem
Adding debian:SecureSign_Root_CA15.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_CYBER_Root_CA.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up maven (3.9.9-1) ...
update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode
Setting up openjdk-21-jre:arm64 (21.0.6+7-1) ...
Setting up ant (1.10.15-1) ...
Setting up junit4 (4.13.2-5) ...
Setting up openjdk-21-jdk-headless:arm64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jre-headless (2:1.21-76) ...
Setting up ant-contrib (1.0~b3+svn177-12) ...
Setting up maven-repo-helper (1.11) ...
Setting up default-jre (2:1.21-76) ...
Setting up libmaven-antrun-plugin-java (3.1.0-1) ...
Setting up libplexus-ant-factory-java (1.0~alpha2.1-5) ...
Setting up openjdk-21-jdk:arm64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up default-jdk-headless (2:1.21-76) ...
Setting up libjsap-java (2.1-5) ...
Setting up r-cran-rjava (1.0-11-1+b1) ...
Setting up libdsiutils-java (2.7.3+dfsg-1) ...
Setting up junit5 (5.10.3-1) ...
Setting up libjson-java (3.1.0+dfsg-2) ...
Setting up libhtsjdk-java (4.1.3+dfsg-2) ...
Setting up libmaven-plugin-tools-java (3.10.2-1) ...
Setting up libgkl-java (0.8.11+dfsg-2) ...
Setting up default-jdk (2:1.21-76) ...
Setting up libpicard-java (3.3.0+dfsg-2) ...
Setting up libsurefire-java (2.22.3-3) ...
Setting up libicb-utils-java (2.0.1+git20161002.afee1d9-5) ...
Processing triggers for sgml-base (1.31) ...
Setting up libvelocity-tools-java (2.0-9) ...
Setting up libdoxia-sitetools-java (2.0.0-1) ...
Setting up libmaven-site-plugin-java (3.21.0-1) ...
Setting up maven-debian-helper (2.6.7) ...
Setting up libmaven-javadoc-plugin-java (3.10.1-2) ...
Setting up libmaven-reporting-impl-java (4.0.0-1) ...
Setting up libmaven-dependency-plugin-java (3.8.1-1) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20240118) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../libgoby-java_3.3.1+dfsg2-11_source.changes
dpkg-buildpackage: info: source package libgoby-java
dpkg-buildpackage: info: source version 3.3.1+dfsg2-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Pierre Gruet <pgt@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean --with javahelper
   dh_auto_clean
	bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
	mh_unpatchpoms -plibgoby-io-java
   jh_clean
Duplicate specification "u=s" for option "u"
   debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
dh_clean
rm -rf goby-distribution/test-data goby-distribution/test-results
rm -rf test-results/
make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
 debian/rules binary
dh binary --with javahelper
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
	mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo
   jh_linkjars
   dh_auto_build
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO]   from goby-io/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.17 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3
[WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:3.1.2 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0
[WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)'
[INFO] 
[INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO]     [mkdir] Created dir: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources
[INFO] Executed tasks
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- resources:3.3.1:resources (default-resources) @ goby-io ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- compiler:3.13.0:compile (default-compile) @ goby-io ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 260 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- antrun:3.1.0:run (default) @ goby-io ---
[WARNING]  Parameter 'tasks' is deprecated: Use target instead. For version 3.0.0, this parameter is only defined to break the build if you use it!
[WARNING] Parameter tasks is deprecated, use target instead
[INFO] Executing tasks
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes
[INFO] Executed tasks
[INFO] 
[INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-io ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources
[INFO] 
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-io ---
[INFO] No sources to compile
[INFO] 
[INFO] --- surefire:2.22.3:test (default-test) @ goby-io ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- jar:3.3.0:jar (default-jar) @ goby-io ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1.jar
[INFO] 
[INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-io >>>
[INFO] 
[INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-io <<<
[INFO] 
[INFO] 
[INFO] --- source:3.3.1:jar (attach-sources) @ goby-io ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-sources.jar
[INFO] 
[INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-io ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlRootElement;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol
[WARNING] @XmlRootElement
[WARNING] ^
[WARNING] symbol: class XmlRootElement
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist
[WARNING] import DistLib.hypergeometric;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol
[WARNING] Rengine rEngine;
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class FisherExactRCalculator
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelTeam;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBContext;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBException;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Unmarshaller;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol
[WARNING] private ParallelTeam team;
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class StatsMode
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist
[WARNING] import org.apache.commons.exec.CommandLine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist
[WARNING] import org.apache.commons.exec.DefaultExecutor;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist
[WARNING] import org.apache.commons.exec.PumpStreamHandler;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBContext;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBException;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Marshaller;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol
[WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException {
[WARNING] ^
[WARNING] symbol:   class JAXBException
[WARNING] location: class MethylStatsMode
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.PJProperties;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.IntegerForLoop;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelRegion;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelTeam;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBContext;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBException;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Marshaller;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol
[WARNING] private ParallelTeam team;
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol
[WARNING] protected synchronized ParallelTeam getParallelTeam() {
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlElement;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlElementWrapper;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlRootElement;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol
[WARNING] @XmlRootElement(name = "info-output")
[WARNING] ^
[WARNING] symbol: class XmlRootElement
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol
[WARNING] private void writeInfoOutput() throws JAXBException, IOException {
[WARNING] ^
[WARNING] symbol:   class JAXBException
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessType;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessorType;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: class XmlAccessorType
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessType;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessorType;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: class XmlAccessorType
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol
[WARNING] class BasenameParallelRegion extends ParallelRegion {
[WARNING] ^
[WARNING] symbol:   class ParallelRegion
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelTeam;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:33: error: cannot find symbol
[WARNING] private ParallelTeam team;
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class DoInParallel
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:47: error: cannot find symbol
[WARNING] protected synchronized ParallelTeam getParallelTeam() {
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class DoInParallel
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.IntegerForLoop;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelRegion;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol
[WARNING] class BasenameParallelRegion extends ParallelRegion {
[WARNING] ^
[WARNING] symbol: class ParallelRegion
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.RMainLoopCallbacks;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol
[WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks {
[WARNING] ^
[WARNING] symbol: class RMainLoopCallbacks
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol
[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol
[WARNING] public void rBusy(final Rengine rengine, final int which) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol
[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol
[WARNING] public void rShowMessage(final Rengine rengine, final String message) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol
[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol
[WARNING] public void rFlushConsole(final Rengine rengine) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol
[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol
[WARNING] public void rLoadHistory(final Rengine re, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.RMainLoopCallbacks;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol
[WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks {
[WARNING] ^
[WARNING] symbol: class RMainLoopCallbacks
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol
[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol
[WARNING] public void rBusy(final Rengine rengine, final int which) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol
[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol
[WARNING] public void rShowMessage(final Rengine rengine, final String message) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol
[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol
[WARNING] public void rFlushConsole(final Rengine rengine) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol
[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol
[WARNING] public void rLoadHistory(final Rengine re, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol
[WARNING] private Rengine rengine;
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class GobyRengine
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol
[WARNING] public Rengine getRengine() {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class GobyRengine
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.REXP;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.RVector;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol
[WARNING] private static Result evaluateFisherExpression(final Rengine rengine,
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class FisherExact
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: variable XmlAccessType
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:35: error: cannot find symbol
[WARNING] @XmlElement(name = "al")
[WARNING] ^
[WARNING] symbol:   class XmlElement
[WARNING] location: class InfoOutput
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:36: error: cannot find symbol
[WARNING] @XmlElementWrapper(name = "annotation-lengths")
[WARNING] ^
[WARNING] symbol:   class XmlElementWrapper
[WARNING] location: class InfoOutput
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: variable XmlAccessType
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:39: error: cannot find symbol
[WARNING] @XmlElement(name = "tc")
[WARNING] ^
[WARNING] symbol:   class XmlElement
[WARNING] location: class InfoOutput
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:40: error: cannot find symbol
[WARNING] @XmlElementWrapper(name = "total-counts")
[WARNING] ^
[WARNING] symbol:   class XmlElementWrapper
[WARNING] location: class InfoOutput
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<'
[WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors).
[WARNING] ^
[WARNING] 100 warnings
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-javadoc.jar
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO]   from goby-distribution/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)'
[INFO] 
[INFO] --- resources:3.3.1:resources (default-resources) @ goby-distribution ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] Copying 72 resources from src/main/java to target/classes
[INFO] 
[INFO] --- compiler:3.13.0:compile (default-compile) @ goby-distribution ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 525 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
  on the class path. A future release of javac may disable annotation processing
  unless at least one processor is specified by name (-processor), or a search
  path is specified (--processor-path, --processor-module-path), or annotation
  processing is enabled explicitly (-proc:only, -proc:full).
  Use -Xlint:-options to suppress this message.
  Use -proc:none to disable annotation processing.
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-distribution ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources
[INFO] 
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-distribution ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 120 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
  on the class path. A future release of javac may disable annotation processing
  unless at least one processor is specified by name (-processor), or a search
  path is specified (--processor-path, --processor-module-path), or annotation
  processing is enabled explicitly (-proc:only, -proc:full).
  Use -Xlint:-options to suppress this message.
  Use -proc:none to disable annotation processing.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- surefire:2.22.3:test (default-test) @ goby-distribution ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- jar:3.3.0:jar (default-jar) @ goby-distribution ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1.jar
[INFO] 
[INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-distribution >>>
[INFO] 
[INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-distribution <<<
[INFO] 
[INFO] 
[INFO] --- source:3.3.1:jar (attach-sources) @ goby-distribution ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-sources.jar
[INFO] 
[INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-distribution ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<'
[WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder
[WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder
[WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J)
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS
[WARNING] * the call, exactly {@link #BITS} excess bits will be present in the
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning: @return tag cannot be used in method with void return type.
[WARNING] void flush(InputBitStream ibs) throws IOException;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS
[WARNING] * @return the current bit stream window in the lower {@link #BITS} bits.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS
[WARNING] * the call, exactly {@link #BITS} excess bits will be present in the
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS
[WARNING] * @return the current bit stream window in the lower {@link #BITS} bits.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS
[WARNING] * the call, exactly {@link #BITS} excess bits will be present in the
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS
[WARNING] * @return the current bit stream window in the lower {@link #BITS} bits.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning: reference not found: org.campagnelab.goby.aligners.LastagAligner
[WARNING] * @see org.campagnelab.goby.aligners.LastagAligner
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:79: warning: reference not found: org.campagnelab.goby.aligners.LastAligner
[WARNING] * @see org.campagnelab.goby.aligners.LastAligner
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:87: warning: reference not found: org.campagnelab.goby.aligners.BWAAligner
[WARNING] * @see org.campagnelab.goby.aligners.BWAAligner
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:95: warning: reference not found: org.campagnelab.goby.aligners.GSnapAligner
[WARNING] * @see org.campagnelab.goby.aligners.GSnapAligner
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:131: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * @return the next {@link edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<'
[WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<'
[WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:43: warning: invalid input: '<'
[WARNING] * @return encoded symbol (post-condition: 0<= encoded-symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:43: warning: invalid input: '<'
[WARNING] * @return encoded symbol (post-condition: 0<= encoded-symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&rct'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&q'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&esrc'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&source'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&cd'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&cts'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&ved'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&url'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&ei'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&usg'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&sig2'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '&'
[WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '<'
[WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:233: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCountComparisonFailures(final boolean countComparisonFailures) {
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:275: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setAllowSourceNs(boolean allowSourceNs) {
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparisonInterface.java:130: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setAllowSourceNs(boolean allowSourceNs);
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java:214: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCheckMate(final boolean checkMate) {
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<'
[WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<'
[WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:176: warning: invalid input: '<'
[WARNING] * Set to <= 0 to process the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '<'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SortMode.java:142: warning: invalid input: '<'
[WARNING] * Set to < 0 for auto-detect number of cores.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/VCFParser.java:179: warning: invalid input: '<'
[WARNING] * Set to <= 0 to scan the entire file. This must be set before calling readHeader() for the value to be used.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] 91 warnings
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-javadoc.jar
[INFO] 
[INFO] --- assembly:3.4.2:single (make-assembly) @ goby-distribution ---
[WARNING]  Parameter 'finalName' is read-only, must not be used in configuration
[INFO] Reading assembly descriptor: assembly/assembly.xml
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-bin.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.076 s]
[INFO] Goby I/O ........................................... SUCCESS [ 19.915 s]
[INFO] Goby Full Distribution ............................. SUCCESS [ 21.899 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  42.041 s
[INFO] Finished at: 2025-03-07T02:57:41-12:00
[INFO] ------------------------------------------------------------------------
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
# Create a symlink to the directory with test data for tests run from the
# goby-distribution directory.
ln -s ../test-data goby-distribution/test-data
# The test-results directory should exist because test classes will write inside.
if [ ! -e test-results ]; then mkdir test-results/; fi
# Putting the JRI location in the path, as indicated in GobyRengine.java.
# Also indicating R_HOME, as found in http://rforge.net/JRI/.
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/R/site-library/rJava/jri" && \
        export R_HOME="/usr/lib/R" && \
        dh_auto_test --no-parallel
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode test
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO]   from goby-io/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.17 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3
[INFO] 
[INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- resources:3.3.1:resources (default-resources) @ goby-io ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] Copying 1 resource from src/main/resources to target/classes
[INFO] 
[INFO] --- compiler:3.13.0:compile (default-compile) @ goby-io ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 260 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- antrun:3.1.0:run (default) @ goby-io ---
[WARNING]  Parameter 'tasks' is deprecated: Use target instead. For version 3.0.0, this parameter is only defined to break the build if you use it!
[WARNING] Parameter tasks is deprecated, use target instead
[INFO] Executing tasks
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes
[INFO] Executed tasks
[INFO] 
[INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-io ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources
[INFO] 
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-io ---
[INFO] No sources to compile
[INFO] 
[INFO] --- surefire:2.22.3:test (default-test) @ goby-io ---
[INFO] No tests to run.
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO]   from goby-distribution/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- resources:3.3.1:resources (default-resources) @ goby-distribution ---
[INFO] Copying 3 resources from src/main/resources to target/classes
[INFO] Copying 72 resources from src/main/java to target/classes
[INFO] 
[INFO] --- compiler:3.13.0:compile (default-compile) @ goby-distribution ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 525 source files with javac [debug target 1.8] to target/classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
  on the class path. A future release of javac may disable annotation processing
  unless at least one processor is specified by name (-processor), or a search
  path is specified (--processor-path, --processor-module-path), or annotation
  processing is enabled explicitly (-proc:only, -proc:full).
  Use -Xlint:-options to suppress this message.
  Use -proc:none to disable annotation processing.
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-distribution ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources
[INFO] 
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-distribution ---
[INFO] Recompiling the module because of changed dependency.
[INFO] Compiling 120 source files with javac [debug target 1.8] to target/test-classes
[WARNING] bootstrap class path not set in conjunction with -source 8
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[INFO] Annotation processing is enabled because one or more processors were found
  on the class path. A future release of javac may disable annotation processing
  unless at least one processor is specified by name (-processor), or a search
  path is specified (--processor-path, --processor-module-path), or annotation
  processing is enabled explicitly (-proc:only, -proc:full).
  Use -Xlint:-options to suppress this message.
  Use -proc:none to disable annotation processing.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- surefire:2.22.3:test (default-test) @ goby-distribution ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
02:57:57.475 INFO  RLoggerMainLoopCallback - 

02:57:57.482 INFO  RLoggerMainLoopCallback - R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu


02:57:57.482 INFO  RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.


02:57:57.482 INFO  RLoggerMainLoopCallback - R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.


02:57:57.483 INFO  RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT 
original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G 
original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT 
original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT 
qPhred=1
qPhred=2
qPhred=3
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qPhred=60
qPhred=61
>1
NNTGAATGAGACCTA

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/share/java/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
02:57:58.001 WARN  GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent.
 0 
AAC 3 
ACC 6 
ATC 9 
AGC 12 
AAC 15 
ACC 18 
ATC 21 
AGC 24 
AAC 27 
ACC 30 
ATC 33 
AGC 36 
AAC 39 
ACC 42 
ATC 45 
AGC 48 
AAC 51 
ACC 54 
ATC 57 
AGC 60 
AAC 63 
ACC 66 
ATC 69 
AGC 72 
AAC 75 
ACC 78 
ATC 81 
AGC02:58:01.823 WARN  MessageChunksWriter - Using chunk-size=10000
02:58:01.823 WARN  MessageChunksWriter - Using chunk-size=9
02:58:01.828 WARN  MessageChunksWriter - Using chunk-size=9
Total logical entries written: 39
Total bytes written: 660
Average bytes/logical entry: 16.923077
Number of bits/base 3.6590436
02:58:01.831 WARN  MessageChunksWriter - Using chunk-size=9
Total logical entries written: 39
Total bytes written: 685
Average bytes/logical entry: 17.564102
Number of bits/base 3.797644
02:58:01.836 WARN  MessageChunksWriter - Using chunk-size=9
Total logical entries written: 39
Total bytes written: 660
Average bytes/logical entry: 16.923077
Number of bits/base 3.6590436
Creating base test directory: test-results/stats
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
02:58:01.967 INFO  BullardUpperQuartileNormalization - normalization denominator 48091.5 for sample B-7
02:58:01.967 INFO  BullardUpperQuartileNormalization - normalization denominator 46853.6 for sample B-3
02:58:01.967 INFO  BullardUpperQuartileNormalization - normalization denominator 92902.6 for sample A-3
02:58:01.967 INFO  BullardUpperQuartileNormalization - normalization denominator 92345.6 for sample A-12
02:58:01.967 INFO  BullardUpperQuartileNormalization - normalization denominator 47225.0 for sample B-15
02:58:01.967 INFO  BullardUpperQuartileNormalization - normalization denominator 47720.1 for sample B-14
02:58:01.967 INFO  BullardUpperQuartileNormalization - normalization denominator 45801.4 for sample B-11
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 90365.0 for sample A-17
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 45430.1 for sample B-2
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 45863.3 for sample B-10
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 90117.4 for sample A-16
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 48091.5 for sample B-8
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 47472.6 for sample B-4
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 92593.2 for sample A-2
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 91355.3 for sample A-0
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 47286.9 for sample B-6
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 94635.7 for sample A-9
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 91293.4 for sample A-8
02:58:01.968 INFO  BullardUpperQuartileNormalization - normalization denominator 94697.5 for sample A-5
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 91479.1 for sample A-4
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 92283.7 for sample A-6
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 94697.5 for sample A-7
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 46606.0 for sample B-5
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 92840.7 for sample A-10
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 93397.8 for sample A-14
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 46110.9 for sample B-9
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 93769.1 for sample A-1
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 45863.3 for sample B-0
02:58:01.969 INFO  BullardUpperQuartileNormalization - normalization denominator 46420.4 for sample B-12
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 46729.8 for sample B-13
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 95564.1 for sample A-19
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 95873.5 for sample A-18
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 90983.9 for sample A-15
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 46172.8 for sample B-1
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 91045.8 for sample A-13
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 92964.5 for sample A-11
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 46482.3 for sample B-16
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 44687.3 for sample B-17
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 45801.4 for sample B-19
02:58:01.970 INFO  BullardUpperQuartileNormalization - normalization denominator 46420.4 for sample B-18
Creating base test directory: test-results/stats-writer
allele: A ref: [CC] alt: [T]02:58:02.035 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
02:58:02.071 INFO  FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
02:58:02.071 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
02:58:02.086 INFO  FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
02:58:02.086 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
02:58:02.227 INFO  FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
02:58:02.279 INFO  FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed.
02:58:02.279 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
02:58:02.392 INFO  FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
02:58:02.414 INFO  FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed.
list3:element-id p-value p-value-BH-FDR-q-value 
[ 0 [2.354054E-7, 1.177027E-5] ]
[ 1 [2.10159E-5, 4.294736666666667E-4] ]
[ 2 [2.576842E-5, 4.294736666666667E-4] ]
[ 3 [9.814783E-5, 9.471342857142858E-4] ]
[ 4 [1.05261E-4, 9.471342857142858E-4] ]
[ 5 [1.241481E-4, 9.471342857142858E-4] ]
[ 6 [1.325988E-4, 9.471342857142858E-4] ]
[ 7 [1.568503E-4, 9.803143750000002E-4] ]
[ 8 [2.254557E-4, 0.0012525316666666666] ]
[ 9 [3.79538E-4, 0.00189769] ]
[ 10 [6.114943E-4, 0.0027795195454545455] ]
[ 11 [0.001613954, 0.006724808333333334] ]
[ 12 [0.00330243, 0.012636935714285714] ]
[ 13 [0.003538342, 0.012636935714285714] ]
[ 14 [0.005236997, 0.017456656666666667] ]
[ 15 [0.006831909, 0.020762429411764708] ]
[ 16 [0.007059226, 0.020762429411764708] ]
[ 17 [0.008805129, 0.024458691666666667] ]
[ 18 [0.00940104, 0.02473957894736842] ]
[ 19 [0.01129798, 0.028244949999999998] ]
[ 20 [0.02115017, 0.050357547619047614] ]
[ 21 [0.04922736, 0.11188036363636364] ]
[ 22 [0.06053298, 0.1304633125] ]
[ 23 [0.06262239, 0.1304633125] ]
[ 24 [0.07395153, 0.14790306] ]
[ 25 [0.08281103, 0.15925198076923075] ]
[ 26 [0.08633331, 0.1598765] ]
[ 27 [0.1190654, 0.21261678571428572] ]
[ 28 [0.1890796, 0.32599931034482754] ]
[ 29 [0.2058494, 0.3430823333333333] ]
[ 30 [0.2209214, 0.3563248387096774] ]
[ 31 [0.2856, 0.44625000000000004] ]
[ 32 [0.3048895, 0.4619537878787878] ]
[ 33 [0.4660682, 0.6835770833333333] ]
[ 34 [0.4830809, 0.6835770833333333] ]
[ 35 [0.4921755, 0.6835770833333333] ]
[ 36 [0.5319453, 0.718845] ]
[ 37 [0.575155, 0.7414352564102564] ]
[ 38 [0.5783195, 0.7414352564102564] ]
[ 39 [0.6185894, 0.7626062790697675] ]
[ 40 [0.636362, 0.7626062790697675] ]
[ 41 [0.6448587, 0.7626062790697675] ]
[ 42 [0.6558414, 0.7626062790697675] ]
[ 43 [0.6885884, 0.7824868181818182] ]
[ 44 [0.7189864, 0.7988737777777778] ]
[ 45 [0.8179539, 0.8802645744680851] ]
[ 46 [0.8274487, 0.8802645744680851] ]
[ 47 [0.89713, 0.9304775510204082] ]
[ 48 [0.911868, 0.9304775510204082] ]
[ 49 [0.943789, 0.943789] ]

element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B 
[ id-1 [0.9973267336151496, 0.5015544660772773, -0.0038618723661262987, -0.9955217167361229, 0.0, 0.0] ]

truncated fdr=3.53108e-05 original=3.53108e-05 
truncated fdr=0.00128842 original=0.00128842 
truncated fdr=0.00128842 original=0.00128842 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00294094 original=0.00294094 
truncated fdr=0.00375760 original=0.00375760 
truncated fdr=0.00569307 original=0.00569307 
truncated fdr=0.00833856 original=0.00833856 
truncated fdr=0.0201744 original=0.0201744 
truncated fdr=0.0379108 original=0.0379108 
truncated fdr=0.0379108 original=0.0379108 
truncated fdr=0.0523700 original=0.0523700 
truncated fdr=0.0622873 original=0.0622873 
truncated fdr=0.0622873 original=0.0622873 
truncated fdr=0.0733761 original=0.0733761 
truncated fdr=0.0742187 original=0.0742187 
truncated fdr=0.0847349 original=0.0847349 
truncated fdr=0.151073 original=0.151073 
truncated fdr=0.335641 original=0.335641 
truncated fdr=0.391390 original=0.391390 
truncated fdr=0.391390 original=0.391390 
truncated fdr=0.443709 original=0.443709 
truncated fdr=0.477756 original=0.477756 
truncated fdr=0.479630 original=0.479630 
truncated fdr=0.637850 original=0.637850 
truncated fdr=0.977998 original=0.977998 
truncated fdr=1.00000 original=1.00000 
truncated fdr=1.00000 original=1.00000 
truncated fdr=1.00000 original=1.00000 
truncated fdr=1.00000 original=1.00000 
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads.
##fileformat=VCFv4.1
##Goby=UNKNOWN
##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data,
##INFO=<ID=p-value1,Number=1,Type=Float,Description="A P-value">
##INFO=<ID=p-value2,Number=1,Type=Float,Description="A P-value">
##INFO=<ID=#Cm_Group[Group_1],Number=1,Type=Float,Description="Some count">
##FORMAT=<ID=Zygosity,Number=1,Type=String,Description="Zygosity">
##FORMAT=<ID=Another,Number=1,Type=String,Description="Another">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SampleA	SampleB

[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
                                               1/1 ..T

Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
Loading test-data/fdr-mode/file1.vcf
Loading test-data/fdr-mode/file2.vcf
Loading test-data/fdr-mode/file3.vcf
adjusting column: PCHI2
Combining test-data/fdr-mode/file1.vcf
Combining test-data/fdr-mode/file2.vcf
Combining test-data/fdr-mode/file3.vcf
Loading test-data/fdr-mode/file-B-1.vcf
Loading test-data/fdr-mode/file-B-2.vcf
adjusting column: PCHI2
Combining test-data/fdr-mode/file-B-1.vcf
Combining test-data/fdr-mode/file-B-2.vcf
Loading test-data/fdr-mode/file-B-1.vcf
Loading test-data/fdr-mode/file-B-2.vcf
adjusting column: PCHI2
Combining test-data/fdr-mode/file-B-1.vcf
Combining test-data/fdr-mode/file-B-2.vcf
Loading test-data/fdr-mode/file1.vcf
Loading test-data/fdr-mode/file2.vcf
Loading test-data/fdr-mode/file3.vcf
Combining test-data/fdr-mode/file1.vcf
Combining test-data/fdr-mode/file2.vcf
Combining test-data/fdr-mode/file3.vcf
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.169 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.173 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.176 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.178 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.181 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.184 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.187 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.189 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.193 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.195 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.322 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.324 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.327 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.329 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.331 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.334 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.336 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.339 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.341 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.343 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.421 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.423 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.425 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.427 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.429 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.431 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.433 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.435 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.437 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.439 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.512 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.514 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.516 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.519 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.521 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.523 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.525 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.527 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.528 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.530 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.632 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.634 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.635 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.638 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.639 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.641 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.643 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.645 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.647 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.650 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.713 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.715 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.717 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.718 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.720 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.722 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.723 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.725 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.727 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.729 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.789 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.791 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.792 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.793 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.795 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.796 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.798 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.800 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.801 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.803 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.858 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.859 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.861 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.862 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.864 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.865 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.867 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.868 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.869 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.871 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.926 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.928 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.929 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.931 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.932 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:15.934 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:15.935 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:15.937 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:15.938 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:15.939 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:15.992 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:15.993 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:15.995 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:15.996 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:15.998 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:16.000 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:16.002 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:16.003 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:16.005 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:16.006 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:16.117 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:16.120 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:16.122 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:16.126 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:16.128 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:16.131 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:16.134 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:16.137 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:16.140 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:16.143 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Methylation format ignores thresholdDistinctReadIndices. Additionally, the minimum coverage needed for a site to be reported can be changed with --minimum-variation-support.
Filtering reads that have these criteria:
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest_mci
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
02:58:16.249 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
02:58:16.251 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
02:58:16.252 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
02:58:16.255 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
02:58:16.256 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
02:58:16.258 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
02:58:16.260 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
02:58:16.263 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
02:58:16.264 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
02:58:16.266 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
info: + ref: A s=0
info: + ref: A s=0
info: + ref: A s=0
info: + ref: A s=0
info: + ref: A s=0
info: +  /T q=40 s=0
info: -  /T q=40 s=0
info: +  /C q=10 s=0
info: +  /C q=20 s=0
info: +  /C q=30 s=0
info: +  /C q=40 s=0
info: +  /C q=40 s=0
info: +  /C q=40 s=0
info: +  /C q=40 s=0
info: +  /C q=10 s=0
info: +  /C q=20 s=0
info: +  /N q=30 s=0
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: +  /T q=40 s=1
info: +  /T q=10 s=1
info: +  /T q=20 s=1
info: +  /T q=30 s=1
info: +  /N q=40 s=1
info: +  /N q=40 s=1
list: pos=-1 #bases: 33 #indels: 0
filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, +  /C q=10 s=0, +  /C q=20 s=0, +  /C q=30 s=0, +  /C q=40 s=0, +  /C q=40 s=0, +  /C q=40 s=0, +  /C q=40 s=0, +  /C q=10 s=0, +  /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, +  /T q=40 s=1, +  /T q=10 s=1, +  /T q=20 s=1, +  /T q=30 s=1, +  /N q=40 s=1, +  /N q=40 s=1}
Scanning target file..
Target file had 1 entries.
Wrote 1 target ids to alignment header.
Setting quality threshold to 0.05
Total logical entries written: 2
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 0
Number of queries: 3
Number of targets: 3
Removed by quality filter: 0
Not best score: 1
Number of alignments written: 2
query_index: 0
target_index: 0
position: 14977972
score: 780.0
matching_reverse_strand: false
multiplicity: 1
number_of_mismatches: 1
number_of_indels: 0
query_length: 142
query_aligned_length: 134
target_aligned_length: 134
sequence_variations {
  to: "T"
  from: "A"
  position: 6
  to_quality: "/"
  read_index: 14
}
fragment_index: 0
query_index_occurrences: 2
ambiguity: 1

TTC[27]->CGT[27] / qual=1:2:3
A[15]->G[20] / qual=20
A[15]->G[20] / qual=20
Processing test-data/sample-qual-scores/30reads.fa
Processed 0 read entries.
Min quality score: 2147483647
Max quality score: -2147483648
Avg quality score: 0
Probable quality encoding scheme: fasta
Processing test-data/sample-qual-scores/30reads.fq
Processed 30 read entries.
Min quality score: 69
Max quality score: 98
Avg quality score: 94
Probable quality encoding scheme: Illumina/Solexa
field CHROM value: 0
field POS value: 145497099
field ID value: .
field REF value: A
field ALT value: G
field QUAL value: 17.1
field FILTER value: .
field INFO[DP] value: 2
field INFO[DP4] value: 0,0,2,0
field INFO[MQ] value: 25
field INFO[FQ] value: -30.8
field INFO[AF1] value: 0.9999
field INFO[CI95] value: 0.5,1
field INFO[PV4] value: 
field INFO[INDEL] value: INDEL
field INFO[PC2] value: 3,3
field INFO[PCHI2] value: 0.752
field INFO[QCHI2] value: 1
field INFO[RP] value: 
field FORMAT[GT] value: 
field FORMAT[GQ] value: 
field FORMAT[GL] value: 
field FORMAT[DP] value: 
field FORMAT[SP] value: 
field FORMAT[PL] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1
field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42
field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0
field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1
field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42
field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0
field CHROM gfi:0 value: 0
field POS gfi:1 value: 145497099
field ID gfi:2 value: .
field REF gfi:3 value: A
field ALT gfi:4 value: G
field QUAL gfi:5 value: 17.1
field FILTER gfi:6 value: .
field FORMAT[GT] gfi:7 value: 
field FORMAT[GQ] gfi:8 value: 
field FORMAT[GL] gfi:9 value: 
field FORMAT[DP] gfi:10 value: 
field FORMAT[SP] gfi:11 value: 
field FORMAT[PL] gfi:12 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1
field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11
field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0
field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1
field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42
field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0
Total logical entries written: 1
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 45
 peak : start :5 count :13 length :100010
 peak : start :100020 count :10 length :1
Appending count: 44478 length: 2
Appending count: 35187 length: 2
Appending count: 15970 length: 9
Appending count: 29386 length: 9
Appending count: 22204 length: 7
Appending count: 24833 length: 1
Appending count: 24726 length: 7
Appending count: 31774 length: 5
Appending count: 35378 length: 9
Appending count: 19759 length: 4
Appending count: 40588 length: 8
Appending count: 23895 length: 3
Appending count: 38556 length: 1
Appending count: 1715 length: 6
Appending count: 37640 length: 10
Appending count: 37482 length: 5
Appending count: 27494 length: 6
Appending count: 44850 length: 3
Appending count: 47919 length: 1
Appending count: 4640 length: 3
Appending count: 23359 length: 7
Appending count: 36855 length: 10
Appending count: 30905 length: 8
Appending count: 36226 length: 6
Appending count: 19368 length: 10
Appending count: 49564 length: 7
Appending count: 15280 length: 2
Appending count: 43228 length: 3
Appending count: 13986 length: 6
Appending count: 24543 length: 5
 position= 0 count= 44478
 position= 1 count= 44478
 position= 2 count= 35187
 position= 3 count= 35187
 position= 4 count= 15970
 position= 5 count= 15970
 position= 6 count= 15970
 position= 7 count= 15970
 position= 8 count= 15970
 position= 9 count= 15970
 position= 10 count= 15970
 position= 11 count= 15970
 position= 12 count= 15970
 position= 13 count= 29386
 position= 14 count= 29386
 position= 15 count= 29386
 position= 16 count= 29386
 position= 17 count= 29386
 position= 18 count= 29386
 position= 19 count= 29386
 position= 20 count= 29386
 position= 21 count= 29386
 position= 22 count= 22204
 position= 23 count= 22204
 position= 24 count= 22204
 position= 25 count= 22204
 position= 26 count= 22204
 position= 27 count= 22204
 position= 28 count= 22204
 position= 29 count= 24833
 position= 30 count= 24726
 position= 31 count= 24726
 position= 32 count= 24726
 position= 33 count= 24726
 position= 34 count= 24726
 position= 35 count= 24726
 position= 36 count= 24726
 position= 37 count= 31774
 position= 38 count= 31774
 position= 39 count= 31774
 position= 40 count= 31774
 position= 41 count= 31774
 position= 42 count= 35378
 position= 43 count= 35378
 position= 44 count= 35378
 position= 45 count= 35378
 position= 46 count= 35378
 position= 47 count= 35378
 position= 48 count= 35378
 position= 49 count= 35378
 position= 50 count= 35378
 position= 51 count= 19759
 position= 52 count= 19759
 position= 53 count= 19759
 position= 54 count= 19759
 position= 55 count= 40588
 position= 56 count= 40588
 position= 57 count= 40588
 position= 58 count= 40588
 position= 59 count= 40588
 position= 60 count= 40588
 position= 61 count= 40588
 position= 62 count= 40588
 position= 63 count= 23895
 position= 64 count= 23895
 position= 65 count= 23895
 position= 66 count= 38556
 position= 67 count= 1715
 position= 68 count= 1715
 position= 69 count= 1715
 position= 70 count= 1715
 position= 71 count= 1715
 position= 72 count= 1715
 position= 73 count= 37640
 position= 74 count= 37640
 position= 75 count= 37640
 position= 76 count= 37640
 position= 77 count= 37640
 position= 78 count= 37640
 position= 79 count= 37640
 position= 80 count= 37640
 position= 81 count= 37640
 position= 82 count= 37640
 position= 83 count= 37482
 position= 84 count= 37482
 position= 85 count= 37482
 position= 86 count= 37482
 position= 87 count= 37482
 position= 88 count= 27494
 position= 89 count= 27494
 position= 90 count= 27494
 position= 91 count= 27494
 position= 92 count= 27494
 position= 93 count= 27494
 position= 94 count= 44850
 position= 95 count= 44850
 position= 96 count= 44850
 position= 97 count= 47919
 position= 98 count= 4640
 position= 99 count= 4640
 position= 100 count= 4640
 position= 101 count= 23359
 position= 102 count= 23359
 position= 103 count= 23359
 position= 104 count= 23359
 position= 105 count= 23359
 position= 106 count= 23359
 position= 107 count= 23359
 position= 108 count= 36855
 position= 109 count= 36855
 position= 110 count= 36855
 position= 111 count= 36855
 position= 112 count= 36855
 position= 113 count= 36855
 position= 114 count= 36855
 position= 115 count= 36855
 position= 116 count= 36855
 position= 117 count= 36855
 position= 118 count= 30905
 position= 119 count= 30905
 position= 120 count= 30905
 position= 121 count= 30905
 position= 122 count= 30905
 position= 123 count= 30905
 position= 124 count= 30905
 position= 125 count= 30905
 position= 126 count= 36226
 position= 127 count= 36226
 position= 128 count= 36226
 position= 129 count= 36226
 position= 130 count= 36226
 position= 131 count= 36226
 position= 132 count= 19368
 position= 133 count= 19368
 position= 134 count= 19368
 position= 135 count= 19368
 position= 136 count= 19368
 position= 137 count= 19368
 position= 138 count= 19368
 position= 139 count= 19368
 position= 140 count= 19368
 position= 141 count= 19368
 position= 142 count= 49564
 position= 143 count= 49564
 position= 144 count= 49564
 position= 145 count= 49564
 position= 146 count= 49564
 position= 147 count= 49564
 position= 148 count= 49564
 position= 149 count= 15280
 position= 150 count= 15280
 position= 151 count= 43228
 position= 152 count= 43228
 position= 153 count= 43228
 position= 154 count= 13986
 position= 155 count= 13986
 position= 156 count= 13986
 position= 157 count= 13986
 position= 158 count= 13986
 position= 159 count= 13986
 position= 160 count= 24543
 position= 161 count= 24543
 position= 162 count= 24543
 position= 163 count= 24543
 position= 164 count= 24543
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=6 count=1 
(0,1)
loading transition for reader[0] position=1 length=3 count=3 
(0,1)(1,4)
loading transition for reader[0] position=4 length=2 count=0 
(0,1)(1,4)(4,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
(0,0)
loading transition for reader[0] position=1 length=1 count=1 
(0,0)(1,1)
loading transition for reader[0] position=2 length=4 count=0 
(0,0)(1,1)(2,0)
loading transition for reader[1] position=4 length=10 count=1 
(0,0)(1,1)(2,0)(4,1)
loading transition for reader[0] position=6 length=2 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)
loading transition for reader[0] position=8 length=1 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)
loading transition for reader[0] position=9 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)
loading transition for reader[0] position=10 length=2 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)
loading transition for reader[0] position=12 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)
loading transition for reader[0] position=13 length=3 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)
loading transition for reader[0] position=16 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
loading transition for reader[0] position=1 length=1 count=1 
loading transition for reader[0] position=2 length=4 count=0 
loading transition for reader[1] position=4 length=10 count=1 
loading transition for reader[0] position=6 length=2 count=1 
loading transition for reader[0] position=8 length=1 count=0 
loading transition for reader[0] position=9 length=1 count=1 
loading transition for reader[0] position=10 length=2 count=0 
loading transition for reader[0] position=12 length=1 count=1 
loading transition for reader[0] position=13 length=3 count=0 
loading transition for reader[0] position=16 length=1 count=1 
02:58:17.764 WARN  WiggleWindow - Not writing 101 7
02:58:17.764 WARN  WiggleWindow - Not writing 111 7
02:58:17.764 WARN  WiggleWindow - Not writing 131 8
02:58:17.764 WARN  WiggleWindow - Not writing 141 8
02:58:17.764 WARN  WiggleWindow - Not writing 151 8
 appending (count=0,length=1)
 appending (count=4,length=3)
 appending (count=1,length=3)
 appending (count=0,length=2)
 appending (count=3,length=1)
 appending (count=1,length=1)
 appending (count=0,length=1)
 appending (count=4,length=3)
 appending (count=0,length=5)
 appending (count=3,length=1)
 appending (count=0,length=2)
 appending (count=2,length=1)
 appending (count=0,length=2)
 appending (count=3,length=1)
 appending (count=2,length=1)
 appending (count=0,length=1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=6 count=1 
(0,1)
loading transition for reader[0] position=1 length=3 count=3 
(0,1)(1,4)
loading transition for reader[0] position=4 length=2 count=0 
(0,1)(1,4)(4,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
(0,0)
loading transition for reader[0] position=1 length=1 count=1 
(0,0)(1,1)
loading transition for reader[0] position=2 length=4 count=0 
(0,0)(1,1)(2,0)
loading transition for reader[1] position=4 length=10 count=1 
(0,0)(1,1)(2,0)(4,1)
loading transition for reader[0] position=6 length=2 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)
loading transition for reader[0] position=8 length=1 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)
loading transition for reader[0] position=9 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)
loading transition for reader[0] position=10 length=2 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)
loading transition for reader[0] position=12 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)
loading transition for reader[0] position=13 length=3 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)
loading transition for reader[0] position=16 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
loading transition for reader[0] position=1 length=1 count=1 
loading transition for reader[0] position=2 length=4 count=0 
loading transition for reader[1] position=4 length=10 count=1 
loading transition for reader[0] position=6 length=2 count=1 
loading transition for reader[0] position=8 length=1 count=0 
loading transition for reader[0] position=9 length=1 count=1 
loading transition for reader[0] position=10 length=2 count=0 
loading transition for reader[0] position=12 length=1 count=1 
loading transition for reader[0] position=13 length=3 count=0 
loading transition for reader[0] position=16 length=1 count=1 
loading transition for reader[0] position=0 length=1 count=0 
(0,0)
loading transition for reader[0] position=1 length=3 count=1 
(0,0)(1,1)
 appending (count=10,length=4)
 appending (count=1,length=0)
 appending (count=2,length=8)
Hello
 appending (count=10,length=4)
02:58:17.784 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 0
Total bytes written: 31
Average bytes/logical entry: Infinity
Min query index: 2147483647
Max query index: -2147483648
Number of queries: 2
Number of targets: 0
97
02:58:17.790 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:17.798 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:17.802 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:17.806 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:17.812 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.818 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.828 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.831 WARN  MessageChunksWriter - Using chunk-size=1000
0
23
Setting quality threshold to 0.02
entry:query_index: 0
target_index: 0
position: 5
score: 5.0
matching_reverse_strand: false
query_length: 20
query_aligned_length: 20
target_aligned_length: 20
sequence_variations {
  to: "CTAG"
  from: "----"
  position: 10
  read_index: 10
}

entry:query_index: 1
target_index: 0
position: 5
matching_reverse_strand: false
query_length: 20
query_aligned_length: 20
target_aligned_length: 20
sequence_variations {
  to: "CTAG"
  from: "----"
  position: 10
  to_quality: "(((("
  read_index: 10
}

entry: query_index: 0
target_index: 0
position: 0
matching_reverse_strand: false
query_length: 10
query_aligned_length: 10
sequence_variations {
  to: "AAA"
  from: "---"
  position: 3
  read_index: 3
}

processing entry on target 0 at position 0 
processing entry on target 0 at position 5 
processing entry on target 1 at position 0 
processing entry on target 1 at position 5 
processing entry on target 4 at position 0 
processing entry on target 4 at position 5 
entry:query_index: 0
target_index: 0
position: 10
matching_reverse_strand: false
query_length: 50
query_aligned_length: 50
sequence_variations {
  to: "AAA"
  from: "---"
  position: 20
  read_index: 20
}

entry:query_index: 1
target_index: 0
position: 1
matching_reverse_strand: false
query_length: 50
query_aligned_length: 50
sequence_variations {
  to: "T"
  from: "A"
  position: 20
  read_index: 20
}

02:58:17.857 WARN  MessageChunksWriter - Using chunk-size=1000
Total logical entries written: 20000
Total bytes written: 77210
Average bytes/logical entry: 3.8605
Min query index: 0
Max query index: 1999
Number of queries: 2000
Number of targets: 10
02:58:17.928 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.930 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.931 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.938 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.940 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.941 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.955 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.956 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.958 WARN  MessageChunksWriter - Using chunk-size=1000
entry.position(): 1
entry.position(): 2
entry.position(): 3
entry.position(): 5
entry.position(): 6
entry.position(): 7
entry.position(): 8
entry.position(): 9
entry.position(): 10
entry.position(): 10
entry.position(): 12
entry.position(): 99
02:58:17.966 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.967 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.968 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.977 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.978 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.979 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.982 INFO  AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-1
02:58:17.983 INFO  AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-2
02:58:17.985 INFO  AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-3
02:58:17.988 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.989 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:17.990 WARN  MessageChunksWriter - Using chunk-size=1000
Processing queryIndex=8 with description '8 perfect start of ref'
Processing queryIndex=9 with description '9 perfect start of ref reverse strand'
Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1'
Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1'
Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1'
Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2'
Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2'
Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2'
Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20'
Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20'
Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2'
Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2'
Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20'
Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)'
Processing queryIndex=0 with description '0  perfect match'
Processing queryIndex=1 with description '1  perfect match on reverse strand'
Processing queryIndex=2 with description '2  mutation'
Processing queryIndex=3 with description '3  mutation on reverse strand'
Processing queryIndex=4 with description '4  insertion'
Processing queryIndex=6 with description '6  deletion'
Processing queryIndex=7 with description '7  deletion on reverse strand'
Processing queryIndex=27 with description '27 padding left & right, deletion then mutation'
Processing queryIndex=24 with description '24 padding left & right, mutation, deletion'
Processing queryIndex=5 with description '5  insertion on reverse strand'
Processing queryIndex=10 with description '10 perfect end of ref'
Processing queryIndex=11 with description '11 perfect end of ref reverse strand'
02:58:18.018 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:18.022 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:18.025 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:18.029 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:18.033 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:18.036 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:18.040 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
02:58:18.046 WARN  MessageChunksWriter - Using chunk-size=1000

02:58:18.049 WARN  MessageChunksWriter - Using chunk-size=1
02:58:18.054 WARN  MessageChunksWriter - Using chunk-size=1
02:58:18.058 WARN  MessageChunksWriter - Using chunk-size=1
02:58:18.062 WARN  MessageChunksWriter - Using chunk-size=1
02:58:18.068 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.070 WARN  MessageChunksWriter - Using chunk-size=1000
entry: score=30.0000 readOriginIndex=0 
entry: score=30.0000 readOriginIndex=0 
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
Scanned 5 entries
02:58:18.076 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.078 WARN  MessageChunksWriter - Using chunk-size=1000
entry: score=30.0000 readOriginIndex=0 
entry: score=30.0000 readOriginIndex=0 
Scanned 2 entries
02:58:18.082 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.083 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.088 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.089 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.094 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.096 WARN  MessageChunksWriter - Using chunk-size=1000
0
2
02:58:18.102 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.103 WARN  MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-101
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-101
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-102
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-102
02:58:18.109 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.110 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.115 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.116 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.121 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.122 WARN  MessageChunksWriter - Using chunk-size=1000
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
entry: score=30.0000 readOriginIndex=0 
entry: score=30.0000 readOriginIndex=0 
Scanned 5 entries
[main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression.
read       =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT
expected   =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT
recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT
read       =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG
expected   =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
read       =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG
expected   =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
read       =TAAAACCTAAAAAAAAAAAAAAACCCC
expected   =TAAAA--TAAAAAAAAAAAAAAACCCC
recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC
read       =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA
expected   =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA
recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA
read       =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG
expected   =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
read       =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT
expected   =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT
recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT
02:58:18.136 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.167 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.169 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.199 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:18.230 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.231 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.239 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.265 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.265 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
02:58:18.265 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 3ms; used/avail/free/total/max mem: 146.33M/15.63G/164.05M/310.38M/15.78G
02:58:18.272 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
found entry: query_index: 0
target_index: 1999
position: 19991
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

02:58:18.308 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.312 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.344 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.344 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.344 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.344 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
02:58:18.344 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.344 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 196.66M/15.58G/113.72M/310.38M/15.78G
02:58:18.347 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.361 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.389 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.412 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.414 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.436 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:18.458 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.459 WARN  MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item]; used/avail/free/total/max mem: 83.05M/15.70G/227.33M/310.38M/15.78G
found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

02:58:18.541 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.564 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.565 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.587 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:18.610 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.611 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.614 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.620 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
02:58:18.620 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
02:58:18.620 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 145.24M/15.63G/165.14M/310.38M/15.78G
02:58:18.623 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
notBestScoreCount=16.6667 % geneAmbiguityCount=33.3333 % 
found entry: query_index: 0
target_index: 1
position: 2
score: 31.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 0
target_index: 2
position: 3
score: 31.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 4
position: 6
score: 30.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

02:58:18.628 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.651 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.652 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.675 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:18.698 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.700 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.702 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.703 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
02:58:18.706 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.706 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
02:58:18.706 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.706 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
02:58:18.706 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.706 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 170.69M/15.61G/139.69M/310.38M/15.78G
02:58:18.708 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.710 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
02:58:18.713 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.736 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.737 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.759 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:18.782 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.783 WARN  MessageChunksWriter - Using chunk-size=1000
Finding max number of reads...
Found input file with 2 target(s)
02:58:18.785 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
Found input file with 2 target(s)
02:58:18.787 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
... max number of reads was 10
First pass: determine which reads should be kept in the merged alignment.
Scanning align-105
Scanning align-106
Found 40 logical alignment entries.
Prepare merged too many hits information.
02:58:18.790 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.790 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
02:58:18.790 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.790 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
02:58:18.790 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.790 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 195.57M/15.58G/114.81M/310.38M/15.78G
Second pass: writing the merged alignment.
02:58:18.792 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.794 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
Wrote 20  skipped: 20 50.000000% too many hits 0.000000% notBestScore: 50.000000%
Total logical entries written: 20
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 9
Number of queries: 10
Number of targets: 4
Percent aligned: 100.0
02:58:18.798 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.821 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.822 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.844 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:18.867 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.868 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.870 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.872 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
02:58:18.872 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
02:58:18.872 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 220.74M/15.56G/89.64M/310.38M/15.78G
02:58:18.874 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
found entry: query_index: 0
target_index: 1
position: 11
score: 40.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1
position: 12
score: 41.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1
position: 13
score: 42.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1
position: 14
score: 43.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1
position: 15
score: 44.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1
position: 16
score: 45.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1
position: 17
score: 46.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1
position: 18
score: 47.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1
position: 19
score: 48.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1
position: 20
score: 49.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

02:58:18.878 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.940 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.942 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:18.980 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:19.006 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:19.007 WARN  MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 94.78M/15.68G/215.60M/310.38M/15.78G
found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

02:58:19.072 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:19.094 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:19.095 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:19.117 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
02:58:19.139 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:19.140 WARN  MessageChunksWriter - Using chunk-size=1000
02:58:19.144 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:19.147 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:19.167 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:19.167 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:19.167 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:19.167 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
02:58:19.167 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:19.167 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 187.06M/15.59G/123.32M/310.38M/15.78G
02:58:19.170 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
02:58:19.181 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
found entry: query_index: 0
target_index: 1999
position: 19991
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 0
target_index: 3999
position: 19991
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 3999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

query_index: 0
target_index: 0
position: 0
query_position: 0
matching_reverse_strand: false
query_length: 75
query_aligned_length: 75
target_aligned_length: 75
mapping_quality: 255
pair_flags: 0
fragment_index: 0
ambiguity: 1

query_index: 1
target_index: 0
position: 1
query_position: 0
matching_reverse_strand: false
query_length: 75
query_aligned_length: 75
target_aligned_length: 75
mapping_quality: 255
pair_flags: 0
fragment_index: 0
ambiguity: 1

02:58:19.283 INFO  TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0
02:58:19.283 INFO  TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds
[ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits
[ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 1
decoding: 2
decoding: 3
decoding: 4
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 1
[ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits
[ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0
 {1} {0}decoding: 4
 {0} {0}decoding: 4
 {0} {0}decoding: 4
 {0}decoding: 4
 {0}decoding: 4
 {0}decoding: 4
decoding: 4
 {0}decoding: 4
 {0}decoding: 4
decoding: 4
 {0}decoding: 4
decoding: 4
 {0}decoding: 4
decoding: 4
 {0} {0} {0} {0} {0}decoding: 1
 {0} {0} {0} {0}decoding: 2
 {0} {0} {0} {0} {0}decoding: 3
decoding: 4
 {0} {0} {0} {0}decoding: 3
 {0} {0} {0}decoding: 1
 {0} {0} {0} {0}decoding: 2
 {0} {0} {0}decoding: 1
 {0} {0} {0}decoding: 2
 {0} {0} {0} {0}decoding: 3
 {0} {0} {0}decoding: 1
 {0} {0} {0}decoding: 2
 {0} {0}decoding: 1
 {0} {0} {0}decoding: 2
 {0} {0}decoding: 1
[ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits
[ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 1
decoding: 2
decoding: 3
decoding: 4
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 1
count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3}
count keys [0, 3, 5, 11, 13]
-1 0.0
0 0.0
1 0.0
2 0.0
3 0.0
4 0.0
5 0.0
6 0.0
7 0.0
8 0.0
9 0.0
10 0.0
11 0.0
12 0.0
13 0.0
14 0.0
15 0.0
16 0.0
17 0.0
18 0.0
19 0.0
20 0.0
21 0.0
22 0.0
23 0.0
24 0.0
25 0.0
26 0.0
27 0.0
28 0.0
29 0.0
30 0.0
overlapping count 3, 4 0.0
overlapping count 15, 17 0.0
overlapping count 9, 18 2.0
overlapping count 3, 8 2.0
overlapping count 11, 12 0.0
overlapping count 9, 10 1.0
overlapping count 8, 9 0.0
overlapping count 8, 8 0.0
overlapping count 5, 6 0.0
overlapping count 3, 3 0.0
overlapping count 3, 12 5.0
overlapping count -1, 2 0.0
overlapping count 0, 45 6.0
overlapping count 13, 15 0.0
-1 0.0
0 0.0
1 0.0
2 0.0
3 2.0
4 2.0
5 3.0
6 3.0
7 3.0
8 3.0
9 3.0
10 3.0
11 2.0
12 2.0
13 0.0
14 0.0
15 1.0
16 1.0
17 1.0
18 1.0
19 0.0
20 0.0
21 0.0
22 0.0
23 0.0
24 0.0
25 0.0
26 0.0
27 0.0
28 0.0
29 0.0
30 0.0
overlapping count 3, 4 2.0
overlapping count 2, 3 2.0
overlapping count 3, 8 4.0
overlapping count 11, 12 2.0
overlapping count 9, 10 3.0
overlapping count 8, 9 4.0
overlapping count 8, 8 3.0
overlapping count 5, 6 3.0
overlapping count 3, 3 2.0
overlapping count 3, 12 5.0
overlapping count -1, 2 0.0
overlapping count 0, 45 6.0
overlapping count 13, 15 1.0
Total logical entries written: 4
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 1
Max query index: 1
Number of queries: 1
Number of targets: 2
Total logical entries written: 4
Total bytes written: 62
Average bytes/logical entry: 15.5
Min query index: 1
Max query index: 1
Number of queries: 1
Number of targets: 2
[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 82.32 s - in TestSuite
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.069 s]
[INFO] Goby I/O ........................................... SUCCESS [  7.140 s]
[INFO] Goby Full Distribution ............................. SUCCESS [01:58 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:05 min
[INFO] Finished at: 2025-03-07T02:59:49-12:00
[INFO] ------------------------------------------------------------------------
make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Ddebian.package=libgoby-io-java -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO]   from pom.xml
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- debian:2.6:install (default-cli) @ goby-framework ---
[INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libgoby-io-java --has-package-version
[INFO] 	--rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO]   from goby-io/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian:2.6:install (default-cli) @ goby-io ---
[INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libgoby-io-java
[INFO] 	--rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules
[INFO] Install jar for goby-io into /usr/share/java
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO]   from goby-distribution/pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian:2.6:install (default-cli) @ goby-distribution ---
[INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=goby-java
[INFO] 	--rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules
[INFO] Install jar for goby-distribution into /usr/share/java
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.400 s]
[INFO] Goby I/O ........................................... SUCCESS [  0.064 s]
[INFO] Goby Full Distribution ............................. SUCCESS [  0.060 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.715 s
[INFO] Finished at: 2025-03-07T02:59:51-12:00
[INFO] ------------------------------------------------------------------------
	mh_resolve_dependencies --non-interactive --offline --build -plibgoby-io-java --base-directory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 --non-explore
Analysing pom.xml...
Analysing goby-distribution/pom.xml...
Checking the parent dependency in the sub project goby-distribution/pom.xml
Analysing goby-io/pom.xml...
Checking the parent dependency in the sub project goby-io/pom.xml
> dpkg --search /usr/share/maven-repo/org/rosuda/REngine/REngine/*/* 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/maven-repo/org/rosuda/REngine/REngine
Mar 07, 2025 2:59:57 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve
SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian
> dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2
Mar 07, 2025 3:00:03 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve
SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian
ERROR:
goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian
goby-io/pom.xml: dependency is not packaged in the Maven repository for Debian: org.itadaki:bzip2:debian
--------
Some problems were found in this project, exiting...
	mh_unpatchpoms -plibgoby-io-java
   dh_install
   jh_installjavadoc
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_lintian
   dh_perl
   dh_link
   jh_installlibs
   jh_classpath
   jh_manifest
   jh_exec
   jh_depends
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined
dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined
dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined
dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined
dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'.
dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-11_all.deb'.
 dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo
 dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/1194656 and its subdirectories
I: Current time: Fri Mar  7 03:00:13 -12 2025
I: pbuilder-time-stamp: 1741359613