I: pbuilder: network access will be disabled during build
I: Current time: Tue Apr 7 20:03:18 -12 2026
I: pbuilder-time-stamp: 1775635398
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/2408174/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='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='a8a84388dcde4ab7b4d914cc0b9f6daf'
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='2408174'
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.4hrWSzCj/pbuilderrc_qifK --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.4hrWSzCj/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2408174/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: amd64
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 ... 19783 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} libdrm-intel1{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} libpciaccess0{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 libgkl-jni 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, 467 newly installed, 0 to remove and 0 not upgraded.
Need to get 386 MB of archives. After unpacking 1014 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 4.1.0~beta5-3 [43.5 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 systemd amd64 257.3-1 [3092 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-1 [177 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.16.2-1 [79.4 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.16.2-1 [51.6 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.16.2-1 [158 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.16.2-1 [52.7 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.16.2-1 [71.0 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 257.3-1 [293 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 44 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0050 [42.7 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.5-1 [1513 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.17.5+ds-3 [51.5 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 48~beta-3 [504 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B]
Get: 64 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.109-1 [1393 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B]
Get: 70 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.15-1 [2163 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 ant-contrib all 1.0~b3+svn177-12 [262 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.55.2-1 [170 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-6 [294 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.16.2-1 [51.5 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-3 [139 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-16 [112 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 131 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2 [463 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.1-3 [26.8 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.1-3 [11.9 kB]
Get: 147 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.1-3 [5860 B]
Get: 148 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB]
Get: 149 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB]
Get: 150 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB]
Get: 151 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB]
Get: 152 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB]
Get: 153 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB]
Get: 154 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB]
Get: 155 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB]
Get: 156 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB]
Get: 157 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB]
Get: 158 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB]
Get: 159 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.124-1 [8180 B]
Get: 160 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.124-1 [38.9 kB]
Get: 161 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB]
Get: 162 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB]
Get: 163 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB]
Get: 164 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB]
Get: 165 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB]
Get: 166 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB]
Get: 167 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.124-1 [22.4 kB]
Get: 168 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB]
Get: 169 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.124-1 [63.8 kB]
Get: 170 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB]
Get: 171 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 172 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB]
Get: 173 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get: 174 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB]
Get: 175 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB]
Get: 176 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB]
Get: 177 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B]
Get: 178 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 25.0.0-1 [9620 kB]
Get: 179 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB]
Get: 180 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 25.0.0-1 [43.9 kB]
Get: 181 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB]
Get: 182 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 25.0.0-1 [45.5 kB]
Get: 183 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 25.0.0-1 [142 kB]
Get: 184 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB]
Get: 185 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB]
Get: 186 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.13-1 [21.1 kB]
Get: 187 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB]
Get: 188 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB]
Get: 189 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 190 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB]
Get: 191 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB]
Get: 192 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B]
Get: 193 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk-headless amd64 21.0.6+7-1 [82.8 MB]
Get: 194 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B]
Get: 195 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk amd64 21.0.6+7-1 [3434 kB]
Get: 196 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.21-76 [1076 B]
Get: 197 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB]
Get: 198 http://deb.debian.org/debian unstable/main amd64 libassuan9 amd64 3.0.2-2 [61.5 kB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 gpgconf amd64 2.2.46-2 [121 kB]
Get: 201 http://deb.debian.org/debian unstable/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB]
Get: 202 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 203 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 204 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 205 http://deb.debian.org/debian unstable/main amd64 libnpth0t64 amd64 1.8-2 [22.9 kB]
Get: 206 http://deb.debian.org/debian unstable/main amd64 dirmngr amd64 2.2.46-2 [369 kB]
Get: 207 http://deb.debian.org/debian unstable/main amd64 gnupg-l10n all 2.2.46-2 [702 kB]
Get: 208 http://deb.debian.org/debian unstable/main amd64 gpg amd64 2.2.46-2 [532 kB]
Get: 209 http://deb.debian.org/debian unstable/main amd64 pinentry-curses amd64 1.3.1-2 [86.4 kB]
Get: 210 http://deb.debian.org/debian unstable/main amd64 gpg-agent amd64 2.2.46-2 [251 kB]
Get: 211 http://deb.debian.org/debian unstable/main amd64 gpgsm amd64 2.2.46-2 [255 kB]
Get: 212 http://deb.debian.org/debian unstable/main amd64 gnupg all 2.2.46-2 [376 kB]
Get: 213 http://deb.debian.org/debian unstable/main amd64 gpgv amd64 2.2.46-2 [220 kB]
Get: 214 http://deb.debian.org/debian unstable/main amd64 sopv-gpgv all 0.1.1-1 [10.7 kB]
Get: 215 http://deb.debian.org/debian unstable/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 216 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 217 http://deb.debian.org/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 218 http://deb.debian.org/debian unstable/main amd64 libfile-touch-perl all 0.12-2 [8816 B]
Get: 219 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB]
Get: 220 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 221 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get: 222 http://deb.debian.org/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB]
Get: 223 http://deb.debian.org/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB]
Get: 224 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get: 225 http://deb.debian.org/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB]
Get: 226 http://deb.debian.org/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB]
Get: 227 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 228 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 229 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 230 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 231 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 232 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 233 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 234 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get: 235 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get: 236 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get: 237 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB]
Get: 238 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB]
Get: 239 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 240 http://deb.debian.org/debian unstable/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB]
Get: 241 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 242 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 243 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get: 244 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get: 245 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 246 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get: 247 http://deb.debian.org/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB]
Get: 248 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB]
Get: 249 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get: 250 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get: 251 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get: 252 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 253 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.78-1 [183 kB]
Get: 254 http://deb.debian.org/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get: 255 http://deb.debian.org/debian unstable/main amd64 wdiff amd64 1.2.2-7 [122 kB]
Get: 256 http://deb.debian.org/debian unstable/main amd64 devscripts all 2.25.5 [1058 kB]
Get: 257 http://deb.debian.org/debian unstable/main amd64 fastjar amd64 2:0.98-7 [80.1 kB]
Get: 258 http://deb.debian.org/debian unstable/main amd64 jarwrapper all 0.80 [9692 B]
Get: 259 http://deb.debian.org/debian unstable/main amd64 javahelper all 0.80 [80.4 kB]
Get: 260 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB]
Get: 261 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-5 [350 kB]
Get: 262 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B]
Get: 263 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B]
Get: 264 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get: 265 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB]
Get: 266 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get: 267 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.3-1 [2459 kB]
Get: 268 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 269 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get: 270 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B]
Get: 271 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7.1-1 [391 kB]
Get: 272 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B]
Get: 273 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 274 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB]
Get: 275 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB]
Get: 276 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get: 277 http://deb.debian.org/debian unstable/main amd64 libjoptsimple-java all 5.0.4-7 [73.7 kB]
Get: 278 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.18.0-1 [304 kB]
Get: 279 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 280 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 281 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 282 http://deb.debian.org/debian unstable/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB]
Get: 283 http://deb.debian.org/debian unstable/main amd64 libmongodb-java all 3.6.3-2 [1901 kB]
Get: 284 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 285 http://deb.debian.org/debian unstable/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB]
Get: 286 http://deb.debian.org/debian unstable/main amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB]
Get: 287 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 288 http://deb.debian.org/debian unstable/main amd64 libbsh-java all 2.0b4-20 [291 kB]
Get: 289 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.18.0-1 [509 kB]
Get: 290 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB]
Get: 291 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get: 292 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 293 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 294 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB]
Get: 295 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB]
Get: 296 http://deb.debian.org/debian unstable/main amd64 libguice-java all 5.1.0-1 [932 kB]
Get: 297 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 43-2 [6252 B]
Get: 298 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 299 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 300 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB]
Get: 301 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 302 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 303 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 304 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB]
Get: 305 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 306 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B]
Get: 307 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-4 [55.3 kB]
Get: 308 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB]
Get: 309 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB]
Get: 310 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB]
Get: 311 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 312 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB]
Get: 313 http://deb.debian.org/debian unstable/main amd64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB]
Get: 314 http://deb.debian.org/debian unstable/main amd64 libbyte-buddy-java all 1.14.19-1 [4756 kB]
Get: 315 http://deb.debian.org/debian unstable/main amd64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB]
Get: 316 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get: 317 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB]
Get: 318 http://deb.debian.org/debian unstable/main amd64 libcommons-collections4-java all 4.4-2 [682 kB]
Get: 319 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB]
Get: 320 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 321 http://deb.debian.org/debian unstable/main amd64 libcommons-configuration-java all 1.10-7 [348 kB]
Get: 322 http://deb.debian.org/debian unstable/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB]
Get: 323 http://deb.debian.org/debian unstable/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get: 324 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 325 http://deb.debian.org/debian unstable/main amd64 libcommons-math-java all 2.2-9 [933 kB]
Get: 326 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB]
Get: 327 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 328 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB]
Get: 329 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B]
Get: 330 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB]
Get: 331 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB]
Get: 332 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 333 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB]
Get: 334 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get: 335 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.13.0-1 [228 kB]
Get: 336 http://deb.debian.org/debian unstable/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB]
Get: 337 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 338 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 339 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 340 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 341 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 342 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 343 http://deb.debian.org/debian unstable/main amd64 libdistlib-java all 1.0-5 [72.5 kB]
Get: 344 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-5 [214 kB]
Get: 345 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB]
Get: 346 http://deb.debian.org/debian unstable/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB]
Get: 347 http://deb.debian.org/debian unstable/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB]
Get: 348 http://deb.debian.org/debian unstable/main amd64 libdoxia-java all 2.0.0-1 [113 kB]
Get: 349 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B]
Get: 350 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-9 [132 kB]
Get: 351 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 352 http://deb.debian.org/debian unstable/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB]
Get: 353 http://deb.debian.org/debian unstable/main amd64 velocity all 1.7-7 [431 kB]
Get: 354 http://deb.debian.org/debian unstable/main amd64 libplexus-velocity-java all 1.2-4 [9676 B]
Get: 355 http://deb.debian.org/debian unstable/main amd64 liboro-java all 2.0.8a-14 [70.5 kB]
Get: 356 http://deb.debian.org/debian unstable/main amd64 libvelocity-tools-java all 2.0-9 [311 kB]
Get: 357 http://deb.debian.org/debian unstable/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB]
Get: 358 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB]
Get: 359 http://deb.debian.org/debian unstable/main amd64 libxpp3-java all 1.1.4c-4 [294 kB]
Get: 360 http://deb.debian.org/debian unstable/main amd64 libxstream-java all 1.4.21-1 [567 kB]
Get: 361 http://deb.debian.org/debian unstable/main amd64 libjsap-java all 2.1-5 [102 kB]
Get: 362 http://deb.debian.org/debian unstable/main amd64 liblogback-java all 1:1.2.11-6 [701 kB]
Get: 363 http://deb.debian.org/debian unstable/main amd64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB]
Get: 364 http://deb.debian.org/debian unstable/main amd64 libobjenesis-java all 3.4-2 [41.3 kB]
Get: 365 http://deb.debian.org/debian unstable/main amd64 libeasymock-java all 5.5.0-1 [134 kB]
Get: 366 http://deb.debian.org/debian unstable/main amd64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 367 http://deb.debian.org/debian unstable/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB]
Get: 368 http://deb.debian.org/debian unstable/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB]
Get: 369 http://deb.debian.org/debian unstable/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B]
Get: 370 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 371 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get: 372 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 373 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 374 http://deb.debian.org/debian unstable/main amd64 libxom-java all 1.3.9-1 [174 kB]
Get: 375 http://deb.debian.org/debian unstable/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB]
Get: 376 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB]
Get: 377 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB]
Get: 378 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB]
Get: 379 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB]
Get: 380 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB]
Get: 381 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB]
Get: 382 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB]
Get: 383 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB]
Get: 384 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.15-1 [1382 kB]
Get: 385 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB]
Get: 386 http://deb.debian.org/debian unstable/main amd64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB]
Get: 387 http://deb.debian.org/debian unstable/main amd64 libicu4j-java all 73.2-1 [16.4 MB]
Get: 388 http://deb.debian.org/debian unstable/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB]
Get: 389 http://deb.debian.org/debian unstable/main amd64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB]
Get: 390 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get: 391 http://deb.debian.org/debian unstable/main amd64 libjansi-java all 2.4.1-2 [100 kB]
Get: 392 http://deb.debian.org/debian unstable/main amd64 libjavassist-java all 1:3.27.0-1 [731 kB]
Get: 393 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 394 http://deb.debian.org/debian unstable/main amd64 libjboss-logging-java all 3.5.3-1 [56.2 kB]
Get: 395 http://deb.debian.org/debian unstable/main amd64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB]
Get: 396 http://deb.debian.org/debian unstable/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB]
Get: 397 http://deb.debian.org/debian unstable/main amd64 libjcommander-java all 1.71-4 [73.0 kB]
Get: 398 http://deb.debian.org/debian unstable/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 399 http://deb.debian.org/debian unstable/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 400 http://deb.debian.org/debian unstable/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 401 http://deb.debian.org/debian unstable/main amd64 libjetty9-java all 9.4.57-1 [2965 kB]
Get: 402 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 403 http://deb.debian.org/debian unstable/main amd64 libjtidy-java all 7+svn20110807-6 [251 kB]
Get: 404 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 405 http://deb.debian.org/debian unstable/main amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB]
Get: 406 http://deb.debian.org/debian unstable/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB]
Get: 407 http://deb.debian.org/debian unstable/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB]
Get: 408 http://deb.debian.org/debian unstable/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB]
Get: 409 http://deb.debian.org/debian unstable/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB]
Get: 410 http://deb.debian.org/debian unstable/main amd64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB]
Get: 411 http://deb.debian.org/debian unstable/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB]
Get: 412 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B]
Get: 413 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB]
Get: 414 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get: 415 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
Get: 416 http://deb.debian.org/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB]
Get: 417 http://deb.debian.org/debian unstable/main amd64 libmaven-dependency-analyzer-java all 1.15.1-1 [38.5 kB]
Get: 418 http://deb.debian.org/debian unstable/main amd64 libmaven-dependency-tree-java all 3.3.0-1 [35.0 kB]
Get: 419 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-impl-java all 4.0.0-1 [17.6 kB]
Get: 420 http://deb.debian.org/debian unstable/main amd64 libmaven-dependency-plugin-java all 3.8.1-1 [191 kB]
Get: 421 http://deb.debian.org/debian unstable/main amd64 libmaven-invoker-java all 3.3.0-1 [29.1 kB]
Get: 422 http://deb.debian.org/debian unstable/main amd64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB]
Get: 423 http://deb.debian.org/debian unstable/main amd64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB]
Get: 424 http://deb.debian.org/debian unstable/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB]
Get: 425 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B]
Get: 426 http://deb.debian.org/debian unstable/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B]
Get: 427 http://deb.debian.org/debian unstable/main amd64 libmaven-plugin-tools-java all 3.10.2-1 [245 kB]
Get: 428 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB]
Get: 429 http://deb.debian.org/debian unstable/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB]
Get: 430 http://deb.debian.org/debian unstable/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB]
Get: 431 http://deb.debian.org/debian unstable/main amd64 libmaven-source-plugin-java all 3.3.1-1 [27.7 kB]
Get: 432 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB]
Get: 433 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB]
Get: 434 http://deb.debian.org/debian unstable/main amd64 libpicard-java all 3.3.0+dfsg-2 [1778 kB]
Get: 435 http://deb.debian.org/debian unstable/main amd64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB]
Get: 436 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 437 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 438 http://deb.debian.org/debian unstable/main amd64 libprotobuf32t64 amd64 3.21.12-10+b6 [981 kB]
Get: 439 http://deb.debian.org/debian unstable/main amd64 libprotobuf-lite32t64 amd64 3.21.12-10+b6 [274 kB]
Get: 440 http://deb.debian.org/debian unstable/main amd64 libprotobuf-dev amd64 3.21.12-10+b6 [1328 kB]
Get: 441 http://deb.debian.org/debian unstable/main amd64 libprotobuf-java all 3.21.12-10 [1268 kB]
Get: 442 http://deb.debian.org/debian unstable/main amd64 libprotoc32t64 amd64 3.21.12-10+b6 [923 kB]
Get: 443 http://deb.debian.org/debian unstable/main amd64 libreflections-java all 0.10.2+dfsg-2 [125 kB]
Get: 444 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB]
Get: 445 http://deb.debian.org/debian unstable/main amd64 libsurefire-java all 2.22.3-3 [1284 kB]
Get: 446 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get: 447 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 448 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get: 449 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB]
Get: 450 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get: 451 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get: 452 http://deb.debian.org/debian unstable/main amd64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 453 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get: 454 http://deb.debian.org/debian unstable/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [99.5 kB]
Get: 455 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB]
Get: 456 http://deb.debian.org/debian unstable/main amd64 maven all 3.9.9-1 [19.7 kB]
Get: 457 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB]
Get: 458 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 459 http://deb.debian.org/debian unstable/main amd64 maven-debian-helper all 2.6.7 [108 kB]
Get: 460 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 461 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 462 http://deb.debian.org/debian unstable/main amd64 protobuf-compiler amd64 3.21.12-10+b6 [84.8 kB]
Get: 463 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB]
Get: 464 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 465 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.3-1 [28.3 MB]
Get: 466 http://deb.debian.org/debian unstable/main amd64 r-cran-rjava amd64 1.0-11-1 [702 kB]
Get: 467 http://deb.debian.org/debian unstable/main amd64 testng all 6.9.12-4 [795 kB]
Fetched 386 MB in 6s (67.2 MB/s)
Preconfiguring packages ...
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Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ...
Unpacking libsystemd-shared:amd64 (257.3-1) ...
Selecting previously unselected package libapparmor1:amd64.
Preparing to unpack .../libapparmor1_4.1.0~beta5-3_amd64.deb ...
Unpacking libapparmor1:amd64 (4.1.0~beta5-3) ...
Setting up libsystemd-shared:amd64 (257.3-1) ...
Selecting previously unselected package systemd.
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Preparing to unpack .../systemd_257.3-1_amd64.deb ...
Unpacking systemd (257.3-1) ...
Setting up libapparmor1:amd64 (4.1.0~beta5-3) ...
Setting up systemd (257.3-1) ...
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.
[0;1;39m/usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring.[0m
Selecting previously unselected package systemd-sysv.
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Preparing to unpack .../00-systemd-sysv_257.3-1_amd64.deb ...
Unpacking systemd-sysv (257.3-1) ...
Selecting previously unselected package libdbus-1-3:amd64.
Preparing to unpack .../01-libdbus-1-3_1.16.2-1_amd64.deb ...
Unpacking libdbus-1-3:amd64 (1.16.2-1) ...
Selecting previously unselected package dbus-bin.
Preparing to unpack .../02-dbus-bin_1.16.2-1_amd64.deb ...
Unpacking dbus-bin (1.16.2-1) ...
Selecting previously unselected package dbus-session-bus-common.
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Unpacking dbus-session-bus-common (1.16.2-1) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../04-libexpat1_2.6.4-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.4-1) ...
Selecting previously unselected package dbus-daemon.
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Unpacking dbus-daemon (1.16.2-1) ...
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Unpacking dbus-system-bus-common (1.16.2-1) ...
Selecting previously unselected package dbus.
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Unpacking dbus (1.16.2-1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.8-1) ...
Selecting previously unselected package binfmt-support.
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Unpacking binfmt-support (2.2.2-7) ...
Selecting previously unselected package libpython3.13-minimal:amd64.
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Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ...
Selecting previously unselected package python3.13-minimal.
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Unpacking python3.13-minimal (3.13.2-1) ...
Setting up libpython3.13-minimal:amd64 (3.13.2-1) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.2-1) ...
Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.13.2-2) ...
Selecting previously unselected package media-types.
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Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
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Unpacking tzdata (2025a-2) ...
Selecting previously unselected package libffi8:amd64.
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Unpacking libffi8:amd64 (3.4.7-1) ...
Selecting previously unselected package readline-common.
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Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:amd64.
Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ...
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:amd64 (8.2-6) ...
Selecting previously unselected package libpython3.13-stdlib:amd64.
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Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ...
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Setting up python3-minimal (3.13.2-2) ...
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Unpacking python3 (3.13.2-2) ...
Selecting previously unselected package sgml-base.
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Unpacking libproc2-0:amd64 (2:4.0.4-7) ...
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Unpacking procps (2:4.0.4-7) ...
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Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package openssl.
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Unpacking openssl (3.4.1-1) ...
Selecting previously unselected package ca-certificates.
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Unpacking ca-certificates (20241223) ...
Selecting previously unselected package libmagic-mgc.
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic1t64:amd64 (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) ...
Selecting previously unselected package libuchardet0:amd64.
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Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
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Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package libpam-systemd:amd64.
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Unpacking libpam-systemd:amd64 (257.3-1) ...
Selecting previously unselected package bsdextrautils.
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Unpacking bsdextrautils (2.40.4-5) ...
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Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package libtext-charwidth-perl:amd64.
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Selecting previously unselected package libtext-wrapi18n-perl.
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Unpacking libtext-wrapi18n-perl (0.06-10) ...
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Moving old data out of the way
Unpacking ucf (3.0050) ...
Selecting previously unselected package libgdk-pixbuf2.0-common.
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invoke-rc.d: policy-rc.d denied execution of start.
Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' -> '/usr/lib/systemd/system/binfmt-support.service'.
Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libjbzip2-java (0.9.1-8) ...
Setting up libipc-run-perl (20231003.0-2) ...
Setting up libpcsclite1:amd64 (2.3.1-1) ...
Setting up pkgconf-bin (1.8.1-4) ...
Setting up libsensors5:amd64 (1:3.6.0-10+b1) ...
Setting up libmongodb-java (3.6.3-2) ...
Setting up libk5crypto3:amd64 (1.21.3-4) ...
Setting up libactivation-java (1.2.0-2) ...
Setting up libhamcrest-java (2.2-2) ...
Setting up libbsh-java (2.0b4-20) ...
Setting up libjsp-api-java (2.3.4-3) ...
Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ...
Setting up libgfortran5:amd64 (14.2.0-17) ...
Setting up libvulkan1:amd64 (1.4.304.0-1) ...
Setting up autoconf (2.72-3) ...
Setting up libnghttp3-9:amd64 (1.8.0-1) ...
Setting up libwebp7:amd64 (1.5.0-0.1) ...
Setting up libcolt-free-java (1.2.0+dfsg-8) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libgif7:amd64 (5.2.2-1+b1) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libffi8:amd64 (3.4.7-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up libplexus-interactivity-api-java (1.3-1) ...
Setting up libfreemarker-java (2.3.32-2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libxshmfence1:amd64 (1.3-1+b3) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.55.2-1) ...
Setting up libcommons-math-java (2.2-9) ...
Setting up gpgv (2.2.46-2) ...
Setting up libtiff6:amd64 (4.5.1+git230720-5) ...
Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ...
Setting up dbus-session-bus-common (1.16.2-1) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libassuan9:amd64 (3.0.2-2) ...
Setting up libxml-commons-external-java (1.4.01-6) ...
Setting up procps (2:4.0.4-7) ...
Setting up libxbean-reflect-java (4.5-9) ...
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:amd64 (4.20.0-2) ...
Setting up libx11-6:amd64 (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:amd64 (1.21.3-4) ...
Setting up libwayland-egl1:amd64 (1.23.1-3) ...
Setting up libmbedcrypto16:amd64 (3.6.2-3) ...
Setting up libpaper2:amd64 (2.2.5-0.3+b1) ...
Setting up libssh2-1t64:amd64 (1.11.1-1) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libjoptsimple-java (5.0.4-7) ...
Setting up libprotoc32t64:amd64 (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:amd64 (1:0.4.6-1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:amd64 (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:amd64 (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:amd64 (1.7.0-2) ...
Setting up libwayland-client0:amd64 (1.23.1-3) ...
Setting up libnet-ssleay-perl:amd64 (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:amd64 (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:amd64 (1.17.0-2+b1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libllvm19:amd64 (1:19.1.7-1+b1) ...
Setting up libwayland-server0:amd64 (1.23.1-3) ...
Setting up libx11-xcb1:amd64 (2:1.8.10-2) ...
Setting up libice6:amd64 (2:1.1.1-1) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up libxstream-java (1.4.21-1) ...
Setting up liblapack3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up gettext (0.23.1-1) ...
Setting up libjetty9-java (9.4.57-1) ...
Setting up libxdamage1:amd64 (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:amd64 (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:amd64 (0.8-16) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:amd64 (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:amd64 (2.3.7-2+b1) ...
Setting up libnss3:amd64 (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:amd64 (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:amd64 (1.8.1-4) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libprotobuf-dev:amd64 (3.21.12-10+b6) ...
Setting up dh-autoreconf (20) ...
Setting up patchutils (0.4.2-1) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:amd64 (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:amd64 (2.83.5-1) ...
Setting up libmbedx509-7:amd64 (3.6.2-3) ...
Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ...
Setting up libxfixes3:amd64 (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:amd64 (0.25.5-3) ...
Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ...
Setting up libxrandr2:amd64 (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:amd64 (3.6.2-3) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libdrm2:amd64 (2.4.124-1) ...
Setting up groff-base (1.23.0-7) ...
Setting up libwayland-cursor0:amd64 (1.23.1-3) ...
Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ...
Setting up gpgconf (2.2.46-2) ...
Setting up libpam-systemd:amd64 (257.3-1) ...
Setting up libcommons-beanutils-java (1.9.4-2) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ...
Setting up libsnappy-java (1.1.10.7-1) ...
Setting up libxss1:amd64 (1:1.2.3-1+b3) ...
Setting up libfontconfig1:amd64 (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:amd64 (2:1.2.4-1) ...
Setting up libreflections-java (0.10.2+dfsg-2) ...
Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ...
Setting up libavahi-client3:amd64 (0.8-16) ...
Setting up libio-socket-ssl-perl (2.089-1) ...
Setting up gpg (2.2.46-2) ...
Setting up libpython3-stdlib:amd64 (3.13.2-2) ...
Setting up libhttp-message-perl (7.00-2) ...
Setting up libdrm-amdgpu1:amd64 (2.4.124-1) ...
Setting up libgnutls30t64:amd64 (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 velocity (1.7-7) ...
Setting up fontconfig (2.15.0-2) ...
Regenerating fonts cache... done.
Setting up libxft2:amd64 (2.3.6-1+b4) ...
Setting up gpg-agent (2.2.46-2) ...
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:amd64 (2.55.2-1) ...
Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxi6:amd64 (2:1.8.2-1) ...
Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ...
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:amd64 (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:amd64 (8.6.16-1) ...
Setting up libdistlib-java (1.0-5) ...
Setting up libxcursor1:amd64 (1:1.2.3-1) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b4) ...
Setting up gpgsm (2.2.46-2) ...
Setting up libpango-1.0-0:amd64 (1.56.1-1) ...
Setting up libdrm-intel1:amd64 (2.4.124-1) ...
Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ...
Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
Setting up libcloudproviders0:amd64 (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:amd64 (1.18.2-2) ...
Setting up libcolord2:amd64 (1.4.7-3) ...
Setting up libdconf1:amd64 (0.40.0-5) ...
Setting up dirmngr (2.2.46-2) ...
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:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libatspi2.0-0t64:amd64 (2.55.2-1) ...
Setting up libxt6t64:amd64 (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 (2.2.46-2) ...
Setting up liblightcouch-java (0.2.0-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libcairo-gobject2:amd64 (1.18.2-2) ...
Setting up libmaven-shared-utils-java (3.4.2-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ...
Setting up libmaven-resources-plugin-java (3.3.1-1) ...
Setting up libcups2t64:amd64 (2.4.10-2+b1) ...
Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ...
Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b2) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ...
Setting up mesa-libgallium:amd64 (25.0.0-1) ...
Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libcommons-compress-java (1.27.1-2) ...
Setting up libcurl4t64:amd64 (8.12.1-3) ...
Setting up libcommons-validator-java (1:1.9.0-1) ...
Setting up libgbm1:amd64 (25.0.0-1) ...
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 libgl1-mesa-dri:amd64 (25.0.0-1) ...
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 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:amd64 (3.0.9+dfsg-7+b2) ...
Setting up libbarclay-java (5.0.0+dfsg-1) ...
Setting up libglx-mesa0:amd64 (25.0.0-1) ...
Setting up libglx0:amd64 (1.7.0-1+b2) ...
Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ...
Setting up libmaven-archiver-java (3.6.2-1) ...
Setting up libgl1:amd64 (1.7.0-1+b2) ...
Setting up libmaven-source-plugin-java (3.3.1-1) ...
Setting up libgtk-3-common (3.24.48-4) ...
Setting up libgtk-3-0t64:amd64 (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 (257.3-1) ...
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=_FÅ‘tanúsÃtvány.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:amd64 (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:amd64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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:amd64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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) ...
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 amd64
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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 [ 0.048 s]
[INFO] Goby I/O ........................................... SUCCESS [ 15.913 s]
[INFO] Goby Full Distribution ............................. SUCCESS [ 23.266 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 39.335 s
[INFO] Finished at: 2026-04-07T20:05:32-12:00
[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
20:05:47.099 INFO RLoggerMainLoopCallback -
20:05:47.103 INFO RLoggerMainLoopCallback - R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
20:05:47.104 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.
20:05:47.104 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.
20:05:47.104 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.
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]
20:05:47.303 WARN MessageChunksWriter - Using chunk-size=10000
20:05:47.331 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.407 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.411 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.446 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:47.475 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.477 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.495 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent.
20:05:47.506 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.
20:05:47.563 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.
20:05:47.563 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
20:05:47.563 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: 2ms [1 items, 1,000.00 items/s, 1.00 ms/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: 6ms; used/avail/free/total/max mem: 46.64M/21.04G/1.30G/1.34G/21.09G
20:05:47.577 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
20:05:47.694 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.
20:05:47.698 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.
20:05:47.742 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.
20:05:47.742 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.
20:05:47.742 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.
20:05:47.742 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
20:05:47.742 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.
20:05:47.743 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: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/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: 53.41M/21.04G/114.37M/167.77M/21.09G
20:05:47.747 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.
20:05:47.764 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.
20:05:47.805 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.833 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.835 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.860 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:47.887 WARN MessageChunksWriter - Using chunk-size=1000
20:05:47.888 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: 27.62M/21.06G/156.93M/184.55M/21.09G
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
20:05:47.991 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.014 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.015 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.038 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:48.061 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.063 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.066 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.
20:05:48.078 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.
20:05:48.078 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
20:05:48.078 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: 2ms; used/avail/free/total/max mem: 87.33M/21.00G/97.22M/184.55M/21.09G
20:05:48.081 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
20:05:48.090 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.114 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.115 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.146 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:48.171 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.172 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.175 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.
20:05:48.178 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.
20:05:48.181 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.
20:05:48.181 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.
20:05:48.181 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.
20:05:48.181 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
20:05:48.181 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.
20:05:48.181 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: 32.83M/21.06G/722.15M/754.97M/21.09G
20:05:48.184 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.
20:05:48.186 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.
20:05:48.190 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.213 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.215 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.238 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:48.261 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.262 WARN MessageChunksWriter - Using chunk-size=1000
Finding max number of reads...
Found input file with 2 target(s)
20:05:48.265 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)
20:05:48.267 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.
20:05:48.271 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.
20:05:48.271 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.
20:05:48.271 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.
20:05:48.271 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
20:05:48.271 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.
20:05:48.271 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: 60.28M/21.03G/694.69M/754.97M/21.09G
Second pass: writing the merged alignment.
20:05:48.275 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.
20:05:48.277 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
20:05:48.282 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.306 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.307 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.330 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:48.355 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.356 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.358 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.
20:05:48.361 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.
20:05:48.361 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
20:05:48.361 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: 85.80M/21.00G/669.17M/754.97M/21.09G
20:05:48.363 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
20:05:48.369 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.393 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.394 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.418 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:48.443 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.445 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: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 142.44M/20.95G/612.54M/754.97M/21.09G
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
20:05:48.544 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.568 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.570 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.594 WARN MessageChunksWriter - Using chunk-size=1000
preparing 105
20:05:48.619 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.620 WARN MessageChunksWriter - Using chunk-size=1000
20:05:48.624 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.
20:05:48.627 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.
20:05:48.661 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.
20:05:48.661 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.
20:05:48.661 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.
20:05:48.661 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
20:05:48.661 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.
20:05:48.661 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: 234.20M/20.85G/520.78M/754.97M/21.09G
20:05:48.665 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.
20:05:48.683 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
20:05:48.832 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
20:05:48.841 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
20:05:48.860 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
20:05:48.864 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
20:05:48.868 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
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
20:05:48.928 WARN MessageChunksWriter - Using chunk-size=1000
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
}
20:05:48.950 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
20:05:49.066 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.069 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
20:05:49.077 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.078 WARN MessageChunksWriter - Using chunk-size=1000
entry: score=30.0000 readOriginIndex=0
entry: score=30.0000 readOriginIndex=0
Scanned 2 entries
20:05:49.083 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.084 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.089 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.090 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.096 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.097 WARN MessageChunksWriter - Using chunk-size=1000
0
2
20:05:49.102 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.104 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
20:05:49.111 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.112 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.117 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.118 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.124 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.125 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
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'
20:05:49.175 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.176 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.177 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.184 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.185 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.186 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.193 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.194 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.195 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
20:05:49.203 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.204 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.205 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.213 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.214 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.215 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.217 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
20:05:49.218 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
20:05:49.219 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
20:05:49.223 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.224 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.225 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.237 WARN MessageChunksWriter - Using chunk-size=1
20:05:49.242 WARN MessageChunksWriter - Using chunk-size=1
20:05:49.246 WARN MessageChunksWriter - Using chunk-size=1
20:05:49.248 WARN MessageChunksWriter - Using chunk-size=1
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
[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.
20:05:49.288 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
20:05:49.292 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
20:05:49.296 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
20:05:49.299 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
20:05:49.302 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
20:05:49.304 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
20:05:49.308 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
Setting quality threshold to 0.02
20:05:49.334 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.336 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.343 WARN MessageChunksWriter - Using chunk-size=1000
20:05:49.344 WARN MessageChunksWriter - Using chunk-size=1000
0
23
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
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
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
[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2
[ {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
20:06:31.713 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0
20:06:31.713 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds
20:06:31.915 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
20:06:31.951 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
20:06:31.951 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
20:06:31.964 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
20:06:31.964 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
20:06:32.061 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
20:06:32.095 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed.
20:06:32.095 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
20:06:32.181 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
20:06:32.187 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 [0.9999251972917639, 0.5018164832652761, -1.0792153267910128E-4, -0.9947682348726232, 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 42 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads.
Creating base test directory: test-results/stats-writer
allele: A ref: [CC] alt: [T]##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
20:06:42.633 INFO BullardUpperQuartileNormalization - normalization denominator 55152.3 for sample B-7
20:06:42.633 INFO BullardUpperQuartileNormalization - normalization denominator 54502.6 for sample B-3
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 110810 for sample A-3
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 110449 for sample A-12
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 56307.3 for sample B-15
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 51903.8 for sample B-14
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 53203.2 for sample B-11
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 110449 for sample A-17
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 55296.7 for sample B-2
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 54935.7 for sample B-10
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 106623 for sample A-16
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 55224.5 for sample B-8
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 54647.0 for sample B-4
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 107489 for sample A-2
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 109510 for sample A-0
20:06:42.634 INFO BullardUpperQuartileNormalization - normalization denominator 53997.3 for sample B-6
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 106984 for sample A-9
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 106839 for sample A-8
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 109366 for sample A-5
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 108211 for sample A-4
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 108355 for sample A-6
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 110160 for sample A-7
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 56162.9 for sample B-5
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 109438 for sample A-10
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 108428 for sample A-14
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 54647.0 for sample B-9
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 111243 for sample A-1
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 53997.3 for sample B-0
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 54069.4 for sample B-12
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 54286.0 for sample B-13
20:06:42.635 INFO BullardUpperQuartileNormalization - normalization denominator 104746 for sample A-19
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 108933 for sample A-18
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 105324 for sample A-15
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 53925.1 for sample B-1
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 107778 for sample A-13
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 108211 for sample A-11
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 54574.8 for sample B-16
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 55585.4 for sample B-17
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 54358.2 for sample B-19
20:06:42.636 INFO BullardUpperQuartileNormalization - normalization denominator 53852.9 for sample B-18
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.
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
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
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
1/1 ..T
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
20:06:43.773 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
20:06:43.774 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
20:06:43.775 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
20:06:43.776 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
20:06:43.777 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
20:06:43.778 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
20:06:43.780 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
20:06:43.781 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
20:06:43.782 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
20:06:43.783 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
20:06:43.845 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
20:06:43.846 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
20:06:43.848 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
20:06:43.849 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
20:06:43.850 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
20:06:43.851 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
20:06:43.852 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
20:06:43.854 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
20:06:43.855 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
20:06:43.856 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
20:06:43.910 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
20:06:43.911 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
20:06:43.912 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
20:06:43.913 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
20:06:43.914 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
20:06:43.915 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
20:06:43.916 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
20:06:43.917 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
20:06:43.918 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
20:06:43.919 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
20:06:44.004 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
20:06:44.005 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
20:06:44.007 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
20:06:44.008 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
20:06:44.009 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
20:06:44.011 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
20:06:44.012 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
20:06:44.013 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
20:06:44.014 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
20:06:44.015 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
20:06:44.065 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
20:06:44.066 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
20:06:44.067 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
20:06:44.068 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
20:06:44.069 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
20:06:44.070 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
20:06:44.071 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
20:06:44.072 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
20:06:44.073 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
20:06:44.074 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
20:06:44.119 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
20:06:44.120 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
20:06:44.121 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
20:06:44.122 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
20:06:44.122 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
20:06:44.124 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
20:06:44.125 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
20:06:44.126 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
20:06:44.127 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
20:06:44.128 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
20:06:44.171 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
20:06:44.172 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
20:06:44.173 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
20:06:44.174 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
20:06:44.175 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
20:06:44.176 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
20:06:44.177 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
20:06:44.177 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
20:06:44.178 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
20:06:44.179 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
20:06:44.222 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
20:06:44.223 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
20:06:44.223 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
20:06:44.224 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
20:06:44.225 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
20:06:44.227 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
20:06:44.227 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
20:06:44.228 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
20:06:44.229 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
20:06:44.230 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
20:06:44.272 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
20:06:44.273 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
20:06:44.274 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
20:06:44.274 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
20:06:44.275 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
20:06:44.276 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
20:06:44.277 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
20:06:44.278 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
20:06:44.279 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
20:06:44.280 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
20:06:44.371 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
20:06:44.372 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
20:06:44.373 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
20:06:44.373 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
20:06:44.375 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
20:06:44.376 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
20:06:44.377 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
20:06:44.378 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
20:06:44.378 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
20:06:44.379 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
20:06:44.422 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
20:06:44.423 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
20:06:44.424 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
20:06:44.425 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
20:06:44.426 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
20:06:44.427 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
20:06:44.428 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
20:06:44.428 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
20:06:44.429 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
20:06:44.430 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
20:06:44.478 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
20:06:44.480 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
20:06:44.481 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
20:06:44.481 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
20:06:44.482 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
20:06:44.483 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
20:06:44.484 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
20:06:44.485 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
20:06:44.486 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
20:06:44.487 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}
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
original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT
original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G
original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT
original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT
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
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
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loading transition for reader[0] position=10 length=2 count=0
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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: 36117 length: 10
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peak : start :5 count :13 length :100010
peak : start :100020 count :10 length :1
20:06:44.954 WARN WiggleWindow - Not writing 101 7
20:06:44.954 WARN WiggleWindow - Not writing 111 7
20:06:44.955 WARN WiggleWindow - Not writing 131 8
20:06:44.955 WARN WiggleWindow - Not writing 141 8
20:06:44.955 WARN WiggleWindow - Not writing 151 8
appending (count=10,length=4)
appending (count=1,length=0)
appending (count=2,length=8)
Hello
appending (count=10,length=4)
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
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ATC 57
AGC 60
AAC 63
ACC 66
ATC 69
AGC 72
AAC 75
ACC 78
ATC 81
AGC20:06:45.005 WARN MessageChunksWriter - Using chunk-size=9
20:06:45.007 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
20:06:45.008 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
20:06:45.012 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
qPhred=1
qPhred=2
qPhred=3
qPhred=4
qPhred=5
qPhred=6
qPhred=7
qPhred=8
qPhred=9
qPhred=10
qPhred=11
qPhred=12
qPhred=13
qPhred=14
qPhred=15
qPhred=16
qPhred=17
qPhred=18
qPhred=19
qPhred=20
qPhred=21
qPhred=22
qPhred=23
qPhred=24
qPhred=25
qPhred=26
qPhred=27
qPhred=28
qPhred=29
qPhred=30
qPhred=31
qPhred=32
qPhred=33
qPhred=34
qPhred=35
qPhred=36
qPhred=37
qPhred=38
qPhred=39
qPhred=40
qPhred=41
qPhred=42
qPhred=43
qPhred=44
qPhred=45
qPhred=46
qPhred=47
qPhred=48
qPhred=49
qPhred=50
qPhred=51
qPhred=52
qPhred=53
qPhred=54
qPhred=55
qPhred=56
qPhred=57
qPhred=58
qPhred=59
qPhred=60
qPhred=61
>1
NNTGAATGAGACCTA
[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 65.837 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 [ 0.047 s]
[INFO] Goby I/O ........................................... SUCCESS [ 7.046 s]
[INFO] Goby Full Distribution ............................. SUCCESS [01:40 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:48 min
[INFO] Finished at: 2026-04-07T20:07:22-12:00
[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 [ 0.342 s]
[INFO] Goby I/O ........................................... SUCCESS [ 0.048 s]
[INFO] Goby Full Distribution ............................. SUCCESS [ 0.034 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.572 s
[INFO] Finished at: 2026-04-07T20:07:24-12:00
[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
Apr 07, 2026 8:07:30 PM 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
Apr 07, 2026 8:07:35 PM 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: 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
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
dh_md5sums
dh_builddeb
dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-11_all.deb'.
dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'.
dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo
dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-11_amd64.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/2408174 and its subdirectories
I: Current time: Tue Apr 7 20:07:48 -12 2026
I: pbuilder-time-stamp: 1775635668