Running as unit: rb-build-arm64_10-69005.service ==================================================================================== Sun Apr 27 18:55:10 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_10) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Sun Apr 27 18:55:10 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-PuQIEshR" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Apr 27 18:55:10 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sun Apr 27 18:55:10 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-9yacRw' Sun Apr 27 18:55:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sun Apr 27 18:55:11 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-pHAWJI' ok, let's check if libgoby-java is building anywhere yet… ok, libgoby-java is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libgoby-java in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Sun Apr 27 18:55:24 UTC 2025 I: starting to build libgoby-java/unstable/arm64 on jenkins on '2025-04-27 18:55' Sun Apr 27 18:55:24 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/69005/console.log 1745780124 arm64 unstable libgoby-java Sun Apr 27 18:55:24 UTC 2025 I: Downloading source for unstable/libgoby-java=3.3.1+dfsg2-11 --2025-04-27 18:55:24-- http://deb.debian.org/debian/pool/main/libg/libgoby-java/libgoby-java_3.3.1%2bdfsg2-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3008 (2.9K) [text/prs.lines.tag] Saving to: ‘libgoby-java_3.3.1+dfsg2-11.dsc’ 0K .. 100% 338M=0s 2025-04-27 18:55:24 (338 MB/s) - ‘libgoby-java_3.3.1+dfsg2-11.dsc’ saved [3008/3008] --2025-04-27 18:55:24-- http://deb.debian.org/debian/pool/main/libg/libgoby-java/libgoby-java_3.3.1%2bdfsg2-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3008 (2.9K) [text/prs.lines.tag] Saving to: ‘libgoby-java_3.3.1+dfsg2-11.dsc’ 0K .. 100% 338M=0s 2025-04-27 18:55:24 (338 MB/s) - ‘libgoby-java_3.3.1+dfsg2-11.dsc’ saved [3008/3008] Sun Apr 27 18:55:24 UTC 2025 I: libgoby-java_3.3.1+dfsg2-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libgoby-java Binary: libgoby-io-java, goby-java Architecture: all Version: 3.3.1+dfsg2-11 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet , Andreas Tille Homepage: https://campagnelab.org/software/goby/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libgoby-java/ Vcs-Git: https://salsa.debian.org/med-team/libgoby-java.git Testsuite: autopkgtest Testsuite-Triggers: default-jdk Build-Depends: debhelper-compat (= 13), maven-debian-helper, javahelper, default-jdk Build-Depends-Indep: 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 Package-List: goby-java deb science optional arch=all libgoby-io-java deb science optional arch=all Checksums-Sha1: f9f9b6c1f4e76c9c403e1a9881d2c81f4d371d1c 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz b26ff390aa68ce3035d8153bb80f2153382882ec 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz Checksums-Sha256: b76b19808f893790e238c91e65680441ff020794cc7708ad6695cf13f0767148 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz db2427807fcc6967f7d3d85e656e4b219bd5af8e88faf8c21bdae07b6f74f468 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz Files: 3a8dbf45ef2c54ec3073240850acbc75 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz ee077d346354fb548086bf2a9f9f11e5 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmZDkf4ACgkQYAMWptwn dHbpoxAArW4ZHQHLR2i3CFyUh7icehts0H7Dw1QPOrrFFMGdEM3NxatGcCXLQr/a oeQbInqiDMzD4nypqLL5AMMSu3JH7nsQ5OvFLfw3dYZnZpKsDzhdorwnOmhpwZ8P rpL+rsNHL+Ond8BysNEHJHQzElxKrpOa39ihu/hgciQ3Spj7BdjE0qUyy9rcHH8D uGF75qN0lTwYntDkdRfUg9JbMfqBXyuqpI7l7aPuQqr9AID9dSA6ilHOEyvFn1v7 67RgMq6gFKztHYK2c2bwWzQ+exmoFglxPa77Nx6NuqZDEyRllzami0iUCI7n+E5m FcpGPLCcHypkhqhTU0kvlKiTYmrgTXRvhfGxfhBB5CF4V3LFYzdsie113QWpaSru qLorRzuMHUJgKbtjy/H9aDQfkqeua7+cnz1wGnOlpBrutfxP5TXUiaeJBW4SSy4T tAYOaxCSkHEEoU0/rNUNDuFc0t4z7L5nsD2OEp1H4sAO7LHSBbuU83NH6Ey4qxJm PBNybPD24etHY0KCFbGaGo+Id0z0lTfU+1QKj6irDrZawnh69V4EwU+mhjVHd86i jCMPZd1SbDQrSJvKF4hHWp2e+D+LjdCaW5If6BaxKQyHEgxAhWpFns20FwzugFIg 63JI+KVPPcxzQ9F7fPbFF8u7txqQsHQEkea1h1PjKRSBTVNbb20= =36L5 -----END PGP SIGNATURE----- Sun Apr 27 18:55:24 UTC 2025 I: Checking whether the package is not for us Sun Apr 27 18:55:24 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun Apr 27 18:55:24 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun Apr 27 18:55:24 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sun Apr 27 18:55:24 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-i4NpkP' ==================================================================================== Sun Apr 27 18:55:26 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 libgoby-java unstable /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp 3.3.1+dfsg2-11" as arguments. Sun Apr 27 18:55:26 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-sTU3cGf6" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Apr 27 18:55:26 UTC 2025 I: Downloading source for unstable/libgoby-java=3.3.1+dfsg2-11 Reading package lists... NOTICE: 'libgoby-java' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgoby-java.git Please use: git clone https://salsa.debian.org/med-team/libgoby-java.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 41.6 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (dsc) [3008 B] Get:2 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (tar) [41.6 MB] Get:3 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (diff) [29.4 kB] Fetched 41.6 MB in 1s (43.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libgoby-java' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgoby-java.git Please use: git clone https://salsa.debian.org/med-team/libgoby-java.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 41.6 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (dsc) [3008 B] Get:2 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (tar) [41.6 MB] Get:3 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (diff) [29.4 kB] Fetched 41.6 MB in 1s (43.5 MB/s) Download complete and in download only mode ============================================================================= Building libgoby-java in unstable on arm64 on codethink04-arm64 now. Date: Sun Apr 27 19:55:27 BST 2025 Date UTC: Sun Apr 27 18:55:27 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 27 06:55:28 -12 2025 I: pbuilder-time-stamp: 1745780128 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/271630/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7a7ac1dbbc154196a2a6c662048efd64' 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='271630' 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.tP9jh8Dp/pbuilderrc_Bir9 --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.tP9jh8Dp/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/271630/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team 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 ... 19953 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} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gpg{a} gpg-agent{a} gpgconf{a} gpgv{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbarclay-java{a} libblas3{a} libbrotli1{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcolord2{a} libcolt-free-java{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdsiutils-java{a} libdynaloader-functions-perl{a} libeasymock-java{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastutil-java{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgbm1{a} libgcrypt20{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicb-utils-java{a} libice6{a} libicu4j-java{a} libicu76{a} libidn2-0{a} libimport-into-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libjansi-java{a} libjavassist-java{a} libjaxb-api-java{a} libjaxen-java{a} libjbig0{a} libjboss-logging-java{a} libjboss-vfs-java{a} libjbzip2-java{a} libjcommander-java{a} libjetty9-java{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjsap-java{a} libjson-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblightcouch-java{a} libllvm19{a} liblog4j1.2-java{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven-source-plugin-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libpcsclite1{a} libpicard-java{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libpj-java{a} libpkgconf3{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} libreflections-java{a} librhino-java{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1t64{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} liburi-perl{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxom-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxss1{a} libxstream-java{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} mesa-libgallium{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sopv-gpgv{a} systemd{a} systemd-sysv{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpg-error-l10n libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjline3-java libjson-perl libkmod2 libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl libnss-systemd librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian linux-sysctl-defaults lynx lzip mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc publicsuffix python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended sopv-doc strace systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 459 newly installed, 0 to remove and 0 not upgraded. Need to get 373 MB of archives. After unpacking 1012 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 257.5-2 [1911 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libapparmor1 arm64 4.1.0-1 [42.9 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 systemd arm64 257.5-2 [2920 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 systemd-sysv arm64 257.5-2 [63.9 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 dbus-bin arm64 1.16.2-2 [78.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 dbus-daemon arm64 1.16.2-2 [152 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 dbus arm64 1.16.2-2 [70.7 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-2 [260 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.5.0-1 [1454 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20250419 [162 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libpam-systemd arm64 257.5-2 [275 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 43 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0051 [42.8 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.84.1-2 [1423 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b2 [756 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1.1 [274 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.7.0-3 [325 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [131 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 4.18.4+ds-2 [51.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 48.0-1 [504 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.110-1 [1292 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.3-1 [55.0 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.7+6-1 [40.6 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.56.1-2 [171 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 dbus-user-session arm64 1.16.2-2 [52.1 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libdconf1 arm64 0.40.0-5 [40.4 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dconf-service arm64 0.40.0-5 [30.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [27.3 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 87 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.56.1-2 [50.0 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libatspi2.0-0t64 arm64 2.56.1-2 [76.5 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libatk-bridge2.0-0t64 arm64 2.56.1-2 [64.8 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.3 [318 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.3 [387 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.4-1+b1 [130 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libcloudproviders0 arm64 0.3.6-2 [27.4 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libcolord2 arm64 1.4.7-3 [130 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-16 [112 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-16 [43.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-16 [46.7 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 129 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.3 [463 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.3-1 [213 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [52.9 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [33.7 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libwayland-client0 arm64 1.23.1-3 [26.1 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libwayland-cursor0 arm64 1.23.1-3 [11.7 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libwayland-egl1 arm64 1.23.1-3 [5952 B] Get: 146 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b4 [20.5 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.3-1 [39.3 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b4 [16.0 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 xkb-data all 2.42-1 [790 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libxkbcommon0 arm64 1.7.0-2 [106 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1+b3 [35.9 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libgtk-3-common all 3.24.49-3 [4908 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libgtk-3-0t64 arm64 3.24.49-3 [2565 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.124-2 [8288 B] Get: 158 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.124-2 [38.3 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.12-1 [247 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b4 [19.2 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.124-2 [21.8 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-3 [23.3 MB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.2-2 [36.4 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3.3-1 [11.1 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 mesa-libgallium arm64 25.0.4-1 [8031 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libwayland-server0 arm64 1.23.1-3 [33.7 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libgbm1 arm64 25.0.4-1 [43.6 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.4.309.0-1 [127 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 25.0.4-1 [45.3 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 25.0.4-1 [142 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.14-1 [21.1 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.14-1 [342 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.5-1 [25.7 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre arm64 21.0.7+6-1 [193 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.21-76 [1068 B] Get: 189 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk-headless arm64 21.0.7+6-1 [81.9 MB] Get: 190 http://deb.debian.org/debian unstable/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 191 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk arm64 21.0.7+6-1 [3557 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 default-jdk arm64 2:1.21-76 [1076 B] Get: 193 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.4.7-16 [121 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-3 [22.9 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.4.7-16 [577 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.3.1-2 [83.5 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.4.7-16 [248 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 203 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 206 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-2 [15.7 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 232 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.78-1 [183 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 gpgv arm64 2.4.7-16 [220 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 sopv-gpgv all 0.1.4-1 [11.3 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-9 [122 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.25.10 [1062 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.80 [9692 B] Get: 246 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.80 [80.4 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 250 http://deb.debian.org/debian unstable/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 251 http://deb.debian.org/debian unstable/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 junit5 all 5.10.3-1 [2459 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 257 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 258 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.8-1 [392 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 260 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libfreemarker-java all 2.3.32-2.1 [1525 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libjoptsimple-java all 5.0.4-7 [73.7 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.18.0-1 [304 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.19.0-1 [524 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libguice-java all 5.1.0-1 [932 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 285 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 291 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 294 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libbyte-buddy-java all 1.14.19-1 [4756 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.10.1-1 [231 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libcommons-configuration-java all 1.10-7 [348 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libcommons-math-java all 2.2-9 [933 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.2-1 [28.3 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.7-1 [6476 B] Get: 317 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libcommons-text-java all 1.13.1-1 [228 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-2 [179 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.13.0-5 [349 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libdistlib-java all 1.0-5 [72.5 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 libdoxia-java all 2.0.0-1 [113 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 341 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 velocity all 1.7-7 [431 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 346 http://deb.debian.org/debian unstable/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 350 http://deb.debian.org/debian unstable/main arm64 libxpp3-java all 1.1.4c-4 [294 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 libxstream-java all 1.4.21-1 [567 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 libjsap-java all 2.1-5 [102 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 liblogback-java all 1:1.2.11-6 [701 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 libobjenesis-java all 3.4-2 [41.3 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 libeasymock-java all 5.5.0-1 [134 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 361 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 libxom-java all 1.3.9-1 [174 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto16 arm64 3.6.3-1 [343 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 libmbedx509-7 arm64 3.6.3-1 [148 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 libmbedtls21 arm64 3.6.3-1 [224 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1096 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 libncbi-ngs3 arm64 3.2.1+dfsg-4 [145 kB] Get: 373 http://deb.debian.org/debian unstable/main arm64 libngs-jni arm64 3.2.1+dfsg-4 [27.7 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 libngs-java arm64 3.2.1+dfsg-4 [114 kB] Get: 375 http://deb.debian.org/debian unstable/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 libicu4j-java all 73.2-1 [16.4 MB] Get: 379 http://deb.debian.org/debian unstable/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-3 [9526 kB] Get: 383 http://deb.debian.org/debian unstable/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 384 http://deb.debian.org/debian unstable/main arm64 libjavassist-java all 1:3.27.0-1 [731 kB] Get: 385 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 386 http://deb.debian.org/debian unstable/main arm64 libjboss-logging-java all 3.5.3-1 [56.2 kB] Get: 387 http://deb.debian.org/debian unstable/main arm64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB] Get: 388 http://deb.debian.org/debian unstable/main arm64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get: 389 http://deb.debian.org/debian unstable/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 390 http://deb.debian.org/debian unstable/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 391 http://deb.debian.org/debian unstable/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 392 http://deb.debian.org/debian unstable/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 393 http://deb.debian.org/debian unstable/main arm64 libjetty9-java all 9.4.57-1 [2965 kB] Get: 394 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 395 http://deb.debian.org/debian unstable/main arm64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 396 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 397 http://deb.debian.org/debian unstable/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 398 http://deb.debian.org/debian unstable/main arm64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 399 http://deb.debian.org/debian unstable/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 400 http://deb.debian.org/debian unstable/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 401 http://deb.debian.org/debian unstable/main arm64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 402 http://deb.debian.org/debian unstable/main arm64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB] Get: 403 http://deb.debian.org/debian unstable/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 404 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 405 http://deb.debian.org/debian unstable/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 406 http://deb.debian.org/debian unstable/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 407 http://deb.debian.org/debian unstable/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 408 http://deb.debian.org/debian unstable/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 409 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-analyzer-java all 1.15.1-1 [38.5 kB] Get: 410 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-tree-java all 3.3.0-1 [35.0 kB] Get: 411 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-impl-java all 4.0.0-1 [17.6 kB] Get: 412 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-plugin-java all 3.8.1-1 [191 kB] Get: 413 http://deb.debian.org/debian unstable/main arm64 libmaven-invoker-java all 3.3.0-1 [29.1 kB] Get: 414 http://deb.debian.org/debian unstable/main arm64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB] Get: 415 http://deb.debian.org/debian unstable/main arm64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB] Get: 416 http://deb.debian.org/debian unstable/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB] Get: 417 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 418 http://deb.debian.org/debian unstable/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 419 http://deb.debian.org/debian unstable/main arm64 libmaven-plugin-tools-java all 3.10.2-2 [245 kB] Get: 420 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 421 http://deb.debian.org/debian unstable/main arm64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 422 http://deb.debian.org/debian unstable/main arm64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 423 http://deb.debian.org/debian unstable/main arm64 libmaven-source-plugin-java all 3.3.1-1 [27.7 kB] Get: 424 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b2 [16.6 kB] Get: 425 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b2 [16.4 kB] Get: 426 http://deb.debian.org/debian unstable/main arm64 libpicard-java all 3.3.0+dfsg-2 [1778 kB] Get: 427 http://deb.debian.org/debian unstable/main arm64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB] Get: 428 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 429 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 430 http://deb.debian.org/debian unstable/main arm64 libprotobuf32t64 arm64 3.21.12-10+b6 [859 kB] Get: 431 http://deb.debian.org/debian unstable/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b6 [250 kB] Get: 432 http://deb.debian.org/debian unstable/main arm64 libprotobuf-dev arm64 3.21.12-10+b6 [1263 kB] Get: 433 http://deb.debian.org/debian unstable/main arm64 libprotobuf-java all 3.21.12-10 [1268 kB] Get: 434 http://deb.debian.org/debian unstable/main arm64 libprotoc32t64 arm64 3.21.12-10+b6 [790 kB] Get: 435 http://deb.debian.org/debian unstable/main arm64 libreflections-java all 0.10.2+dfsg-2 [125 kB] Get: 436 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.6-1 [36.4 kB] Get: 437 http://deb.debian.org/debian unstable/main arm64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 438 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 439 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get: 440 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.6+ds-1 [79.1 kB] Get: 441 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 442 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 443 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 444 http://deb.debian.org/debian unstable/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 445 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 446 http://deb.debian.org/debian unstable/main arm64 libxml2-utils arm64 2.12.7+dfsg+really2.9.14-0.4 [98.3 kB] Get: 447 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 448 http://deb.debian.org/debian unstable/main arm64 maven all 3.9.9-1 [19.7 kB] Get: 449 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 450 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-29 [163 kB] Get: 451 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.7 [108 kB] Get: 452 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 453 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 454 http://deb.debian.org/debian unstable/main arm64 protobuf-compiler arm64 3.21.12-10+b6 [84.9 kB] Get: 455 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-15 [227 kB] Get: 456 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 457 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.5.0-2 [28.4 MB] Get: 458 http://deb.debian.org/debian unstable/main arm64 r-cran-rjava arm64 1.0-11-2 [712 kB] Get: 459 http://deb.debian.org/debian unstable/main arm64 testng all 6.9.12-4 [795 kB] Fetched 373 MB in 3s (118 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19953 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.5-2_arm64.deb ... Unpacking libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package libapparmor1:arm64. Preparing to unpack .../libapparmor1_4.1.0-1_arm64.deb ... Unpacking libapparmor1:arm64 (4.1.0-1) ... Setting up libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package systemd. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../systemd_257.5-2_arm64.deb ... Unpacking systemd (257.5-2) ... Setting up libapparmor1:arm64 (4.1.0-1) ... Setting up systemd (257.5-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20904 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.5-2_arm64.deb ... Unpacking systemd-sysv (257.5-2) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../01-libdbus-1-3_1.16.2-2_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.16.2-2) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.16.2-2_arm64.deb ... Unpacking dbus-bin (1.16.2-2) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../03-dbus-session-bus-common_1.16.2-2_all.deb ... Unpacking dbus-session-bus-common (1.16.2-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../04-libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../05-dbus-daemon_1.16.2-2_arm64.deb ... Unpacking dbus-daemon (1.16.2-2) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../06-dbus-system-bus-common_1.16.2-2_all.deb ... Unpacking dbus-system-bus-common (1.16.2-2) ... Selecting previously unselected package dbus. Preparing to unpack .../07-dbus_1.16.2-2_arm64.deb ... Unpacking dbus (1.16.2-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../09-binfmt-support_2.2.2-7+b1_arm64.deb ... Unpacking binfmt-support (2.2.2-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../10-libpython3.13-minimal_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../11-python3.13-minimal_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21354 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_arm64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.8-2_arm64.deb ... Unpacking libffi8:arm64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22366 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.3-1_arm64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-8_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-8) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-8_arm64.deb ... Unpacking procps (2:4.0.4-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.5.0-1_arm64.deb ... Unpacking openssl (3.5.0-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../007-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package libpam-systemd:arm64. Preparing to unpack .../012-libpam-systemd_257.5-2_arm64.deb ... Unpacking libpam-systemd:arm64 (257.5-2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../015-libtext-charwidth-perl_0.04-11+b4_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../016-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../017-ucf_3.0051_all.deb ... Moving old data out of the way Unpacking ucf (3.0051) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../018-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../019-libglib2.0-0t64_2.84.1-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.84.1-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../020-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../021-shared-mime-info_2.4-5+b2_arm64.deb ... Unpacking shared-mime-info (2.4-5+b2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../022-libjpeg62-turbo_1%3a2.1.5-3.1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../023-libpng16-16t64_1.6.47-1.1_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.47-1.1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../024-libdeflate0_1.23-2_arm64.deb ... Unpacking libdeflate0:arm64 (1.23-2) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../025-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../026-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../027-libsharpyuv0_1.5.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../028-libwebp7_1.5.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../029-libtiff6_4.7.0-3_arm64.deb ... Unpacking libtiff6:arm64 (4.7.0-3) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. Preparing to unpack .../030-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ... Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../031-gtk-update-icon-cache_4.18.4+ds-2_arm64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.18.4+ds-2) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../032-hicolor-icon-theme_0.18-2_all.deb ... Unpacking hicolor-icon-theme (0.18-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../033-adwaita-icon-theme_48.0-1_all.deb ... Unpacking adwaita-icon-theme (48.0-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../034-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../035-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../036-liblcms2-2_2.16-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.16-2) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../037-libnspr4_2%3a4.36-1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.36-1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../038-libnss3_2%3a3.110-1_arm64.deb ... Unpacking libnss3:arm64 (2:3.110-1) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../039-libpcsclite1_2.3.3-1_arm64.deb ... Unpacking libpcsclite1:arm64 (2.3.3-1) ... Selecting previously unselected package openjdk-21-jre-headless:arm64. Preparing to unpack .../040-openjdk-21-jre-headless_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jre-headless:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../041-default-jre-headless_2%3a1.21-76_arm64.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../042-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package ant-contrib. Preparing to unpack .../043-ant-contrib_1.0~b3+svn177-12_all.deb ... Unpacking ant-contrib (1.0~b3+svn177-12) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../044-at-spi2-common_2.56.1-2_all.deb ... Unpacking at-spi2-common (2.56.1-2) ... Selecting previously unselected package m4. Preparing to unpack .../045-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../046-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../047-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../048-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../049-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package dbus-user-session. Preparing to unpack .../050-dbus-user-session_1.16.2-2_arm64.deb ... Unpacking dbus-user-session (1.16.2-2) ... Selecting previously unselected package libdconf1:arm64. Preparing to unpack .../051-libdconf1_0.40.0-5_arm64.deb ... Unpacking libdconf1:arm64 (0.40.0-5) ... Selecting previously unselected package dconf-service. Preparing to unpack .../052-dconf-service_0.40.0-5_arm64.deb ... Unpacking dconf-service (0.40.0-5) ... Selecting previously unselected package dconf-gsettings-backend:arm64. Preparing to unpack .../053-dconf-gsettings-backend_0.40.0-5_arm64.deb ... Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../054-dctrl-tools_2.24-3+b1_arm64.deb ... Unpacking dctrl-tools (2.24-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../055-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../056-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../057-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../058-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../059-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../060-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../061-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../062-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../063-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package gettext. Preparing to unpack .../064-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../065-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../066-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../067-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libatk1.0-0t64:arm64. Preparing to unpack .../068-libatk1.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatk1.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../069-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../070-libxdmcp6_1%3a1.1.5-1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../071-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../072-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../073-libx11-6_2%3a1.8.12-1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.12-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../074-libxext6_2%3a1.3.4-1+b3_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../075-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libatspi2.0-0t64:arm64. Preparing to unpack .../076-libatspi2.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatspi2.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libatk-bridge2.0-0t64:arm64. Preparing to unpack .../077-libatk-bridge2.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatk-bridge2.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../078-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../079-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../080-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../081-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../082-fontconfig-config_2.15.0-2.3_arm64.deb ... Unpacking fontconfig-config (2.15.0-2.3) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../083-libfontconfig1_2.15.0-2.3_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-2.3) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../084-libpixman-1-0_0.44.0-3_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.44.0-3) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../085-libxcb-render0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../086-libxcb-shm0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../087-libxrender1_1%3a0.9.12-1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.12-1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../088-libcairo2_1.18.4-1+b1_arm64.deb ... Unpacking libcairo2:arm64 (1.18.4-1+b1) ... Selecting previously unselected package libcairo-gobject2:arm64. Preparing to unpack .../089-libcairo-gobject2_1.18.4-1+b1_arm64.deb ... Unpacking libcairo-gobject2:arm64 (1.18.4-1+b1) ... Selecting previously unselected package libcloudproviders0:arm64. Preparing to unpack .../090-libcloudproviders0_0.3.6-2_arm64.deb ... Unpacking libcloudproviders0:arm64 (0.3.6-2) ... Selecting previously unselected package libcolord2:arm64. Preparing to unpack .../091-libcolord2_1.4.7-3_arm64.deb ... Unpacking libcolord2:arm64 (1.4.7-3) ... Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../092-libavahi-common-data_0.8-16_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-16) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../093-libavahi-common3_0.8-16_arm64.deb ... Unpacking libavahi-common3:arm64 (0.8-16) ... Selecting previously unselected package libavahi-client3:arm64. Preparing to unpack .../094-libavahi-client3_0.8-16_arm64.deb ... Unpacking libavahi-client3:arm64 (0.8-16) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../095-libidn2-0_2.3.8-2_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-2) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../096-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../097-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../098-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../099-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../100-libcom-err2_1.47.2-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../101-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../102-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../103-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../104-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libcups2t64:arm64. Preparing to unpack .../105-libcups2t64_2.4.10-2+b1_arm64.deb ... Unpacking libcups2t64:arm64 (2.4.10-2+b1) ... Selecting previously unselected package libepoxy0:arm64. Preparing to unpack .../106-libepoxy0_1.5.10-2_arm64.deb ... Unpacking libepoxy0:arm64 (1.5.10-2) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../107-libfribidi0_1.0.16-1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.16-1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../108-libgraphite2-3_1.3.14-2+b1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../109-libharfbuzz0b_10.2.0-1+b1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.2.0-1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../110-fontconfig_2.15.0-2.3_arm64.deb ... Unpacking fontconfig (2.15.0-2.3) ... Selecting previously unselected package libthai-data. Preparing to unpack .../111-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../112-libdatrie1_0.2.13-3+b1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3+b1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../113-libthai0_0.1.29-2+b1_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../114-libpango-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../115-libpangoft2-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../116-libpangocairo-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libwayland-client0:arm64. Preparing to unpack .../117-libwayland-client0_1.23.1-3_arm64.deb ... Unpacking libwayland-client0:arm64 (1.23.1-3) ... Selecting previously unselected package libwayland-cursor0:arm64. Preparing to unpack .../118-libwayland-cursor0_1.23.1-3_arm64.deb ... Unpacking libwayland-cursor0:arm64 (1.23.1-3) ... Selecting previously unselected package libwayland-egl1:arm64. Preparing to unpack .../119-libwayland-egl1_1.23.1-3_arm64.deb ... Unpacking libwayland-egl1:arm64 (1.23.1-3) ... Selecting previously unselected package libxcomposite1:arm64. Preparing to unpack .../120-libxcomposite1_1%3a0.4.6-1_arm64.deb ... Unpacking libxcomposite1:arm64 (1:0.4.6-1) ... Selecting previously unselected package libxfixes3:arm64. Preparing to unpack .../121-libxfixes3_1%3a6.0.0-2+b4_arm64.deb ... Unpacking libxfixes3:arm64 (1:6.0.0-2+b4) ... Selecting previously unselected package libxcursor1:arm64. Preparing to unpack .../122-libxcursor1_1%3a1.2.3-1_arm64.deb ... Unpacking libxcursor1:arm64 (1:1.2.3-1) ... Selecting previously unselected package libxdamage1:arm64. Preparing to unpack .../123-libxdamage1_1%3a1.1.6-1+b2_arm64.deb ... Unpacking libxdamage1:arm64 (1:1.1.6-1+b2) ... Selecting previously unselected package libxinerama1:arm64. Preparing to unpack .../124-libxinerama1_2%3a1.1.4-3+b4_arm64.deb ... Unpacking libxinerama1:arm64 (2:1.1.4-3+b4) ... Selecting previously unselected package xkb-data. Preparing to unpack .../125-xkb-data_2.42-1_all.deb ... Unpacking xkb-data (2.42-1) ... Selecting previously unselected package libxkbcommon0:arm64. Preparing to unpack .../126-libxkbcommon0_1.7.0-2_arm64.deb ... Unpacking libxkbcommon0:arm64 (1.7.0-2) ... Selecting previously unselected package libxrandr2:arm64. Preparing to unpack .../127-libxrandr2_2%3a1.5.4-1+b3_arm64.deb ... Unpacking libxrandr2:arm64 (2:1.5.4-1+b3) ... Selecting previously unselected package libgtk-3-common. Preparing to unpack .../128-libgtk-3-common_3.24.49-3_all.deb ... Unpacking libgtk-3-common (3.24.49-3) ... Selecting previously unselected package libgtk-3-0t64:arm64. Preparing to unpack .../129-libgtk-3-0t64_3.24.49-3_arm64.deb ... Unpacking libgtk-3-0t64:arm64 (3.24.49-3) ... Selecting previously unselected package libglvnd0:arm64. Preparing to unpack .../130-libglvnd0_1.7.0-1+b2_arm64.deb ... Unpacking libglvnd0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../131-libdrm-common_2.4.124-2_all.deb ... Unpacking libdrm-common (2.4.124-2) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../132-libdrm2_2.4.124-2_arm64.deb ... Unpacking libdrm2:arm64 (2.4.124-2) ... Selecting previously unselected package libx11-xcb1:arm64. Preparing to unpack .../133-libx11-xcb1_2%3a1.8.12-1_arm64.deb ... Unpacking libx11-xcb1:arm64 (2:1.8.12-1) ... Selecting previously unselected package libxcb-dri3-0:arm64. Preparing to unpack .../134-libxcb-dri3-0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-glx0:arm64. Preparing to unpack .../135-libxcb-glx0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-glx0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-present0:arm64. Preparing to unpack .../136-libxcb-present0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-present0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-xfixes0:arm64. Preparing to unpack .../137-libxcb-xfixes0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxxf86vm1:arm64. Preparing to unpack .../138-libxxf86vm1_1%3a1.1.4-1+b4_arm64.deb ... Unpacking libxxf86vm1:arm64 (1:1.1.4-1+b4) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../139-libdrm-amdgpu1_2.4.124-2_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.124-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../140-libedit2_3.1-20250104-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20250104-1) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../141-libz3-4_4.13.3-1_arm64.deb ... Unpacking libz3-4:arm64 (4.13.3-1) ... Selecting previously unselected package libllvm19:arm64. Preparing to unpack .../142-libllvm19_1%3a19.1.7-3_arm64.deb ... Unpacking libllvm19:arm64 (1:19.1.7-3) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../143-libsensors-config_1%3a3.6.2-2_all.deb ... Unpacking libsensors-config (1:3.6.2-2) ... Selecting previously unselected package libsensors5:arm64. Preparing to unpack .../144-libsensors5_1%3a3.6.2-2_arm64.deb ... Unpacking libsensors5:arm64 (1:3.6.2-2) ... Selecting previously unselected package libxcb-randr0:arm64. Preparing to unpack .../145-libxcb-randr0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-randr0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-sync1:arm64. Preparing to unpack .../146-libxcb-sync1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-sync1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxshmfence1:arm64. Preparing to unpack .../147-libxshmfence1_1.3.3-1_arm64.deb ... Unpacking libxshmfence1:arm64 (1.3.3-1) ... Selecting previously unselected package mesa-libgallium:arm64. Preparing to unpack .../148-mesa-libgallium_25.0.4-1_arm64.deb ... Unpacking mesa-libgallium:arm64 (25.0.4-1) ... Selecting previously unselected package libwayland-server0:arm64. Preparing to unpack .../149-libwayland-server0_1.23.1-3_arm64.deb ... Unpacking libwayland-server0:arm64 (1.23.1-3) ... Selecting previously unselected package libgbm1:arm64. Preparing to unpack .../150-libgbm1_25.0.4-1_arm64.deb ... Unpacking libgbm1:arm64 (25.0.4-1) ... Selecting previously unselected package libvulkan1:arm64. Preparing to unpack .../151-libvulkan1_1.4.309.0-1_arm64.deb ... Unpacking libvulkan1:arm64 (1.4.309.0-1) ... Selecting previously unselected package libgl1-mesa-dri:arm64. Preparing to unpack .../152-libgl1-mesa-dri_25.0.4-1_arm64.deb ... Unpacking libgl1-mesa-dri:arm64 (25.0.4-1) ... Selecting previously unselected package libglx-mesa0:arm64. Preparing to unpack .../153-libglx-mesa0_25.0.4-1_arm64.deb ... Unpacking libglx-mesa0:arm64 (25.0.4-1) ... Selecting previously unselected package libglx0:arm64. Preparing to unpack .../154-libglx0_1.7.0-1+b2_arm64.deb ... Unpacking libglx0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libgl1:arm64. Preparing to unpack .../155-libgl1_1.7.0-1+b2_arm64.deb ... Unpacking libgl1:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../156-libasound2-data_1.2.14-1_all.deb ... Unpacking libasound2-data (1.2.14-1) ... Selecting previously unselected package libasound2t64:arm64. Preparing to unpack .../157-libasound2t64_1.2.14-1_arm64.deb ... Unpacking libasound2t64:arm64 (1.2.14-1) ... Selecting previously unselected package libgif7:arm64. Preparing to unpack .../158-libgif7_5.2.2-1+b1_arm64.deb ... Unpacking libgif7:arm64 (5.2.2-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../159-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package libxtst6:arm64. Preparing to unpack .../160-libxtst6_2%3a1.2.5-1_arm64.deb ... Unpacking libxtst6:arm64 (2:1.2.5-1) ... Selecting previously unselected package openjdk-21-jre:arm64. Preparing to unpack .../161-openjdk-21-jre_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jre:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jre. Preparing to unpack .../162-default-jre_2%3a1.21-76_arm64.deb ... Unpacking default-jre (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk-headless:arm64. Preparing to unpack .../163-openjdk-21-jdk-headless_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jdk-headless:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../164-default-jdk-headless_2%3a1.21-76_arm64.deb ... Unpacking default-jdk-headless (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk:arm64. Preparing to unpack .../165-openjdk-21-jdk_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jdk:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jdk. Preparing to unpack .../166-default-jdk_2%3a1.21-76_arm64.deb ... Unpacking default-jdk (2:1.21-76) ... Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../167-libgpg-error0_1.51-4_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-4) ... Selecting previously unselected package libassuan9:arm64. Preparing to unpack .../168-libassuan9_3.0.2-2_arm64.deb ... Unpacking libassuan9:arm64 (3.0.2-2) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../169-libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../170-gpgconf_2.4.7-16_arm64.deb ... Unpacking gpgconf (2.4.7-16) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../171-libksba8_1.6.7-2+b1_arm64.deb ... Unpacking libksba8:arm64 (1.6.7-2+b1) ... Selecting previously unselected package libnpth0t64:arm64. Preparing to unpack .../172-libnpth0t64_1.8-3_arm64.deb ... Unpacking libnpth0t64:arm64 (1.8-3) ... Selecting previously unselected package gpg. Preparing to unpack .../173-gpg_2.4.7-16_arm64.deb ... Unpacking gpg (2.4.7-16) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../174-pinentry-curses_1.3.1-2_arm64.deb ... Unpacking pinentry-curses (1.3.1-2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../175-gpg-agent_2.4.7-16_arm64.deb ... Unpacking gpg-agent (2.4.7-16) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../176-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../177-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../178-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../179-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../180-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../181-libclass-xsaccessor-perl_1.19-4+b5_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b5) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../182-libb-hooks-op-check-perl_0.22-3+b2_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../183-libdynaloader-functions-perl_0.004-2_all.deb ... Unpacking libdynaloader-functions-perl (0.004-2) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../184-libdevel-callchecker-perl_0.009-2_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.009-2) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../185-libparams-classify-perl_0.015-2+b4_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b4) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../186-libmodule-runtime-perl_0.018-1_all.deb ... Unpacking libmodule-runtime-perl (0.018-1) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../187-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../188-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../189-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../190-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../191-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../192-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../193-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../194-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../195-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../196-liburi-perl_5.30-1_all.deb ... Unpacking liburi-perl (5.30-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../197-libhtml-parser-perl_3.83-1+b2_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.83-1+b2) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../198-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../199-libclone-perl_0.47-1+b1_arm64.deb ... Unpacking libclone-perl:arm64 (0.47-1+b1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../200-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../201-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../202-libhttp-message-perl_7.00-2_all.deb ... Unpacking libhttp-message-perl (7.00-2) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../203-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../204-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:arm64. Preparing to unpack .../205-perl-openssl-defaults_7+b2_arm64.deb ... Unpacking perl-openssl-defaults:arm64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:arm64. Preparing to unpack .../206-libnet-ssleay-perl_1.94-3_arm64.deb ... Unpacking libnet-ssleay-perl:arm64 (1.94-3) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../207-libio-socket-ssl-perl_2.089-1_all.deb ... Unpacking libio-socket-ssl-perl (2.089-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../208-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../209-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../210-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../211-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../212-libwww-perl_6.78-1_all.deb ... Unpacking libwww-perl (6.78-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../213-patchutils_0.4.2-1+b1_arm64.deb ... Unpacking patchutils (0.4.2-1+b1) ... Selecting previously unselected package gpgv. Preparing to unpack .../214-gpgv_2.4.7-16_arm64.deb ... Unpacking gpgv (2.4.7-16) ... Selecting previously unselected package sopv-gpgv. Preparing to unpack .../215-sopv-gpgv_0.1.4-1_all.deb ... Unpacking sopv-gpgv (0.1.4-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../216-wdiff_1.2.2-9_arm64.deb ... Unpacking wdiff (1.2.2-9) ... Selecting previously unselected package devscripts. Preparing to unpack .../217-devscripts_2.25.10_all.deb ... Unpacking devscripts (2.25.10) ... Selecting previously unselected package fastjar. Preparing to unpack .../218-fastjar_2%3a0.98-7+b1_arm64.deb ... Unpacking fastjar (2:0.98-7+b1) ... Selecting previously unselected package jarwrapper. Preparing to unpack .../219-jarwrapper_0.80_all.deb ... Unpacking jarwrapper (0.80) ... Selecting previously unselected package javahelper. Preparing to unpack .../220-javahelper_0.80_all.deb ... Unpacking javahelper (0.80) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../221-libhamcrest-java_2.2-2_all.deb ... Unpacking libhamcrest-java (2.2-2) ... Selecting previously unselected package junit4. Preparing to unpack .../222-junit4_4.13.2-5_all.deb ... Unpacking junit4 (4.13.2-5) ... Selecting previously unselected package libapiguardian-java. Preparing to unpack .../223-libapiguardian-java_1.1.2-1_all.deb ... Unpacking libapiguardian-java (1.1.2-1) ... Selecting previously unselected package libopentest4j-java. Preparing to unpack .../224-libopentest4j-java_1.2.0-4_all.deb ... Unpacking libopentest4j-java (1.2.0-4) ... Selecting previously unselected package libopentest4j-reporting-java. Preparing to unpack .../225-libopentest4j-reporting-java_0.1.0-M1-2_all.deb ... Unpacking libopentest4j-reporting-java (0.1.0-M1-2) ... Selecting previously unselected package libpicocli-java. Preparing to unpack .../226-libpicocli-java_4.6.2-2_all.deb ... Unpacking libpicocli-java (4.6.2-2) ... Selecting previously unselected package libunivocity-parsers-java. Preparing to unpack .../227-libunivocity-parsers-java_2.9.1-1_all.deb ... Unpacking libunivocity-parsers-java (2.9.1-1) ... Selecting previously unselected package junit5. Preparing to unpack .../228-junit5_5.10.3-1_all.deb ... Unpacking junit5 (5.10.3-1) ... Selecting previously unselected package libactivation-java. Preparing to unpack .../229-libactivation-java_1.2.0-2_all.deb ... Unpacking libactivation-java (1.2.0-2) ... Selecting previously unselected package libaopalliance-java. Preparing to unpack .../230-libaopalliance-java_20070526-7_all.deb ... Unpacking libaopalliance-java (20070526-7) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../231-libapache-pom-java_33-2_all.deb ... Unpacking libapache-pom-java (33-2) ... Selecting previously unselected package libasm-java. Preparing to unpack .../232-libasm-java_9.8-1_all.deb ... Unpacking libasm-java (9.8-1) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../233-libatinject-jsr330-api-java_1.0+ds1-6_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-6) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../234-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-lang3-java. Preparing to unpack .../235-libcommons-lang3-java_3.17.0-1_all.deb ... Unpacking libcommons-lang3-java (3.17.0-1) ... Selecting previously unselected package libfreemarker-java. Preparing to unpack .../236-libfreemarker-java_2.3.32-2.1_all.deb ... Unpacking libfreemarker-java (2.3.32-2.1) ... Selecting previously unselected package libgoogle-gson-java. Preparing to unpack .../237-libgoogle-gson-java_2.10.1-1_all.deb ... Unpacking libgoogle-gson-java (2.10.1-1) ... Selecting previously unselected package libjoptsimple-java. Preparing to unpack .../238-libjoptsimple-java_5.0.4-7_all.deb ... Unpacking libjoptsimple-java (5.0.4-7) ... Selecting previously unselected package libcommons-codec-java. Preparing to unpack .../239-libcommons-codec-java_1.18.0-1_all.deb ... Unpacking libcommons-codec-java (1.18.0-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../240-libcommons-logging-java_1.3.0-1_all.deb ... Unpacking libcommons-logging-java (1.3.0-1) ... Selecting previously unselected package libhttpcore-java. Preparing to unpack .../241-libhttpcore-java_4.4.16-1_all.deb ... Unpacking libhttpcore-java (4.4.16-1) ... Selecting previously unselected package libhttpclient-java. Preparing to unpack .../242-libhttpclient-java_4.5.14-1_all.deb ... Unpacking libhttpclient-java (4.5.14-1) ... Selecting previously unselected package liblightcouch-java. Preparing to unpack .../243-liblightcouch-java_0.2.0-1_all.deb ... Unpacking liblightcouch-java (0.2.0-1) ... Selecting previously unselected package libmongodb-java. Preparing to unpack .../244-libmongodb-java_3.6.3-2_all.deb ... Unpacking libmongodb-java (3.6.3-2) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../245-libslf4j-java_1.7.32-1_all.deb ... Unpacking libslf4j-java (1.7.32-1) ... Selecting previously unselected package liblog4j2-java. Preparing to unpack .../246-liblog4j2-java_2.19.0-2_all.deb ... Unpacking liblog4j2-java (2.19.0-2) ... Selecting previously unselected package libbarclay-java. Preparing to unpack .../247-libbarclay-java_5.0.0+dfsg-1_all.deb ... Unpacking libbarclay-java (5.0.0+dfsg-1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../248-libblas3_3.12.1-2_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-2) ... Selecting previously unselected package libbsh-java. Preparing to unpack .../249-libbsh-java_2.0b4-20_all.deb ... Unpacking libbsh-java (2.0b4-20) ... Selecting previously unselected package libcommons-io-java. Preparing to unpack .../250-libcommons-io-java_2.19.0-1_all.deb ... Unpacking libcommons-io-java (2.19.0-1) ... Selecting previously unselected package libmaven-shared-utils-java. Preparing to unpack .../251-libmaven-shared-utils-java_3.4.2-1_all.deb ... Unpacking libmaven-shared-utils-java (3.4.2-1) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../252-libcommons-cli-java_1.6.0-1_all.deb ... Unpacking libcommons-cli-java (1.6.0-1) ... Selecting previously unselected package libgeronimo-annotation-1.3-spec-java. Preparing to unpack .../253-libgeronimo-annotation-1.3-spec-java_1.3-1_all.deb ... Unpacking libgeronimo-annotation-1.3-spec-java (1.3-1) ... Selecting previously unselected package liberror-prone-java. Preparing to unpack .../254-liberror-prone-java_2.18.0-1_all.deb ... Unpacking liberror-prone-java (2.18.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../255-libjsr305-java_0.1~+svn49-12_all.deb ... Unpacking libjsr305-java (0.1~+svn49-12) ... Selecting previously unselected package libguava-java. Preparing to unpack .../256-libguava-java_32.0.1-1_all.deb ... Unpacking libguava-java (32.0.1-1) ... Selecting previously unselected package libguice-java. Preparing to unpack .../257-libguice-java_5.1.0-1_all.deb ... Unpacking libguice-java (5.1.0-1) ... Selecting previously unselected package libmaven-parent-java. Preparing to unpack .../258-libmaven-parent-java_43-2_all.deb ... Unpacking libmaven-parent-java (43-2) ... Selecting previously unselected package libplexus-utils2-java. Preparing to unpack .../259-libplexus-utils2-java_3.4.2-1_all.deb ... Unpacking libplexus-utils2-java (3.4.2-1) ... Selecting previously unselected package libwagon-provider-api-java. Preparing to unpack .../260-libwagon-provider-api-java_3.5.3-1_all.deb ... Unpacking libwagon-provider-api-java (3.5.3-1) ... Selecting previously unselected package libmaven-resolver-java. Preparing to unpack .../261-libmaven-resolver-java_1.9.22-1_all.deb ... Unpacking libmaven-resolver-java (1.9.22-1) ... Selecting previously unselected package libplexus-cipher-java. Preparing to unpack .../262-libplexus-cipher-java_2.0-1_all.deb ... Unpacking libplexus-cipher-java (2.0-1) ... Selecting previously unselected package libplexus-classworlds-java. Preparing to unpack .../263-libplexus-classworlds-java_2.7.0-1_all.deb ... Unpacking libplexus-classworlds-java (2.7.0-1) ... Selecting previously unselected package libplexus-component-annotations-java. Preparing to unpack .../264-libplexus-component-annotations-java_2.1.1-1_all.deb ... Unpacking libplexus-component-annotations-java (2.1.1-1) ... Selecting previously unselected package libplexus-interpolation-java. Preparing to unpack .../265-libplexus-interpolation-java_1.27-1_all.deb ... Unpacking libplexus-interpolation-java (1.27-1) ... Selecting previously unselected package libplexus-sec-dispatcher-java. Preparing to unpack .../266-libplexus-sec-dispatcher-java_2.0-3_all.deb ... Unpacking libplexus-sec-dispatcher-java (2.0-3) ... Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java. Preparing to unpack .../267-libgeronimo-interceptor-3.0-spec-java_1.0.1-5_all.deb ... Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Selecting previously unselected package libcdi-api-java. Preparing to unpack .../268-libcdi-api-java_1.2-4_all.deb ... Unpacking libcdi-api-java (1.2-4) ... Selecting previously unselected package libsisu-inject-java. Preparing to unpack .../269-libsisu-inject-java_0.3.5-1_all.deb ... Unpacking libsisu-inject-java (0.3.5-1) ... Selecting previously unselected package libsisu-plexus-java. Preparing to unpack .../270-libsisu-plexus-java_0.3.5-1_all.deb ... Unpacking libsisu-plexus-java (0.3.5-1) ... Selecting previously unselected package libmaven3-core-java. Preparing to unpack .../271-libmaven3-core-java_3.9.9-1_all.deb ... Unpacking libmaven3-core-java (3.9.9-1) ... Selecting previously unselected package libmaven-shared-io-java. Preparing to unpack .../272-libmaven-shared-io-java_3.0.0-4_all.deb ... Unpacking libmaven-shared-io-java (3.0.0-4) ... Selecting previously unselected package libmaven-file-management-java. Preparing to unpack .../273-libmaven-file-management-java_3.0.0-2_all.deb ... Unpacking libmaven-file-management-java (3.0.0-2) ... Selecting previously unselected package libbuild-helper-maven-plugin-java. Preparing to unpack .../274-libbuild-helper-maven-plugin-java_3.3.0-1_all.deb ... Unpacking libbuild-helper-maven-plugin-java (3.3.0-1) ... Selecting previously unselected package libbyte-buddy-java. Preparing to unpack .../275-libbyte-buddy-java_1.14.19-1_all.deb ... Unpacking libbyte-buddy-java (1.14.19-1) ... Selecting previously unselected package libcolt-free-java. Preparing to unpack .../276-libcolt-free-java_1.2.0+dfsg-8_all.deb ... Unpacking libcolt-free-java (1.2.0+dfsg-8) ... Selecting previously unselected package libcommons-collections3-java. Preparing to unpack .../277-libcommons-collections3-java_3.2.2-3_all.deb ... Unpacking libcommons-collections3-java (3.2.2-3) ... Selecting previously unselected package libcommons-beanutils-java. Preparing to unpack .../278-libcommons-beanutils-java_1.10.1-1_all.deb ... Unpacking libcommons-beanutils-java (1.10.1-1) ... Selecting previously unselected package libcommons-collections4-java. Preparing to unpack .../279-libcommons-collections4-java_4.4-2_all.deb ... Unpacking libcommons-collections4-java (4.4-2) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../280-libcommons-compress-java_1.27.1-2_all.deb ... Unpacking libcommons-compress-java (1.27.1-2) ... Selecting previously unselected package libcommons-lang-java. Preparing to unpack .../281-libcommons-lang-java_2.6-10_all.deb ... Unpacking libcommons-lang-java (2.6-10) ... Selecting previously unselected package libcommons-configuration-java. Preparing to unpack .../282-libcommons-configuration-java_1.10-7_all.deb ... Unpacking libcommons-configuration-java (1.10-7) ... Selecting previously unselected package libcommons-digester-java. Preparing to unpack .../283-libcommons-digester-java_1.8.1-7_all.deb ... Unpacking libcommons-digester-java (1.8.1-7) ... Selecting previously unselected package libcommons-exec-java. Preparing to unpack .../284-libcommons-exec-java_1.3-2_all.deb ... Unpacking libcommons-exec-java (1.3-2) ... Selecting previously unselected package libcommons-jexl2-java. Preparing to unpack .../285-libcommons-jexl2-java_2.1.1-6_all.deb ... Unpacking libcommons-jexl2-java (2.1.1-6) ... Selecting previously unselected package libcommons-math-java. Preparing to unpack .../286-libcommons-math-java_2.2-9_all.deb ... Unpacking libcommons-math-java (2.2-9) ... Selecting previously unselected package libcommons-math3-java. Preparing to unpack .../287-libcommons-math3-java_3.6.1-4_all.deb ... Unpacking libcommons-math3-java (3.6.1-4) ... Selecting previously unselected package libplexus-io-java. Preparing to unpack .../288-libplexus-io-java_3.3.1-2_all.deb ... Unpacking libplexus-io-java (3.3.1-2) ... Selecting previously unselected package libsnappy1v5:arm64. Preparing to unpack .../289-libsnappy1v5_1.2.2-1_arm64.deb ... Unpacking libsnappy1v5:arm64 (1.2.2-1) ... Selecting previously unselected package libsnappy-jni. Preparing to unpack .../290-libsnappy-jni_1.1.10.7-1_arm64.deb ... Unpacking libsnappy-jni (1.1.10.7-1) ... Selecting previously unselected package libsnappy-java. Preparing to unpack .../291-libsnappy-java_1.1.10.7-1_all.deb ... Unpacking libsnappy-java (1.1.10.7-1) ... Selecting previously unselected package libxz-java. Preparing to unpack .../292-libxz-java_1.9-1_all.deb ... Unpacking libxz-java (1.9-1) ... Selecting previously unselected package libplexus-archiver-java. Preparing to unpack .../293-libplexus-archiver-java_4.6.1-1_all.deb ... Unpacking libplexus-archiver-java (4.6.1-1) ... Selecting previously unselected package libmaven-archiver-java. Preparing to unpack .../294-libmaven-archiver-java_3.6.2-1_all.deb ... Unpacking libmaven-archiver-java (3.6.2-1) ... Selecting previously unselected package libmaven-jar-plugin-java. Preparing to unpack .../295-libmaven-jar-plugin-java_3.3.0-2_all.deb ... Unpacking libmaven-jar-plugin-java (3.3.0-2) ... Selecting previously unselected package libcommons-text-java. Preparing to unpack .../296-libcommons-text-java_1.13.1-1_all.deb ... Unpacking libcommons-text-java (1.13.1-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../297-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package libcommons-validator-java. Preparing to unpack .../298-libcommons-validator-java_1%3a1.9.0-1_all.deb ... Unpacking libcommons-validator-java (1:1.9.0-1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../299-libsasl2-modules-db_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../300-libsasl2-2_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../301-libldap2_2.6.9+dfsg-2_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-2) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../302-libnghttp2-14_1.64.0-1.1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../303-libnghttp3-9_1.8.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.8.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../304-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../305-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../306-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../307-libcurl4t64_8.13.0-5_arm64.deb ... Unpacking libcurl4t64:arm64 (8.13.0-5) ... Selecting previously unselected package libdistlib-java. Preparing to unpack .../308-libdistlib-java_1.0-5_all.deb ... Unpacking libdistlib-java (1.0-5) ... Selecting previously unselected package libjaxen-java. Preparing to unpack .../309-libjaxen-java_1.1.6-5_all.deb ... Unpacking libjaxen-java (1.1.6-5) ... Selecting previously unselected package libdom4j-java. Preparing to unpack .../310-libdom4j-java_2.1.4-1_all.deb ... Unpacking libdom4j-java (2.1.4-1) ... Selecting previously unselected package libdoxia-core-java. Preparing to unpack .../311-libdoxia-core-java_2.0.0-1_all.deb ... Unpacking libdoxia-core-java (2.0.0-1) ... Selecting previously unselected package libplexus-xml-java. Preparing to unpack .../312-libplexus-xml-java_3.0.1-2_all.deb ... Unpacking libplexus-xml-java (3.0.1-2) ... Selecting previously unselected package libdoxia-java. Preparing to unpack .../313-libdoxia-java_2.0.0-1_all.deb ... Unpacking libdoxia-java (2.0.0-1) ... Selecting previously unselected package libmaven-reporting-api-java. Preparing to unpack .../314-libmaven-reporting-api-java_4.0.0-1_all.deb ... Unpacking libmaven-reporting-api-java (4.0.0-1) ... Selecting previously unselected package libxbean-reflect-java. Preparing to unpack .../315-libxbean-reflect-java_4.5-9_all.deb ... Unpacking libxbean-reflect-java (4.5-9) ... Selecting previously unselected package libplexus-container-default-java. Preparing to unpack .../316-libplexus-container-default-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default-java (2.1.1-1) ... Selecting previously unselected package libplexus-i18n-java. Preparing to unpack .../317-libplexus-i18n-java_1.0-beta-10-6_all.deb ... Unpacking libplexus-i18n-java (1.0-beta-10-6) ... Selecting previously unselected package velocity. Preparing to unpack .../318-velocity_1.7-7_all.deb ... Unpacking velocity (1.7-7) ... Selecting previously unselected package libplexus-velocity-java. Preparing to unpack .../319-libplexus-velocity-java_1.2-4_all.deb ... Unpacking libplexus-velocity-java (1.2-4) ... Selecting previously unselected package liboro-java. Preparing to unpack .../320-liboro-java_2.0.8a-14_all.deb ... Unpacking liboro-java (2.0.8a-14) ... Selecting previously unselected package libvelocity-tools-java. Preparing to unpack .../321-libvelocity-tools-java_2.0-9_all.deb ... Unpacking libvelocity-tools-java (2.0-9) ... Selecting previously unselected package libdoxia-sitetools-java. Preparing to unpack .../322-libdoxia-sitetools-java_2.0.0-1_all.deb ... Unpacking libdoxia-sitetools-java (2.0.0-1) ... Selecting previously unselected package libfastutil-java. Preparing to unpack .../323-libfastutil-java_8.5.15+dfsg-1_all.deb ... Unpacking libfastutil-java (8.5.15+dfsg-1) ... Selecting previously unselected package libxpp3-java. Preparing to unpack .../324-libxpp3-java_1.1.4c-4_all.deb ... Unpacking libxpp3-java (1.1.4c-4) ... Selecting previously unselected package libxstream-java. Preparing to unpack .../325-libxstream-java_1.4.21-1_all.deb ... Unpacking libxstream-java (1.4.21-1) ... Selecting previously unselected package libjsap-java. Preparing to unpack .../326-libjsap-java_2.1-5_all.deb ... Unpacking libjsap-java (2.1-5) ... Selecting previously unselected package liblogback-java. Preparing to unpack .../327-liblogback-java_1%3a1.2.11-6_all.deb ... Unpacking liblogback-java (1:1.2.11-6) ... Selecting previously unselected package libdsiutils-java. Preparing to unpack .../328-libdsiutils-java_2.7.3+dfsg-1_all.deb ... Unpacking libdsiutils-java (2.7.3+dfsg-1) ... Selecting previously unselected package libobjenesis-java. Preparing to unpack .../329-libobjenesis-java_3.4-2_all.deb ... Unpacking libobjenesis-java (3.4-2) ... Selecting previously unselected package libeasymock-java. Preparing to unpack .../330-libeasymock-java_5.5.0-1_all.deb ... Unpacking libeasymock-java (5.5.0-1) ... Selecting previously unselected package libel-api-java. Preparing to unpack .../331-libel-api-java_3.0.0-3_all.deb ... Unpacking libel-api-java (3.0.0-3) ... Selecting previously unselected package libexec-maven-plugin-java. Preparing to unpack .../332-libexec-maven-plugin-java_3.1.0-2_all.deb ... Unpacking libexec-maven-plugin-java (3.1.0-2) ... Selecting previously unselected package libezmorph-java. Preparing to unpack .../333-libezmorph-java_1.0.6-4_all.deb ... Unpacking libezmorph-java (1.0.6-4) ... Selecting previously unselected package libgatk-native-bindings-java. Preparing to unpack .../334-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../335-libgfortran5_14.2.0-19_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-19) ... Selecting previously unselected package libxml-commons-external-java. Preparing to unpack .../336-libxml-commons-external-java_1.4.01-6_all.deb ... Unpacking libxml-commons-external-java (1.4.01-6) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Preparing to unpack .../337-libxml-commons-resolver1.1-java_1.2-11_all.deb ... Unpacking libxml-commons-resolver1.1-java (1.2-11) ... Selecting previously unselected package libxerces2-java. Preparing to unpack .../338-libxerces2-java_2.12.2-1_all.deb ... Unpacking libxerces2-java (2.12.2-1) ... Selecting previously unselected package libxom-java. Preparing to unpack .../339-libxom-java_1.3.9-1_all.deb ... Unpacking libxom-java (1.3.9-1) ... Selecting previously unselected package libjson-java. Preparing to unpack .../340-libjson-java_3.1.0+dfsg-2_all.deb ... Unpacking libjson-java (3.1.0+dfsg-2) ... Selecting previously unselected package libmbedcrypto16:arm64. Preparing to unpack .../341-libmbedcrypto16_3.6.3-1_arm64.deb ... Unpacking libmbedcrypto16:arm64 (3.6.3-1) ... Selecting previously unselected package libmbedx509-7:arm64. Preparing to unpack .../342-libmbedx509-7_3.6.3-1_arm64.deb ... Unpacking libmbedx509-7:arm64 (3.6.3-1) ... Selecting previously unselected package libmbedtls21:arm64. Preparing to unpack .../343-libmbedtls21_3.6.3-1_arm64.deb ... Unpacking libmbedtls21:arm64 (3.6.3-1) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../344-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:arm64. Preparing to unpack .../345-libncbi-vdb3_3.2.1+dfsg-2_arm64.deb ... Unpacking libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-ngs3:arm64. Preparing to unpack .../346-libncbi-ngs3_3.2.1+dfsg-4_arm64.deb ... Unpacking libncbi-ngs3:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package libngs-jni:arm64. Preparing to unpack .../347-libngs-jni_3.2.1+dfsg-4_arm64.deb ... Unpacking libngs-jni:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package libngs-java:arm64. Preparing to unpack .../348-libngs-java_3.2.1+dfsg-4_arm64.deb ... Unpacking libngs-java:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package librhino-java. Preparing to unpack .../349-librhino-java_1.7.15-1_all.deb ... Unpacking librhino-java (1.7.15-1) ... Selecting previously unselected package libhtsjdk-java. Preparing to unpack .../350-libhtsjdk-java_4.1.3+dfsg-2_all.deb ... Unpacking libhtsjdk-java (4.1.3+dfsg-2) ... Selecting previously unselected package libgkl-java. Preparing to unpack .../351-libgkl-java_0.8.11+dfsg-2_all.deb ... Unpacking libgkl-java (0.8.11+dfsg-2) ... Selecting previously unselected package libicu4j-java. Preparing to unpack .../352-libicu4j-java_73.2-1_all.deb ... Unpacking libicu4j-java (73.2-1) ... Selecting previously unselected package liblog4j1.2-java. Preparing to unpack .../353-liblog4j1.2-java_1.2.17-11_all.deb ... Unpacking liblog4j1.2-java (1.2.17-11) ... Selecting previously unselected package libicb-utils-java. Preparing to unpack .../354-libicb-utils-java_2.0.1+git20161002.afee1d9-5_all.deb ... Unpacking libicb-utils-java (2.0.1+git20161002.afee1d9-5) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../355-libice6_2%3a1.1.1-1_arm64.deb ... Unpacking libice6:arm64 (2:1.1.1-1) ... Selecting previously unselected package libicu76:arm64. Preparing to unpack .../356-libicu76_76.1-3_arm64.deb ... Unpacking libicu76:arm64 (76.1-3) ... Selecting previously unselected package libjansi-java. Preparing to unpack .../357-libjansi-java_2.4.1-2_all.deb ... Unpacking libjansi-java (2.4.1-2) ... Selecting previously unselected package libjavassist-java. Preparing to unpack .../358-libjavassist-java_1%3a3.27.0-1_all.deb ... Unpacking libjavassist-java (1:3.27.0-1) ... Selecting previously unselected package libjaxb-api-java. Preparing to unpack .../359-libjaxb-api-java_2.3.1-1_all.deb ... Unpacking libjaxb-api-java (2.3.1-1) ... Selecting previously unselected package libjboss-logging-java. Preparing to unpack .../360-libjboss-logging-java_3.5.3-1_all.deb ... Unpacking libjboss-logging-java (3.5.3-1) ... Selecting previously unselected package libjboss-vfs-java. Preparing to unpack .../361-libjboss-vfs-java_3.2.15.Final-3_all.deb ... Unpacking libjboss-vfs-java (3.2.15.Final-3) ... Selecting previously unselected package libjbzip2-java. Preparing to unpack .../362-libjbzip2-java_0.9.1-8_all.deb ... Unpacking libjbzip2-java (0.9.1-8) ... Selecting previously unselected package libjcommander-java. Preparing to unpack .../363-libjcommander-java_1.71-4_all.deb ... Unpacking libjcommander-java (1.71-4) ... Selecting previously unselected package libjsp-api-java. Preparing to unpack .../364-libjsp-api-java_2.3.4-3_all.deb ... Unpacking libjsp-api-java (2.3.4-3) ... Selecting previously unselected package libservlet-api-java. Preparing to unpack .../365-libservlet-api-java_4.0.1-2_all.deb ... Unpacking libservlet-api-java (4.0.1-2) ... Selecting previously unselected package libwebsocket-api-java. Preparing to unpack .../366-libwebsocket-api-java_1.1-2_all.deb ... Unpacking libwebsocket-api-java (1.1-2) ... Selecting previously unselected package libjetty9-java. Preparing to unpack .../367-libjetty9-java_9.4.57-1_all.deb ... Unpacking libjetty9-java (9.4.57-1) ... Selecting previously unselected package libjsoup-java. Preparing to unpack .../368-libjsoup-java_1.15.3-1_all.deb ... Unpacking libjsoup-java (1.15.3-1) ... Selecting previously unselected package libjtidy-java. Preparing to unpack .../369-libjtidy-java_7+svn20110807-6_all.deb ... Unpacking libjtidy-java (7+svn20110807-6) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../370-liblapack3_3.12.1-2_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-2) ... Selecting previously unselected package libmaven-antrun-plugin-java. Preparing to unpack .../371-libmaven-antrun-plugin-java_3.1.0-1_all.deb ... Unpacking libmaven-antrun-plugin-java (3.1.0-1) ... Selecting previously unselected package libmaven-common-artifact-filters-java. Preparing to unpack .../372-libmaven-common-artifact-filters-java_3.4.0-1_all.deb ... Unpacking libmaven-common-artifact-filters-java (3.4.0-1) ... Selecting previously unselected package libmaven-artifact-transfer-java. Preparing to unpack .../373-libmaven-artifact-transfer-java_0.13.1-2_all.deb ... Unpacking libmaven-artifact-transfer-java (0.13.1-2) ... Selecting previously unselected package libplexus-build-api-java. Preparing to unpack .../374-libplexus-build-api-java_0.0.7-4_all.deb ... Unpacking libplexus-build-api-java (0.0.7-4) ... Selecting previously unselected package libmaven-filtering-java. Preparing to unpack .../375-libmaven-filtering-java_3.4.0-1_all.deb ... Unpacking libmaven-filtering-java (3.4.0-1) ... Selecting previously unselected package libmaven-assembly-plugin-java. Preparing to unpack .../376-libmaven-assembly-plugin-java_3.4.2-2_all.deb ... Unpacking libmaven-assembly-plugin-java (3.4.2-2) ... Selecting previously unselected package libmaven-clean-plugin-java. Preparing to unpack .../377-libmaven-clean-plugin-java_3.2.0-2_all.deb ... Unpacking libmaven-clean-plugin-java (3.2.0-2) ... Selecting previously unselected package libmaven-shared-incremental-java. Preparing to unpack .../378-libmaven-shared-incremental-java_1.1-6_all.deb ... Unpacking libmaven-shared-incremental-java (1.1-6) ... Selecting previously unselected package libplexus-compiler-java. Preparing to unpack .../379-libplexus-compiler-java_2.13.0-1_all.deb ... Unpacking libplexus-compiler-java (2.13.0-1) ... Selecting previously unselected package libqdox2-java. Preparing to unpack .../380-libqdox2-java_2.0.3-1_all.deb ... Unpacking libqdox2-java (2.0.3-1) ... Selecting previously unselected package libplexus-languages-java. Preparing to unpack .../381-libplexus-languages-java_1.1.1-2_all.deb ... Unpacking libplexus-languages-java (1.1.1-2) ... Selecting previously unselected package libmaven-compiler-plugin-java. Preparing to unpack .../382-libmaven-compiler-plugin-java_3.13.0-1_all.deb ... Unpacking libmaven-compiler-plugin-java (3.13.0-1) ... Selecting previously unselected package libmaven-dependency-analyzer-java. Preparing to unpack .../383-libmaven-dependency-analyzer-java_1.15.1-1_all.deb ... Unpacking libmaven-dependency-analyzer-java (1.15.1-1) ... Selecting previously unselected package libmaven-dependency-tree-java. Preparing to unpack .../384-libmaven-dependency-tree-java_3.3.0-1_all.deb ... Unpacking libmaven-dependency-tree-java (3.3.0-1) ... Selecting previously unselected package libmaven-reporting-impl-java. Preparing to unpack .../385-libmaven-reporting-impl-java_4.0.0-1_all.deb ... Unpacking libmaven-reporting-impl-java (4.0.0-1) ... Selecting previously unselected package libmaven-dependency-plugin-java. Preparing to unpack .../386-libmaven-dependency-plugin-java_3.8.1-1_all.deb ... Unpacking libmaven-dependency-plugin-java (3.8.1-1) ... Selecting previously unselected package libmaven-invoker-java. Preparing to unpack .../387-libmaven-invoker-java_3.3.0-1_all.deb ... Unpacking libmaven-invoker-java (3.3.0-1) ... Selecting previously unselected package libplexus-interactivity-api-java. Preparing to unpack .../388-libplexus-interactivity-api-java_1.3-1_all.deb ... Unpacking libplexus-interactivity-api-java (1.3-1) ... Selecting previously unselected package libmaven-javadoc-plugin-java. Preparing to unpack .../389-libmaven-javadoc-plugin-java_3.10.1-2_all.deb ... Unpacking libmaven-javadoc-plugin-java (3.10.1-2) ... Selecting previously unselected package libplexus-ant-factory-java. Preparing to unpack .../390-libplexus-ant-factory-java_1.0~alpha2.1-5_all.deb ... Unpacking libplexus-ant-factory-java (1.0~alpha2.1-5) ... Selecting previously unselected package libplexus-container-default1.5-java. Preparing to unpack .../391-libplexus-container-default1.5-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default1.5-java (2.1.1-1) ... Selecting previously unselected package libplexus-bsh-factory-java. Preparing to unpack .../392-libplexus-bsh-factory-java_1.0~alpha7-5_all.deb ... Unpacking libplexus-bsh-factory-java (1.0~alpha7-5) ... Selecting previously unselected package libmaven-plugin-tools-java. Preparing to unpack .../393-libmaven-plugin-tools-java_3.10.2-2_all.deb ... Unpacking libmaven-plugin-tools-java (3.10.2-2) ... Selecting previously unselected package libmaven-reporting-exec-java. Preparing to unpack .../394-libmaven-reporting-exec-java_2.0.0-1_all.deb ... Unpacking libmaven-reporting-exec-java (2.0.0-1) ... Selecting previously unselected package libmaven-resources-plugin-java. Preparing to unpack .../395-libmaven-resources-plugin-java_3.3.1-1_all.deb ... Unpacking libmaven-resources-plugin-java (3.3.1-1) ... Selecting previously unselected package libmaven-site-plugin-java. Preparing to unpack .../396-libmaven-site-plugin-java_3.21.0-1_all.deb ... Unpacking libmaven-site-plugin-java (3.21.0-1) ... Selecting previously unselected package libmaven-source-plugin-java. Preparing to unpack .../397-libmaven-source-plugin-java_3.3.1-1_all.deb ... Unpacking libmaven-source-plugin-java (3.3.1-1) ... Selecting previously unselected package libpaper2:arm64. Preparing to unpack .../398-libpaper2_2.2.5-0.3+b2_arm64.deb ... Unpacking libpaper2:arm64 (2.2.5-0.3+b2) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../399-libpaper-utils_2.2.5-0.3+b2_arm64.deb ... Unpacking libpaper-utils (2.2.5-0.3+b2) ... Selecting previously unselected package libpicard-java. Preparing to unpack .../400-libpicard-java_3.3.0+dfsg-2_all.deb ... Unpacking libpicard-java (3.3.0+dfsg-2) ... Selecting previously unselected package libpj-java. Preparing to unpack .../401-libpj-java_0.0~20150107+dfsg-5_all.deb ... Unpacking libpj-java (0.0~20150107+dfsg-5) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../402-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../403-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libprotobuf32t64:arm64. Preparing to unpack .../404-libprotobuf32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-lite32t64:arm64. Preparing to unpack .../405-libprotobuf-lite32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf-lite32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-dev:arm64. Preparing to unpack .../406-libprotobuf-dev_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf-dev:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-java. Preparing to unpack .../407-libprotobuf-java_3.21.12-10_all.deb ... Unpacking libprotobuf-java (3.21.12-10) ... Selecting previously unselected package libprotoc32t64:arm64. Preparing to unpack .../408-libprotoc32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotoc32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libreflections-java. Preparing to unpack .../409-libreflections-java_0.10.2+dfsg-2_all.deb ... Unpacking libreflections-java (0.10.2+dfsg-2) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../410-libsm6_2%3a1.2.6-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.6-1) ... Selecting previously unselected package libsurefire-java. Preparing to unpack .../411-libsurefire-java_2.22.3-3_all.deb ... Unpacking libsurefire-java (2.22.3-3) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../412-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../413-libtirpc-common_1.3.6+ds-1_all.deb ... Unpacking libtirpc-common (1.3.6+ds-1) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../414-libtirpc3t64_1.3.6+ds-1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.6+ds-1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../415-libxft2_2.3.6-1+b4_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b4) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../416-libxss1_1%3a1.2.3-1+b3_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../417-libtk8.6_8.6.16-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.16-1) ... Selecting previously unselected package libwagon-file-java. Preparing to unpack .../418-libwagon-file-java_3.5.3-1_all.deb ... Unpacking libwagon-file-java (3.5.3-1) ... Selecting previously unselected package libwagon-http-java. Preparing to unpack .../419-libwagon-http-java_3.5.3-1_all.deb ... Unpacking libwagon-http-java (3.5.3-1) ... Selecting previously unselected package libxml2-utils. Preparing to unpack .../420-libxml2-utils_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2-utils (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../421-libxt6t64_1%3a1.2.1-1.2+b2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Selecting previously unselected package maven. Preparing to unpack .../422-maven_3.9.9-1_all.deb ... Unpacking maven (3.9.9-1) ... Selecting previously unselected package maven-repo-helper. Preparing to unpack .../423-maven-repo-helper_1.11_all.deb ... Unpacking maven-repo-helper (1.11) ... Selecting previously unselected package unzip. Preparing to unpack .../424-unzip_6.0-29_arm64.deb ... Unpacking unzip (6.0-29) ... Selecting previously unselected package maven-debian-helper. Preparing to unpack .../425-maven-debian-helper_2.6.7_all.deb ... Unpacking maven-debian-helper (2.6.7) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../426-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../427-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package protobuf-compiler. Preparing to unpack .../428-protobuf-compiler_3.21.12-10+b6_arm64.deb ... Unpacking protobuf-compiler (3.21.12-10+b6) ... Selecting previously unselected package zip. Preparing to unpack .../429-zip_3.0-15_arm64.deb ... Unpacking zip (3.0-15) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../430-xdg-utils_1.2.1-2_all.deb ... Unpacking xdg-utils (1.2.1-2) ... Selecting previously unselected package r-base-core. Preparing to unpack .../431-r-base-core_4.5.0-2_arm64.deb ... Unpacking r-base-core (4.5.0-2) ... Selecting previously unselected package r-cran-rjava. Preparing to unpack .../432-r-cran-rjava_1.0-11-2_arm64.deb ... Unpacking r-cran-rjava (1.0-11-2) ... Selecting previously unselected package testng. Preparing to unpack .../433-testng_6.9.12-4_all.deb ... Unpacking testng (6.9.12-4) ... Setting up libprotobuf-lite32t64:arm64 (3.21.12-10+b6) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up fastjar (2:0.98-7+b1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libjcommander-java (1.71-4) ... Setting up libfastutil-java (8.5.15+dfsg-1) ... Setting up libtext-charwidth-perl:arm64 (0.04-11+b4) ... Setting up wdiff (1.2.2-9) ... Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libprotobuf32t64:arm64 (3.21.12-10+b6) ... Setting up libfile-which-perl (1.27-2) ... Setting up systemd-sysv (257.5-2) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:arm64 (1.8-3) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up bsdextrautils (2.41-4) ... Setting up hicolor-icon-theme (0.18-2) ... Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... Setting up libgpg-error0:arm64 (1.51-4) ... Setting up libicu4j-java (73.2-1) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libobjenesis-java (3.4-2) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up liblogback-java (1:1.2.11-6) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:arm64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libtirpc-common (1.3.6+ds-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxcb-glx0:arm64 (1.17.0-2+b1) ... Setting up unzip (6.0-29) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libedit2:arm64 (3.1-20250104-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.8-1) ... Setting up x11-common (1:7.7+24) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.2-2) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libel-api-java (3.0.0-3) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up xkb-data (2.42-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2-1+b1) ... Setting up file (1:5.46-5) ... Setting up libjboss-logging-java (3.5.3-1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:arm64 (1.2.2-1) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 27 18:57:29 UTC 2025. Universal Time is now: Sun Apr 27 18:57:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.14-1) ... Setting up libjavassist-java (1:3.27.0-1) ... Setting up zip (3.0-15) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libasound2t64:arm64 (1.2.14-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libepoxy0:arm64 (1.5.10-2) ... Setting up libnspr4:arm64 (2:4.36-1) ... Setting up libxcb-sync1:arm64 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-6) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-16) ... Setting up libxpp3-java (1.1.4c-4) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:arm64 (1.16.2-2) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libproc2-0:arm64 (2:4.0.4-8) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.47-1.1) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-2) ... Setting up binfmt-support (2.2.2-7+b1) ... Running in chroot, ignoring request. 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:arm64 (0.22-3+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libpcsclite1:arm64 (2.3.3-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libsensors5:arm64 (1:3.6.2-2) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... 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:arm64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:arm64 (14.2.0-19) ... Setting up libvulkan1:arm64 (1.4.309.0-1) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libwebp7:arm64 (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:arm64 (5.2.2-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up libplexus-interactivity-api-java (1.3-1) ... Setting up libfreemarker-java (2.3.32-2.1) ... Setting up sensible-utils (0.0.25) ... Setting up libxshmfence1:arm64 (1.3.3-1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.56.1-2) ... Setting up libcommons-math-java (2.2-9) ... Setting up gpgv (2.4.7-16) ... Setting up libtiff6:arm64 (4.7.0-3) ... Setting up libxcb-randr0:arm64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.2-2) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libassuan9:arm64 (3.0.2-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-8) ... 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:arm64 (4.20.0-2) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.5) ... Setting up libcommons-math3-java (3.6.1-4) ... Setting up sgml-base (1.31+nmu1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libwayland-egl1:arm64 (1.23.1-3) ... Setting up libicu76:arm64 (76.1-3) ... Setting up libmbedcrypto16:arm64 (3.6.3-1) ... Setting up libpaper2:arm64 (2.2.5-0.3+b2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-7) ... Setting up libprotoc32t64:arm64 (3.21.12-10+b6) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up libfile-homedir-perl (1.006-2) ... Setting up libpj-java (0.0~20150107+dfsg-5) ... Setting up openssl (3.5.0-1) ... Setting up libdrm-common (2.4.124-2) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:arm64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-2) ... Setting up liburi-perl (5.30-1) ... Setting up dbus-bin (1.16.2-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libxkbcommon0:arm64 (1.7.0-2) ... Setting up libwayland-client0:arm64 (1.23.1-3) ... Setting up libnet-ssleay-perl:arm64 (1.94-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.1-2) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:arm64 (1:19.1.7-3) ... Setting up libwayland-server0:arm64 (1.23.1-3) ... Setting up libx11-xcb1:arm64 (2:1.8.12-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxstream-java (1.4.21-1) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libjetty9-java (9.4.57-1) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up protobuf-compiler (3.21.12-10+b6) ... Setting up libjboss-vfs-java (3.2.15.Final-3) ... Setting up libxrender1:arm64 (1:0.9.12-1) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:arm64 (2.3.8-2) ... Setting up libnss3:arm64 (2:3.110-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libpaper-utils (2.2.5-0.3+b2) ... Setting up libxom-java (1.3.9-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libmaven-dependency-analyzer-java (1.15.1-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:arm64 (3.21.12-10+b6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1+b1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:arm64 (2.84.1-2) ... Setting up libmbedx509-7:arm64 (3.6.3-1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b4) ... Setting up testng (6.9.12-4) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b4) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libxrandr2:arm64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0051) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:arm64 (3.6.3-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:arm64 (2.4.124-2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:arm64 (1.23.1-3) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gpgconf (2.4.7-16) ... Setting up libpam-systemd:arm64 (257.5-2) ... Setting up libcommons-beanutils-java (1.10.1-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2.3) ... 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+really2.9.14-0.4) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up libsm6:arm64 (2:1.2.6-1) ... Setting up libreflections-java (0.10.2+dfsg-2) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libavahi-client3:arm64 (0.8-16) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.4.7-16) ... Created symlink '/etc/systemd/user/sockets.target.wants/keyboxd.socket' -> '/usr/lib/systemd/user/keyboxd.socket'. Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.124-2) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.18.4+ds-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up mesa-libgallium:arm64 (25.0.4-1) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-2.3) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.6-1+b4) ... Setting up gpg-agent (2.4.7-16) ... Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'. Setting up libatk1.0-0t64:arm64 (2.56.1-2) ... Setting up openjdk-21-jre-headless:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libtirpc3t64:arm64 (1.3.6+ds-1) ... Setting up libgbm1:arm64 (25.0.4-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.3-2) ... Setting up libcommons-io-java (2.19.0-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:arm64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:arm64 (1:1.2.3-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libpango-1.0-0:arm64 (1.56.3-1) ... Setting up libgl1-mesa-dri:arm64 (25.0.4-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Setting up libcloudproviders0:arm64 (0.3.6-2) ... Setting up python3 (3.13.3-1) ... Setting up sopv-gpgv (0.1.4-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up libcolord2:arm64 (1.4.7-3) ... Setting up libdconf1:arm64 (0.40.0-5) ... Setting up libmaven-filtering-java (3.4.0-1) ... Setting up dbus-user-session (1.16.2-2) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (48.0-1) ... 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 (0.018-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:arm64 (2.56.1-2) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up libmaven-dependency-tree-java (3.3.0-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:arm64 (1.18.4-1+b1) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... Setting up libncbi-ngs3:arm64 (3.2.1+dfsg-4) ... Setting up libatk-bridge2.0-0t64:arm64 (2.56.1-2) ... Setting up libngs-jni:arm64 (3.2.1+dfsg-4) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:arm64 (25.0.4-1) ... Setting up libglx0:arm64 (1.7.0-1+b2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:arm64 (8.13.0-5) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libmaven-invoker-java (3.3.0-1) ... Setting up debhelper (13.24.2) ... Setting up dconf-service (0.40.0-5) ... Setting up libgl1:arm64 (1.7.0-1+b2) ... Setting up r-base-core (4.5.0-2) ... Creating config file /etc/R/Renviron with new version Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:arm64 (3.2.1+dfsg-4) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libmaven-source-plugin-java (3.3.1-1) ... Setting up libgtk-3-common (3.24.49-3) ... Setting up libgtk-3-0t64:arm64 (3.24.49-3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.78-1) ... Setting up devscripts (2.25.10) ... 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 (1.13.1-1) ... 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 (2.41-7) ... Processing triggers for systemd (257.5-2) ... 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_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_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: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:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven (3.9.9-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:arm64 (21.0.7+6-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up ant-contrib (1.0~b3+svn177-12) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.21-76) ... Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-5) ... Setting up openjdk-21-jdk:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up libjsap-java (2.1-5) ... Setting up r-cran-rjava (1.0-11-2) ... 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 (3.10.2-2) ... 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+nmu1) ... 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 (20250419) ... 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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with javahelper dh_auto_clean bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibgoby-io-java jh_clean Duplicate specification "unlink|u" for option "u" debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' dh_clean rm -rf goby-distribution/test-data goby-distribution/test-results rm -rf test-results/ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo jh_linkjars dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1 [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16 [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15 [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Goby Framework [pom] [INFO] Goby I/O [jar] [INFO] Goby Full Distribution [jar] [INFO] [INFO] ----------------< org.campagnelab.goby:goby-framework >----------------- [INFO] Building Goby Framework 3.3.1 [1/3] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] from goby-io/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.17 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:3.1.2 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)' [INFO] [INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ goby-io --- [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ goby-io --- [INFO] Recompiling the module because of changed source code. [INFO] Compiling 260 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- antrun:3.1.0:run (default) @ goby-io --- [WARNING] Parameter 'tasks' is deprecated: Use target instead. For version 3.0.0, this parameter is only defined to break the build if you use it! [WARNING] Parameter tasks is deprecated, use target instead [INFO] Executing tasks [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2 [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-io --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-io --- [INFO] No sources to compile [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ goby-io --- [INFO] Tests are skipped. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1.jar [INFO] [INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-io >>> [INFO] [INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-io <<< [INFO] [INFO] [INFO] --- source:3.3.1:jar (attach-sources) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-sources.jar [INFO] [INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-io --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol [WARNING] @XmlRootElement [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist [WARNING] import DistLib.hypergeometric; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol [WARNING] Rengine rEngine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExactRCalculator [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Unmarshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class StatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.CommandLine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.DefaultExecutor; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.PumpStreamHandler; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol [WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class MethylStatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.PJProperties; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElementWrapper; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol [WARNING] @XmlRootElement(name = "info-output") [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol [WARNING] private void writeInfoOutput() throws JAXBException, IOException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:33: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:47: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol [WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol [WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol [WARNING] private Rengine rengine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol [WARNING] public Rengine getRengine() { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.REXP; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RVector; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol [WARNING] private static Result evaluateFisherExpression(final Rengine rengine, [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExact [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:35: error: cannot find symbol [WARNING] @XmlElement(name = "al") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:36: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "annotation-lengths") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:39: error: cannot find symbol [WARNING] @XmlElement(name = "tc") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:40: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "total-counts") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-javadoc.jar [INFO] [INFO] ---------------< org.campagnelab.goby:goby-distribution >--------------- [INFO] Building Goby Full Distribution 3.3.1 [3/3] [INFO] from goby-distribution/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ goby-distribution --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] Copying 72 resources from src/main/java to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ goby-distribution --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 525 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-distribution --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-distribution --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 120 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ goby-distribution --- [INFO] Tests are skipped. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1.jar [INFO] [INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-distribution >>> [INFO] [INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-distribution <<< [INFO] [INFO] [INFO] --- source:3.3.1:jar (attach-sources) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-sources.jar [INFO] [INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-distribution --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J). [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J) [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning: @return tag cannot be used in method with void return type. [WARNING] void flush(InputBitStream ibs) throws IOException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning: reference not found: org.campagnelab.goby.aligners.LastagAligner [WARNING] * @see org.campagnelab.goby.aligners.LastagAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:79: warning: reference not found: org.campagnelab.goby.aligners.LastAligner [WARNING] * @see org.campagnelab.goby.aligners.LastAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:87: warning: reference not found: org.campagnelab.goby.aligners.BWAAligner [WARNING] * @see org.campagnelab.goby.aligners.BWAAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:95: warning: reference not found: org.campagnelab.goby.aligners.GSnapAligner [WARNING] * @see org.campagnelab.goby.aligners.GSnapAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:131: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * @return the next {@link edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<' [WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol ?@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 [ 0.133 s] [INFO] Goby I/O ........................................... SUCCESS [ 40.749 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 43.490 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:24 min [INFO] Finished at: 2025-04-27T07:00:27-12:00 [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 07:01:01.252 INFO RLoggerMainLoopCallback - 07:01:01.257 INFO RLoggerMainLoopCallback - R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 07:01:01.257 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. 07:01:01.257 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. 07:01:01.258 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT qPhred=1 qPhred=2 qPhred=3 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 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] 07:01:02.380 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. 0 AAC 3 ACC 6 ATC 9 AGC 12 AAC 15 ACC 18 ATC 21 AGC 24 AAC 27 ACC 30 ATC 33 AGC 36 AAC 39 ACC 42 ATC 45 AGC 48 AAC 51 ACC 54 ATC 57 AGC 60 AAC 63 ACC 66 ATC 69 AGC 72 AAC 75 ACC 78 ATC 81 AGC07:01:09.707 WARN MessageChunksWriter - Using chunk-size=10000 07:01:09.708 WARN MessageChunksWriter - Using chunk-size=9 07:01:09.713 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 07:01:09.724 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 07:01:09.731 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 Number of bits/base 3.6590436 Creating base test directory: test-results/stats [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. 07:01:10.072 INFO BullardUpperQuartileNormalization - normalization denominator 49719.7 for sample B-7 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 48867.0 for sample B-3 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 99505.1 for sample A-3 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-12 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49588.6 for sample B-15 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 51097.2 for sample B-14 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49326.2 for sample B-11 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 94520.0 for sample A-17 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49916.5 for sample B-2 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 47358.4 for sample B-10 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 98586.8 for sample A-16 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 50703.6 for sample B-8 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 48735.8 for sample B-4 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-2 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 98521.2 for sample A-0 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49326.2 for sample B-6 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97996.4 for sample A-9 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98062.0 for sample A-8 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98980.3 for sample A-5 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97537.3 for sample A-4 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 99964.2 for sample A-6 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98390.0 for sample A-7 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48211.1 for sample B-5 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-10 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 100030 for sample A-14 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 50769.2 for sample B-9 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97865.2 for sample A-1 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48735.8 for sample B-0 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48604.7 for sample B-12 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 49719.7 for sample B-13 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 93536.1 for sample A-19 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97799.6 for sample A-18 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 96750.1 for sample A-15 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48014.3 for sample B-1 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97012.5 for sample A-13 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98258.8 for sample A-11 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 49588.6 for sample B-16 07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 49785.3 for sample B-17 07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 47292.8 for sample B-19 07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 48342.3 for sample B-18 Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T]07:01:10.230 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 07:01:10.309 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 07:01:10.309 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 07:01:10.345 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 07:01:10.346 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 07:01:10.563 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 07:01:10.629 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. 07:01:10.629 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 07:01:10.785 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 07:01:10.808 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 [1.0042223266471022, 0.5016882445373338, 0.006078705586435645, -0.9951369613424312, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00294094 original=0.00294094 truncated fdr=0.00375760 original=0.00375760 truncated fdr=0.00569307 original=0.00569307 truncated fdr=0.00833856 original=0.00833856 truncated fdr=0.0201744 original=0.0201744 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0523700 original=0.0523700 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0733761 original=0.0733761 truncated fdr=0.0742187 original=0.0742187 truncated fdr=0.0847349 original=0.0847349 truncated fdr=0.151073 original=0.151073 truncated fdr=0.335641 original=0.335641 truncated fdr=0.391390 original=0.391390 truncated fdr=0.391390 original=0.391390 truncated fdr=0.443709 original=0.443709 truncated fdr=0.477756 original=0.477756 truncated fdr=0.479630 original=0.479630 truncated fdr=0.637850 original=0.637850 truncated fdr=0.977998 original=0.977998 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. ##fileformat=VCFv4.1 ##Goby=UNKNOWN ##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 1/1 ..T Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 07:01:34.553 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 07:01:34.557 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 07:01:34.564 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 07:01:34.567 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 07:01:34.578 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 07:01:34.585 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 07:01:34.592 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 07:01:34.595 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 07:01:34.598 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 07:01:34.609 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 07:01:34.919 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 07:01:34.930 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 07:01:34.933 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 07:01:34.939 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 07:01:34.942 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 07:01:34.953 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 07:01:34.955 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 07:01:34.958 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 07:01:34.968 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 07:01:34.971 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 07:01:35.166 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 07:01:35.176 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 07:01:35.179 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 07:01:35.185 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 07:01:35.192 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 07:01:35.194 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 07:01:35.201 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 07:01:35.203 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 07:01:35.213 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 07:01:35.216 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 07:01:35.377 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 07:01:35.384 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 07:01:35.386 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 07:01:35.392 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 07:01:35.394 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 07:01:35.413 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 07:01:35.415 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 07:01:35.418 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 07:01:35.424 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 07:01:35.426 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 07:01:35.670 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 07:01:35.680 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 07:01:35.682 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 07:01:35.685 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 07:01:35.686 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 07:01:35.693 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 07:01:35.695 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 07:01:35.698 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 07:01:35.700 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 07:01:35.702 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 07:01:35.803 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 07:01:35.805 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 07:01:35.806 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 07:01:35.817 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 07:01:35.827 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 07:01:35.830 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 07:01:35.831 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 07:01:35.833 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 07:01:35.835 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 07:01:35.841 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 07:01:35.928 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 07:01:35.930 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 07:01:35.933 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 07:01:35.935 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 07:01:35.936 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 07:01:35.938 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 07:01:35.948 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 07:01:35.950 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 07:01:35.960 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 07:01:35.962 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 07:01:36.091 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 07:01:36.101 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 07:01:36.102 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 07:01:36.104 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 07:01:36.106 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 07:01:36.115 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 07:01:36.117 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 07:01:36.119 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 07:01:36.120 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 07:01:36.122 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 07:01:36.246 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 07:01:36.252 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 07:01:36.254 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 07:01:36.264 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 07:01:36.265 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 07:01:36.267 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 07:01:36.269 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 07:01:36.270 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 07:01:36.280 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 07:01:36.282 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 07:01:36.361 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 07:01:36.363 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 07:01:36.364 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 07:01:36.366 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 07:01:36.367 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 07:01:36.369 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 07:01:36.370 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 07:01:36.373 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 07:01:36.374 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 07:01:36.376 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 07:01:36.504 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 07:01:36.506 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 07:01:36.512 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 07:01:36.513 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 07:01:36.515 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 07:01:36.521 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 07:01:36.522 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 07:01:36.528 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 07:01:36.530 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 07:01:36.536 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 07:01:36.690 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 07:01:36.691 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 07:01:36.701 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 07:01:36.702 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 07:01:36.704 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 07:01:36.706 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 07:01:36.715 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 07:01:36.717 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 07:01:36.719 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 07:01:36.721 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + /T q=40 s=0 info: - /T q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /C q=30 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /N q=30 s=0 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + /T q=40 s=1 info: + /T q=10 s=1 info: + /T q=20 s=1 info: + /T q=30 s=1 info: + /N q=40 s=1 info: + /N q=40 s=1 list: pos=-1 #bases: 33 #indels: 0 filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1} Scanning target file.. Target file had 1 entries. Wrote 1 target ids to alignment header. Setting quality threshold to 0.05 Total logical entries written: 2 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 3 Number of targets: 3 Removed by quality filter: 0 Not best score: 1 Number of alignments written: 2 query_index: 0 target_index: 0 position: 14977972 score: 780.0 matching_reverse_strand: false multiplicity: 1 number_of_mismatches: 1 number_of_indels: 0 query_length: 142 query_aligned_length: 134 target_aligned_length: 134 sequence_variations { to: "T" from: "A" position: 6 to_quality: "/" read_index: 14 } fragment_index: 0 query_index_occurrences: 2 ambiguity: 1 TTC[27]->CGT[27] / qual=1:2:3 A[15]->G[20] / qual=20 A[15]->G[20] / qual=20 Processing test-data/sample-qual-scores/30reads.fa Processed 0 read entries. Min quality score: 2147483647 Max quality score: -2147483648 Avg quality score: 0 Probable quality encoding scheme: fasta Processing test-data/sample-qual-scores/30reads.fq Processed 30 read entries. Min quality score: 69 Max quality score: 98 Avg quality score: 94 Probable quality encoding scheme: Illumina/Solexa field CHROM value: 0 field POS value: 145497099 field ID value: . field REF value: A field ALT value: G field QUAL value: 17.1 field FILTER value: . field INFO[DP] value: 2 field INFO[DP4] value: 0,0,2,0 field INFO[MQ] value: 25 field INFO[FQ] value: -30.8 field INFO[AF1] value: 0.9999 field INFO[CI95] value: 0.5,1 field INFO[PV4] value: field INFO[INDEL] value: INDEL field INFO[PC2] value: 3,3 field INFO[PCHI2] value: 0.752 field INFO[QCHI2] value: 1 field INFO[RP] value: field FORMAT[GT] value: field FORMAT[GQ] value: field FORMAT[GL] value: field FORMAT[DP] value: field FORMAT[SP] value: field FORMAT[PL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 field CHROM gfi:0 value: 0 field POS gfi:1 value: 145497099 field ID gfi:2 value: . field REF gfi:3 value: A field ALT gfi:4 value: G field QUAL gfi:5 value: 17.1 field FILTER gfi:6 value: . field FORMAT[GT] gfi:7 value: field FORMAT[GQ] gfi:8 value: field FORMAT[GL] gfi:9 value: field FORMAT[DP] gfi:10 value: field FORMAT[SP] gfi:11 value: field FORMAT[PL] gfi:12 value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 Total logical entries written: 1 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 45 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 Appending count: 16576 length: 10 Appending count: 35371 length: 4 Appending count: 23073 length: 1 Appending count: 22583 length: 2 Appending count: 17646 length: 5 Appending count: 19398 length: 1 Appending count: 12875 length: 9 Appending count: 39440 length: 1 Appending count: 46977 length: 7 Appending count: 39057 length: 10 Appending count: 7950 length: 9 Appending count: 1004 length: 8 Appending count: 14153 length: 2 Appending count: 2284 length: 6 Appending count: 5888 length: 1 Appending count: 36281 length: 7 Appending count: 45232 length: 3 Appending count: 4131 length: 6 Appending count: 28736 length: 2 Appending count: 6015 length: 6 Appending count: 26795 length: 10 Appending count: 9739 length: 3 Appending count: 49032 length: 9 Appending count: 9375 length: 3 Appending count: 8631 length: 9 Appending count: 21777 length: 7 Appending count: 38666 length: 9 Appending count: 38565 length: 10 Appending count: 30414 length: 6 Appending count: 27984 length: 5 position= 0 count= 16576 position= 1 count= 16576 position= 2 count= 16576 position= 3 count= 16576 position= 4 count= 16576 position= 5 count= 16576 position= 6 count= 16576 position= 7 count= 16576 position= 8 count= 16576 position= 9 count= 16576 position= 10 count= 35371 position= 11 count= 35371 position= 12 count= 35371 position= 13 count= 35371 position= 14 count= 23073 position= 15 count= 22583 position= 16 count= 22583 position= 17 count= 17646 position= 18 count= 17646 position= 19 count= 17646 position= 20 count= 17646 position= 21 count= 17646 position= 22 count= 19398 position= 23 count= 12875 position= 24 count= 12875 position= 25 count= 12875 position= 26 count= 12875 position= 27 count= 12875 position= 28 count= 12875 position= 29 count= 12875 position= 30 count= 12875 position= 31 count= 12875 position= 32 count= 39440 position= 33 count= 46977 position= 34 count= 46977 position= 35 count= 46977 position= 36 count= 46977 position= 37 count= 46977 position= 38 count= 46977 position= 39 count= 46977 position= 40 count= 39057 position= 41 count= 39057 position= 42 count= 39057 position= 43 count= 39057 position= 44 count= 39057 position= 45 count= 39057 position= 46 count= 39057 position= 47 count= 39057 position= 48 count= 39057 position= 49 count= 39057 position= 50 count= 7950 position= 51 count= 7950 position= 52 count= 7950 position= 53 count= 7950 position= 54 count= 7950 position= 55 count= 7950 position= 56 count= 7950 position= 57 count= 7950 position= 58 count= 7950 position= 59 count= 1004 position= 60 count= 1004 position= 61 count= 1004 position= 62 count= 1004 position= 63 count= 1004 position= 64 count= 1004 position= 65 count= 1004 position= 66 count= 1004 position= 67 count= 14153 position= 68 count= 14153 position= 69 count= 2284 position= 70 count= 2284 position= 71 count= 2284 position= 72 count= 2284 position= 73 count= 2284 position= 74 count= 2284 position= 75 count= 5888 position= 76 count= 36281 position= 77 count= 36281 position= 78 count= 36281 position= 79 count= 36281 position= 80 count= 36281 position= 81 count= 36281 position= 82 count= 36281 position= 83 count= 45232 position= 84 count= 45232 position= 85 count= 45232 position= 86 count= 4131 position= 87 count= 4131 position= 88 count= 4131 position= 89 count= 4131 position= 90 count= 4131 position= 91 count= 4131 position= 92 count= 28736 position= 93 count= 28736 position= 94 count= 6015 position= 95 count= 6015 position= 96 count= 6015 position= 97 count= 6015 position= 98 count= 6015 position= 99 count= 6015 position= 100 count= 26795 position= 101 count= 26795 position= 102 count= 26795 position= 103 count= 26795 position= 104 count= 26795 position= 105 count= 26795 position= 106 count= 26795 position= 107 count= 26795 position= 108 count= 26795 position= 109 count= 26795 position= 110 count= 9739 position= 111 count= 9739 position= 112 count= 9739 position= 113 count= 49032 position= 114 count= 49032 position= 115 count= 49032 position= 116 count= 49032 position= 117 count= 49032 position= 118 count= 49032 position= 119 count= 49032 position= 120 count= 49032 position= 121 count= 49032 position= 122 count= 9375 position= 123 count= 9375 position= 124 count= 9375 position= 125 count= 8631 position= 126 count= 8631 position= 127 count= 8631 position= 128 count= 8631 position= 129 count= 8631 position= 130 count= 8631 position= 131 count= 8631 position= 132 count= 8631 position= 133 count= 8631 position= 134 count= 21777 position= 135 count= 21777 position= 136 count= 21777 position= 137 count= 21777 position= 138 count= 21777 position= 139 count= 21777 position= 140 count= 21777 position= 141 count= 38666 position= 142 count= 38666 position= 143 count= 38666 position= 144 count= 38666 position= 145 count= 38666 position= 146 count= 38666 position= 147 count= 38666 position= 148 count= 38666 position= 149 count= 38666 position= 150 count= 38565 position= 151 count= 38565 position= 152 count= 38565 position= 153 count= 38565 position= 154 count= 38565 position= 155 count= 38565 position= 156 count= 38565 position= 157 count= 38565 position= 158 count= 38565 position= 159 count= 38565 position= 160 count= 30414 position= 161 count= 30414 position= 162 count= 30414 position= 163 count= 30414 position= 164 count= 30414 position= 165 count= 30414 position= 166 count= 27984 position= 167 count= 27984 position= 168 count= 27984 position= 169 count= 27984 position= 170 count= 27984 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 07:01:39.310 WARN WiggleWindow - Not writing 101 7 07:01:39.310 WARN WiggleWindow - Not writing 111 7 07:01:39.310 WARN WiggleWindow - Not writing 131 8 07:01:39.310 WARN WiggleWindow - Not writing 141 8 07:01:39.310 WARN WiggleWindow - Not writing 151 8 appending (count=0,length=1) appending (count=4,length=3) appending (count=1,length=3) appending (count=0,length=2) appending (count=3,length=1) appending (count=1,length=1) appending (count=0,length=1) appending (count=4,length=3) appending (count=0,length=5) appending (count=3,length=1) appending (count=0,length=2) appending (count=2,length=1) appending (count=0,length=2) appending (count=3,length=1) appending (count=2,length=1) appending (count=0,length=1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) loading transition for reader[0] position=1 length=3 count=3 (0,1)(1,4) loading transition for reader[0] position=4 length=2 count=0 (0,1)(1,4)(4,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 (0,0) loading transition for reader[0] position=1 length=1 count=1 (0,0)(1,1) loading transition for reader[0] position=2 length=4 count=0 (0,0)(1,1)(2,0) loading transition for reader[1] position=4 length=10 count=1 (0,0)(1,1)(2,0)(4,1) loading transition for reader[0] position=6 length=2 count=1 (0,0)(1,1)(2,0)(4,1)(6,2) loading transition for reader[0] position=8 length=1 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1) loading transition for reader[0] position=9 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) loading transition for reader[0] position=10 length=2 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) loading transition for reader[0] position=12 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) loading transition for reader[0] position=13 length=3 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) loading transition for reader[0] position=16 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 loading transition for reader[0] position=1 length=1 count=1 loading transition for reader[0] position=2 length=4 count=0 loading transition for reader[1] position=4 length=10 count=1 loading transition for reader[0] position=6 length=2 count=1 loading transition for reader[0] position=8 length=1 count=0 loading transition for reader[0] position=9 length=1 count=1 loading transition for reader[0] position=10 length=2 count=0 loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 loading transition for reader[0] position=0 length=1 count=0 (0,0) loading transition for reader[0] position=1 length=3 count=1 (0,0)(1,1) appending (count=10,length=4) appending (count=1,length=0) appending (count=2,length=8) Hello appending (count=10,length=4) 07:01:39.366 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 07:01:39.373 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 07:01:39.381 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 07:01:39.384 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 07:01:39.388 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 07:01:39.394 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.401 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.412 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.416 WARN MessageChunksWriter - Using chunk-size=1000 0 23 Setting quality threshold to 0.02 entry:query_index: 0 target_index: 0 position: 5 score: 5.0 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 read_index: 10 } entry:query_index: 1 target_index: 0 position: 5 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 to_quality: "((((" read_index: 10 } entry: query_index: 0 target_index: 0 position: 0 matching_reverse_strand: false query_length: 10 query_aligned_length: 10 sequence_variations { to: "AAA" from: "---" position: 3 read_index: 3 } processing entry on target 0 at position 0 processing entry on target 0 at position 5 processing entry on target 1 at position 0 processing entry on target 1 at position 5 processing entry on target 4 at position 0 processing entry on target 4 at position 5 entry:query_index: 0 target_index: 0 position: 10 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "AAA" from: "---" position: 20 read_index: 20 } entry:query_index: 1 target_index: 0 position: 1 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "T" from: "A" position: 20 read_index: 20 } 07:01:39.454 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 07:01:39.543 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.545 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.546 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.556 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.557 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.558 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.569 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.570 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.573 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 07:01:39.583 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.586 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.587 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.601 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.603 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.604 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.607 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 07:01:39.609 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 07:01:39.611 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 07:01:39.615 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.616 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.617 WARN MessageChunksWriter - Using chunk-size=1000 Processing queryIndex=8 with description '8 perfect start of ref' Processing queryIndex=9 with description '9 perfect start of ref reverse strand' Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' Processing queryIndex=0 with description '0 perfect match' Processing queryIndex=1 with description '1 perfect match on reverse strand' Processing queryIndex=2 with description '2 mutation' Processing queryIndex=3 with description '3 mutation on reverse strand' Processing queryIndex=4 with description '4 insertion' Processing queryIndex=6 with description '6 deletion' Processing queryIndex=7 with description '7 deletion on reverse strand' Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' Processing queryIndex=5 with description '5 insertion on reverse strand' Processing queryIndex=10 with description '10 perfect end of ref' Processing queryIndex=11 with description '11 perfect end of ref reverse strand' 07:01:39.646 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 07:01:39.651 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 07:01:39.657 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 07:01:39.661 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 07:01:39.665 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 07:01:39.669 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 07:01:39.673 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 07:01:39.680 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.683 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.688 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.693 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.696 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.702 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.712 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 07:01:39.718 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.728 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries 07:01:39.732 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.733 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.745 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.747 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.761 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.762 WARN MessageChunksWriter - Using chunk-size=1000 0 2 07:01:39.776 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.778 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 07:01:39.793 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.794 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.808 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.809 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.823 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.824 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 5 entries [main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TAAAACCTAAAAAAAAAAAAAAACCCC expected =TAAAA--TAAAAAAAAAAAAAAACCCC recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT 07:01:39.860 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.926 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.927 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.992 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:40.049 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.051 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.067 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. 07:01:40.110 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. 07:01:40.110 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 07:01:40.110 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 5ms; used/avail/free/total/max mem: 895.63M/7.51G/178.11M/1.07G/8.40G 07:01:40.121 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 07:01:40.175 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. 07:01:40.186 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. 07:01:40.244 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. 07:01:40.244 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. 07:01:40.244 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. 07:01:40.244 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 07:01:40.244 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. 07:01:40.244 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: 945.96M/7.46G/127.78M/1.07G/8.40G 07:01:40.247 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. 07:01:40.261 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. 07:01:40.312 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.354 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.356 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.387 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:40.411 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.413 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: 1.04G/7.37G/37.60M/1.07G/8.40G 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 07:01:40.613 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.661 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.662 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.714 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:40.763 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.764 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.767 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. 07:01:40.818 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. 07:01:40.818 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 07:01:40.818 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: 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: 1ms; used/avail/free/total/max mem: 436.14M/7.97G/645.99M/1.08G/8.40G 07:01:40.822 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 07:01:40.838 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.914 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.920 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.962 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.009 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.010 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.021 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. 07:01:41.022 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. 07:01:41.025 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. 07:01:41.025 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. 07:01:41.025 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. 07:01:41.026 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 07:01:41.026 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. 07:01:41.026 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: 80.86M/8.32G/103.69M/184.55M/8.40G 07:01:41.036 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. 07:01:41.038 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. 07:01:41.041 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.088 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.089 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.136 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.182 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.186 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) 07:01:41.188 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) 07:01:41.189 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. 07:01:41.201 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. 07:01:41.201 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. 07:01:41.201 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. 07:01:41.201 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 07:01:41.201 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. 07:01:41.201 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 108.12M/8.29G/76.43M/184.55M/8.40G Second pass: writing the merged alignment. 07:01:41.207 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. 07:01:41.209 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 07:01:41.216 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.265 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.266 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.313 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.363 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.365 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.367 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. 07:01:41.373 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. 07:01:41.373 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 07:01:41.373 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: 1ms; used/avail/free/total/max mem: 133.28M/8.27G/51.26M/184.55M/8.40G 07:01:41.375 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 07:01:41.387 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.430 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.431 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.516 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.554 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.555 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 89.94M/8.31G/94.61M/184.55M/8.40G 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 07:01:41.691 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.730 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.740 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.782 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.838 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.839 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.851 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. 07:01:41.854 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. 07:01:41.899 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. 07:01:41.899 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. 07:01:41.899 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. 07:01:41.899 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 07:01:41.899 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. 07:01:41.899 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: 72.43M/8.33G/112.12M/184.55M/8.40G 07:01:41.902 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. 07:01:41.925 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 1999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 0 target_index: 3999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 3999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 query_index: 0 target_index: 0 position: 0 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 query_index: 1 target_index: 0 position: 1 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 07:01:42.041 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 07:01:42.041 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 [ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits [ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 {1} {0}decoding: 4 {0} {0}decoding: 4 {0} {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0} {0} {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0} {0} {0}decoding: 3 decoding: 4 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 [ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits [ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} count keys [0, 3, 5, 11, 13] -1 0.0 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 0.0 overlapping count 15, 17 0.0 overlapping count 9, 18 2.0 overlapping count 3, 8 2.0 overlapping count 11, 12 0.0 overlapping count 9, 10 1.0 overlapping count 8, 9 0.0 overlapping count 8, 8 0.0 overlapping count 5, 6 0.0 overlapping count 3, 3 0.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 0.0 -1 0.0 0 0.0 1 0.0 2 0.0 3 2.0 4 2.0 5 3.0 6 3.0 7 3.0 8 3.0 9 3.0 10 3.0 11 2.0 12 2.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 2.0 overlapping count 2, 3 2.0 overlapping count 3, 8 4.0 overlapping count 11, 12 2.0 overlapping count 9, 10 3.0 overlapping count 8, 9 4.0 overlapping count 8, 8 3.0 overlapping count 5, 6 3.0 overlapping count 3, 3 2.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 1.0 Total logical entries written: 4 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Total logical entries written: 4 Total bytes written: 62 Average bytes/logical entry: 15.5 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 Annotations loaded Annotations loaded Annotations loaded Annotations loaded Annotations loaded [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 106.692 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 [ 0.115 s] [INFO] Goby I/O ........................................... SUCCESS [ 15.391 s] [INFO] Goby Full Distribution ............................. SUCCESS [02:29 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:45 min [INFO] Finished at: 2025-04-27T07:03:16-12:00 [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 [ 0.337 s] [INFO] Goby I/O ........................................... SUCCESS [ 0.055 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 0.037 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.597 s [INFO] Finished at: 2025-04-27T07:03:18-12:00 [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 27, 2025 7:03:24 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian > dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2 Apr 27, 2025 7:03:29 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian ERROR: goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian goby-io/pom.xml: dependency is not packaged in the Maven repository for Debian: org.itadaki:bzip2:debian -------- Some problems were found in this project, exiting... mh_unpatchpoms -plibgoby-io-java dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package 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: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} 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 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'. dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-11_all.deb'. dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/271630 and its subdirectories I: Current time: Sun Apr 27 07:03:40 -12 2025 I: pbuilder-time-stamp: 1745780620 Sun Apr 27 19:03:40 UTC 2025 I: Signing ./b1/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo as libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc Sun Apr 27 19:03:40 UTC 2025 I: Signed ./b1/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo as ./b1/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc Sun Apr 27 19:03:40 UTC 2025 - build #1 for libgoby-java/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Sun Apr 27 19:03:40 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-sTU3cGf6, removing. /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp: total 20 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 19:03 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 18:55 b2 -rw-r--r-- 1 jenkins jenkins 3008 May 14 2024 libgoby-java_3.3.1+dfsg2-11.dsc -rw------- 1 jenkins jenkins 4193 Apr 27 18:55 rbuildlog.0ltXdoE /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b1: total 3024 -rw-r--r-- 1 jenkins jenkins 446610 Apr 27 19:03 build.log -rw-r--r-- 1 jenkins jenkins 1575696 Apr 27 19:03 goby-java_3.3.1+dfsg2-11_all.deb -rw-r--r-- 1 jenkins jenkins 978952 Apr 27 19:03 libgoby-io-java_3.3.1+dfsg2-11_all.deb -rw-r--r-- 1 jenkins jenkins 29428 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 3008 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11.dsc -rw-r--r-- 1 jenkins jenkins 19044 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 19926 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1651 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_arm64.changes -rw-r--r-- 1 jenkins jenkins 1494 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b2: total 0 Sun Apr 27 19:03:43 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 27 06:55:28 -12 2025 I: pbuilder-time-stamp: 1745780128 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/271630/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7a7ac1dbbc154196a2a6c662048efd64' 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='271630' 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.tP9jh8Dp/pbuilderrc_Bir9 --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.tP9jh8Dp/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/271630/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team 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 ... 19953 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} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gpg{a} gpg-agent{a} gpgconf{a} gpgv{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbarclay-java{a} libblas3{a} libbrotli1{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcolord2{a} libcolt-free-java{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdsiutils-java{a} libdynaloader-functions-perl{a} libeasymock-java{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastutil-java{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgbm1{a} libgcrypt20{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicb-utils-java{a} libice6{a} libicu4j-java{a} libicu76{a} libidn2-0{a} libimport-into-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libjansi-java{a} libjavassist-java{a} libjaxb-api-java{a} libjaxen-java{a} libjbig0{a} libjboss-logging-java{a} libjboss-vfs-java{a} libjbzip2-java{a} libjcommander-java{a} libjetty9-java{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjsap-java{a} libjson-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblightcouch-java{a} libllvm19{a} liblog4j1.2-java{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven-source-plugin-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libpcsclite1{a} libpicard-java{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libpj-java{a} libpkgconf3{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} libreflections-java{a} librhino-java{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1t64{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} liburi-perl{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxom-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxss1{a} libxstream-java{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} mesa-libgallium{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sopv-gpgv{a} systemd{a} systemd-sysv{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpg-error-l10n libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjline3-java libjson-perl libkmod2 libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl libnss-systemd librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian linux-sysctl-defaults lynx lzip mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc publicsuffix python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended sopv-doc strace systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 459 newly installed, 0 to remove and 0 not upgraded. Need to get 373 MB of archives. After unpacking 1012 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 257.5-2 [1911 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libapparmor1 arm64 4.1.0-1 [42.9 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 systemd arm64 257.5-2 [2920 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 systemd-sysv arm64 257.5-2 [63.9 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 dbus-bin arm64 1.16.2-2 [78.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 dbus-daemon arm64 1.16.2-2 [152 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 dbus arm64 1.16.2-2 [70.7 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-2 [260 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.5.0-1 [1454 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20250419 [162 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libpam-systemd arm64 257.5-2 [275 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 43 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0051 [42.8 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.84.1-2 [1423 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b2 [756 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1.1 [274 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.7.0-3 [325 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [131 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 4.18.4+ds-2 [51.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 48.0-1 [504 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.110-1 [1292 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.3-1 [55.0 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.7+6-1 [40.6 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.56.1-2 [171 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 dbus-user-session arm64 1.16.2-2 [52.1 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libdconf1 arm64 0.40.0-5 [40.4 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dconf-service arm64 0.40.0-5 [30.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [27.3 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 87 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.56.1-2 [50.0 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libatspi2.0-0t64 arm64 2.56.1-2 [76.5 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libatk-bridge2.0-0t64 arm64 2.56.1-2 [64.8 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.3 [318 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.3 [387 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.4-1+b1 [130 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libcloudproviders0 arm64 0.3.6-2 [27.4 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libcolord2 arm64 1.4.7-3 [130 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-16 [112 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-16 [43.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-16 [46.7 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 129 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.3 [463 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.3-1 [213 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [52.9 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [33.7 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libwayland-client0 arm64 1.23.1-3 [26.1 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libwayland-cursor0 arm64 1.23.1-3 [11.7 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libwayland-egl1 arm64 1.23.1-3 [5952 B] Get: 146 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b4 [20.5 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.3-1 [39.3 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b4 [16.0 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 xkb-data all 2.42-1 [790 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libxkbcommon0 arm64 1.7.0-2 [106 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1+b3 [35.9 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libgtk-3-common all 3.24.49-3 [4908 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libgtk-3-0t64 arm64 3.24.49-3 [2565 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.124-2 [8288 B] Get: 158 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.124-2 [38.3 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.12-1 [247 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b4 [19.2 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.124-2 [21.8 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-3 [23.3 MB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.2-2 [36.4 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3.3-1 [11.1 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 mesa-libgallium arm64 25.0.4-1 [8031 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libwayland-server0 arm64 1.23.1-3 [33.7 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libgbm1 arm64 25.0.4-1 [43.6 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.4.309.0-1 [127 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 25.0.4-1 [45.3 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 25.0.4-1 [142 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.14-1 [21.1 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.14-1 [342 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.5-1 [25.7 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre arm64 21.0.7+6-1 [193 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.21-76 [1068 B] Get: 189 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk-headless arm64 21.0.7+6-1 [81.9 MB] Get: 190 http://deb.debian.org/debian unstable/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 191 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk arm64 21.0.7+6-1 [3557 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 default-jdk arm64 2:1.21-76 [1076 B] Get: 193 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.4.7-16 [121 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-3 [22.9 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.4.7-16 [577 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.3.1-2 [83.5 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.4.7-16 [248 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 203 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 206 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-2 [15.7 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 232 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.78-1 [183 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 gpgv arm64 2.4.7-16 [220 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 sopv-gpgv all 0.1.4-1 [11.3 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-9 [122 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.25.10 [1062 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.80 [9692 B] Get: 246 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.80 [80.4 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 250 http://deb.debian.org/debian unstable/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 251 http://deb.debian.org/debian unstable/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 junit5 all 5.10.3-1 [2459 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 257 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 258 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.8-1 [392 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 260 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libfreemarker-java all 2.3.32-2.1 [1525 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libjoptsimple-java all 5.0.4-7 [73.7 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.18.0-1 [304 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.19.0-1 [524 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libguice-java all 5.1.0-1 [932 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 285 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 291 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 294 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libbyte-buddy-java all 1.14.19-1 [4756 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.10.1-1 [231 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libcommons-configuration-java all 1.10-7 [348 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libcommons-math-java all 2.2-9 [933 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.2-1 [28.3 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.7-1 [6476 B] Get: 317 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libcommons-text-java all 1.13.1-1 [228 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-2 [179 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.13.0-5 [349 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libdistlib-java all 1.0-5 [72.5 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 libdoxia-java all 2.0.0-1 [113 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 341 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 velocity all 1.7-7 [431 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 346 http://deb.debian.org/debian unstable/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 350 http://deb.debian.org/debian unstable/main arm64 libxpp3-java all 1.1.4c-4 [294 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 libxstream-java all 1.4.21-1 [567 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 libjsap-java all 2.1-5 [102 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 liblogback-java all 1:1.2.11-6 [701 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 libobjenesis-java all 3.4-2 [41.3 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 libeasymock-java all 5.5.0-1 [134 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 361 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 libxom-java all 1.3.9-1 [174 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto16 arm64 3.6.3-1 [343 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 libmbedx509-7 arm64 3.6.3-1 [148 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 libmbedtls21 arm64 3.6.3-1 [224 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1096 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 libncbi-ngs3 arm64 3.2.1+dfsg-4 [145 kB] Get: 373 http://deb.debian.org/debian unstable/main arm64 libngs-jni arm64 3.2.1+dfsg-4 [27.7 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 libngs-java arm64 3.2.1+dfsg-4 [114 kB] Get: 375 http://deb.debian.org/debian unstable/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 libicu4j-java all 73.2-1 [16.4 MB] Get: 379 http://deb.debian.org/debian unstable/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-3 [9526 kB] Get: 383 http://deb.debian.org/debian unstable/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 384 http://deb.debian.org/debian unstable/main arm64 libjavassist-java all 1:3.27.0-1 [731 kB] Get: 385 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 386 http://deb.debian.org/debian unstable/main arm64 libjboss-logging-java all 3.5.3-1 [56.2 kB] Get: 387 http://deb.debian.org/debian unstable/main arm64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB] Get: 388 http://deb.debian.org/debian unstable/main arm64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get: 389 http://deb.debian.org/debian unstable/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 390 http://deb.debian.org/debian unstable/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 391 http://deb.debian.org/debian unstable/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 392 http://deb.debian.org/debian unstable/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 393 http://deb.debian.org/debian unstable/main arm64 libjetty9-java all 9.4.57-1 [2965 kB] Get: 394 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 395 http://deb.debian.org/debian unstable/main arm64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 396 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 397 http://deb.debian.org/debian unstable/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 398 http://deb.debian.org/debian unstable/main arm64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 399 http://deb.debian.org/debian unstable/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 400 http://deb.debian.org/debian unstable/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 401 http://deb.debian.org/debian unstable/main arm64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 402 http://deb.debian.org/debian unstable/main arm64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB] Get: 403 http://deb.debian.org/debian unstable/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 404 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 405 http://deb.debian.org/debian unstable/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 406 http://deb.debian.org/debian unstable/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 407 http://deb.debian.org/debian unstable/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 408 http://deb.debian.org/debian unstable/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 409 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-analyzer-java all 1.15.1-1 [38.5 kB] Get: 410 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-tree-java all 3.3.0-1 [35.0 kB] Get: 411 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-impl-java all 4.0.0-1 [17.6 kB] Get: 412 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-plugin-java all 3.8.1-1 [191 kB] Get: 413 http://deb.debian.org/debian unstable/main arm64 libmaven-invoker-java all 3.3.0-1 [29.1 kB] Get: 414 http://deb.debian.org/debian unstable/main arm64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB] Get: 415 http://deb.debian.org/debian unstable/main arm64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB] Get: 416 http://deb.debian.org/debian unstable/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB] Get: 417 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 418 http://deb.debian.org/debian unstable/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 419 http://deb.debian.org/debian unstable/main arm64 libmaven-plugin-tools-java all 3.10.2-2 [245 kB] Get: 420 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 421 http://deb.debian.org/debian unstable/main arm64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 422 http://deb.debian.org/debian unstable/main arm64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 423 http://deb.debian.org/debian unstable/main arm64 libmaven-source-plugin-java all 3.3.1-1 [27.7 kB] Get: 424 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b2 [16.6 kB] Get: 425 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b2 [16.4 kB] Get: 426 http://deb.debian.org/debian unstable/main arm64 libpicard-java all 3.3.0+dfsg-2 [1778 kB] Get: 427 http://deb.debian.org/debian unstable/main arm64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB] Get: 428 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 429 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 430 http://deb.debian.org/debian unstable/main arm64 libprotobuf32t64 arm64 3.21.12-10+b6 [859 kB] Get: 431 http://deb.debian.org/debian unstable/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b6 [250 kB] Get: 432 http://deb.debian.org/debian unstable/main arm64 libprotobuf-dev arm64 3.21.12-10+b6 [1263 kB] Get: 433 http://deb.debian.org/debian unstable/main arm64 libprotobuf-java all 3.21.12-10 [1268 kB] Get: 434 http://deb.debian.org/debian unstable/main arm64 libprotoc32t64 arm64 3.21.12-10+b6 [790 kB] Get: 435 http://deb.debian.org/debian unstable/main arm64 libreflections-java all 0.10.2+dfsg-2 [125 kB] Get: 436 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.6-1 [36.4 kB] Get: 437 http://deb.debian.org/debian unstable/main arm64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 438 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 439 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get: 440 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.6+ds-1 [79.1 kB] Get: 441 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 442 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 443 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 444 http://deb.debian.org/debian unstable/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 445 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 446 http://deb.debian.org/debian unstable/main arm64 libxml2-utils arm64 2.12.7+dfsg+really2.9.14-0.4 [98.3 kB] Get: 447 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 448 http://deb.debian.org/debian unstable/main arm64 maven all 3.9.9-1 [19.7 kB] Get: 449 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 450 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-29 [163 kB] Get: 451 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.7 [108 kB] Get: 452 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 453 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 454 http://deb.debian.org/debian unstable/main arm64 protobuf-compiler arm64 3.21.12-10+b6 [84.9 kB] Get: 455 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-15 [227 kB] Get: 456 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 457 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.5.0-2 [28.4 MB] Get: 458 http://deb.debian.org/debian unstable/main arm64 r-cran-rjava arm64 1.0-11-2 [712 kB] Get: 459 http://deb.debian.org/debian unstable/main arm64 testng all 6.9.12-4 [795 kB] Fetched 373 MB in 3s (118 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19953 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.5-2_arm64.deb ... Unpacking libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package libapparmor1:arm64. Preparing to unpack .../libapparmor1_4.1.0-1_arm64.deb ... Unpacking libapparmor1:arm64 (4.1.0-1) ... Setting up libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package systemd. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../systemd_257.5-2_arm64.deb ... Unpacking systemd (257.5-2) ... Setting up libapparmor1:arm64 (4.1.0-1) ... Setting up systemd (257.5-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20904 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.5-2_arm64.deb ... Unpacking systemd-sysv (257.5-2) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../01-libdbus-1-3_1.16.2-2_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.16.2-2) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.16.2-2_arm64.deb ... Unpacking dbus-bin (1.16.2-2) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../03-dbus-session-bus-common_1.16.2-2_all.deb ... Unpacking dbus-session-bus-common (1.16.2-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../04-libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../05-dbus-daemon_1.16.2-2_arm64.deb ... Unpacking dbus-daemon (1.16.2-2) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../06-dbus-system-bus-common_1.16.2-2_all.deb ... Unpacking dbus-system-bus-common (1.16.2-2) ... Selecting previously unselected package dbus. Preparing to unpack .../07-dbus_1.16.2-2_arm64.deb ... Unpacking dbus (1.16.2-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../09-binfmt-support_2.2.2-7+b1_arm64.deb ... Unpacking binfmt-support (2.2.2-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../10-libpython3.13-minimal_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../11-python3.13-minimal_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21354 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_arm64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.8-2_arm64.deb ... Unpacking libffi8:arm64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22366 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.3-1_arm64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-8_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-8) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-8_arm64.deb ... Unpacking procps (2:4.0.4-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.5.0-1_arm64.deb ... Unpacking openssl (3.5.0-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../007-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package libpam-systemd:arm64. Preparing to unpack .../012-libpam-systemd_257.5-2_arm64.deb ... Unpacking libpam-systemd:arm64 (257.5-2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../015-libtext-charwidth-perl_0.04-11+b4_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../016-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../017-ucf_3.0051_all.deb ... Moving old data out of the way Unpacking ucf (3.0051) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../018-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../019-libglib2.0-0t64_2.84.1-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.84.1-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../020-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../021-shared-mime-info_2.4-5+b2_arm64.deb ... Unpacking shared-mime-info (2.4-5+b2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../022-libjpeg62-turbo_1%3a2.1.5-3.1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../023-libpng16-16t64_1.6.47-1.1_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.47-1.1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../024-libdeflate0_1.23-2_arm64.deb ... Unpacking libdeflate0:arm64 (1.23-2) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../025-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../026-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../027-libsharpyuv0_1.5.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../028-libwebp7_1.5.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../029-libtiff6_4.7.0-3_arm64.deb ... Unpacking libtiff6:arm64 (4.7.0-3) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. Preparing to unpack .../030-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ... Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../031-gtk-update-icon-cache_4.18.4+ds-2_arm64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.18.4+ds-2) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../032-hicolor-icon-theme_0.18-2_all.deb ... Unpacking hicolor-icon-theme (0.18-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../033-adwaita-icon-theme_48.0-1_all.deb ... Unpacking adwaita-icon-theme (48.0-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../034-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../035-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../036-liblcms2-2_2.16-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.16-2) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../037-libnspr4_2%3a4.36-1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.36-1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../038-libnss3_2%3a3.110-1_arm64.deb ... Unpacking libnss3:arm64 (2:3.110-1) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../039-libpcsclite1_2.3.3-1_arm64.deb ... Unpacking libpcsclite1:arm64 (2.3.3-1) ... Selecting previously unselected package openjdk-21-jre-headless:arm64. Preparing to unpack .../040-openjdk-21-jre-headless_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jre-headless:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../041-default-jre-headless_2%3a1.21-76_arm64.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../042-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package ant-contrib. Preparing to unpack .../043-ant-contrib_1.0~b3+svn177-12_all.deb ... Unpacking ant-contrib (1.0~b3+svn177-12) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../044-at-spi2-common_2.56.1-2_all.deb ... Unpacking at-spi2-common (2.56.1-2) ... Selecting previously unselected package m4. Preparing to unpack .../045-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../046-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../047-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../048-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../049-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package dbus-user-session. Preparing to unpack .../050-dbus-user-session_1.16.2-2_arm64.deb ... Unpacking dbus-user-session (1.16.2-2) ... Selecting previously unselected package libdconf1:arm64. Preparing to unpack .../051-libdconf1_0.40.0-5_arm64.deb ... Unpacking libdconf1:arm64 (0.40.0-5) ... Selecting previously unselected package dconf-service. Preparing to unpack .../052-dconf-service_0.40.0-5_arm64.deb ... Unpacking dconf-service (0.40.0-5) ... Selecting previously unselected package dconf-gsettings-backend:arm64. Preparing to unpack .../053-dconf-gsettings-backend_0.40.0-5_arm64.deb ... Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../054-dctrl-tools_2.24-3+b1_arm64.deb ... Unpacking dctrl-tools (2.24-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../055-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../056-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../057-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../058-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../059-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../060-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../061-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../062-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../063-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package gettext. Preparing to unpack .../064-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../065-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../066-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../067-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libatk1.0-0t64:arm64. Preparing to unpack .../068-libatk1.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatk1.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../069-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../070-libxdmcp6_1%3a1.1.5-1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../071-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../072-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../073-libx11-6_2%3a1.8.12-1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.12-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../074-libxext6_2%3a1.3.4-1+b3_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../075-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libatspi2.0-0t64:arm64. Preparing to unpack .../076-libatspi2.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatspi2.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libatk-bridge2.0-0t64:arm64. Preparing to unpack .../077-libatk-bridge2.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatk-bridge2.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../078-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../079-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../080-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../081-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../082-fontconfig-config_2.15.0-2.3_arm64.deb ... Unpacking fontconfig-config (2.15.0-2.3) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../083-libfontconfig1_2.15.0-2.3_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-2.3) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../084-libpixman-1-0_0.44.0-3_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.44.0-3) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../085-libxcb-render0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../086-libxcb-shm0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../087-libxrender1_1%3a0.9.12-1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.12-1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../088-libcairo2_1.18.4-1+b1_arm64.deb ... Unpacking libcairo2:arm64 (1.18.4-1+b1) ... Selecting previously unselected package libcairo-gobject2:arm64. Preparing to unpack .../089-libcairo-gobject2_1.18.4-1+b1_arm64.deb ... Unpacking libcairo-gobject2:arm64 (1.18.4-1+b1) ... Selecting previously unselected package libcloudproviders0:arm64. Preparing to unpack .../090-libcloudproviders0_0.3.6-2_arm64.deb ... Unpacking libcloudproviders0:arm64 (0.3.6-2) ... Selecting previously unselected package libcolord2:arm64. Preparing to unpack .../091-libcolord2_1.4.7-3_arm64.deb ... Unpacking libcolord2:arm64 (1.4.7-3) ... Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../092-libavahi-common-data_0.8-16_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-16) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../093-libavahi-common3_0.8-16_arm64.deb ... Unpacking libavahi-common3:arm64 (0.8-16) ... Selecting previously unselected package libavahi-client3:arm64. Preparing to unpack .../094-libavahi-client3_0.8-16_arm64.deb ... Unpacking libavahi-client3:arm64 (0.8-16) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../095-libidn2-0_2.3.8-2_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-2) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../096-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../097-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../098-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../099-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../100-libcom-err2_1.47.2-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../101-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../102-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../103-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../104-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libcups2t64:arm64. Preparing to unpack .../105-libcups2t64_2.4.10-2+b1_arm64.deb ... Unpacking libcups2t64:arm64 (2.4.10-2+b1) ... Selecting previously unselected package libepoxy0:arm64. Preparing to unpack .../106-libepoxy0_1.5.10-2_arm64.deb ... Unpacking libepoxy0:arm64 (1.5.10-2) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../107-libfribidi0_1.0.16-1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.16-1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../108-libgraphite2-3_1.3.14-2+b1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../109-libharfbuzz0b_10.2.0-1+b1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.2.0-1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../110-fontconfig_2.15.0-2.3_arm64.deb ... Unpacking fontconfig (2.15.0-2.3) ... Selecting previously unselected package libthai-data. Preparing to unpack .../111-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../112-libdatrie1_0.2.13-3+b1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3+b1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../113-libthai0_0.1.29-2+b1_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../114-libpango-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../115-libpangoft2-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../116-libpangocairo-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libwayland-client0:arm64. Preparing to unpack .../117-libwayland-client0_1.23.1-3_arm64.deb ... Unpacking libwayland-client0:arm64 (1.23.1-3) ... Selecting previously unselected package libwayland-cursor0:arm64. Preparing to unpack .../118-libwayland-cursor0_1.23.1-3_arm64.deb ... Unpacking libwayland-cursor0:arm64 (1.23.1-3) ... Selecting previously unselected package libwayland-egl1:arm64. Preparing to unpack .../119-libwayland-egl1_1.23.1-3_arm64.deb ... Unpacking libwayland-egl1:arm64 (1.23.1-3) ... Selecting previously unselected package libxcomposite1:arm64. Preparing to unpack .../120-libxcomposite1_1%3a0.4.6-1_arm64.deb ... Unpacking libxcomposite1:arm64 (1:0.4.6-1) ... Selecting previously unselected package libxfixes3:arm64. Preparing to unpack .../121-libxfixes3_1%3a6.0.0-2+b4_arm64.deb ... Unpacking libxfixes3:arm64 (1:6.0.0-2+b4) ... Selecting previously unselected package libxcursor1:arm64. Preparing to unpack .../122-libxcursor1_1%3a1.2.3-1_arm64.deb ... Unpacking libxcursor1:arm64 (1:1.2.3-1) ... Selecting previously unselected package libxdamage1:arm64. Preparing to unpack .../123-libxdamage1_1%3a1.1.6-1+b2_arm64.deb ... Unpacking libxdamage1:arm64 (1:1.1.6-1+b2) ... Selecting previously unselected package libxinerama1:arm64. Preparing to unpack .../124-libxinerama1_2%3a1.1.4-3+b4_arm64.deb ... Unpacking libxinerama1:arm64 (2:1.1.4-3+b4) ... Selecting previously unselected package xkb-data. Preparing to unpack .../125-xkb-data_2.42-1_all.deb ... Unpacking xkb-data (2.42-1) ... Selecting previously unselected package libxkbcommon0:arm64. Preparing to unpack .../126-libxkbcommon0_1.7.0-2_arm64.deb ... Unpacking libxkbcommon0:arm64 (1.7.0-2) ... Selecting previously unselected package libxrandr2:arm64. Preparing to unpack .../127-libxrandr2_2%3a1.5.4-1+b3_arm64.deb ... Unpacking libxrandr2:arm64 (2:1.5.4-1+b3) ... Selecting previously unselected package libgtk-3-common. Preparing to unpack .../128-libgtk-3-common_3.24.49-3_all.deb ... Unpacking libgtk-3-common (3.24.49-3) ... Selecting previously unselected package libgtk-3-0t64:arm64. Preparing to unpack .../129-libgtk-3-0t64_3.24.49-3_arm64.deb ... Unpacking libgtk-3-0t64:arm64 (3.24.49-3) ... Selecting previously unselected package libglvnd0:arm64. Preparing to unpack .../130-libglvnd0_1.7.0-1+b2_arm64.deb ... Unpacking libglvnd0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../131-libdrm-common_2.4.124-2_all.deb ... Unpacking libdrm-common (2.4.124-2) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../132-libdrm2_2.4.124-2_arm64.deb ... Unpacking libdrm2:arm64 (2.4.124-2) ... Selecting previously unselected package libx11-xcb1:arm64. Preparing to unpack .../133-libx11-xcb1_2%3a1.8.12-1_arm64.deb ... Unpacking libx11-xcb1:arm64 (2:1.8.12-1) ... Selecting previously unselected package libxcb-dri3-0:arm64. Preparing to unpack .../134-libxcb-dri3-0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-glx0:arm64. Preparing to unpack .../135-libxcb-glx0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-glx0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-present0:arm64. Preparing to unpack .../136-libxcb-present0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-present0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-xfixes0:arm64. Preparing to unpack .../137-libxcb-xfixes0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxxf86vm1:arm64. Preparing to unpack .../138-libxxf86vm1_1%3a1.1.4-1+b4_arm64.deb ... Unpacking libxxf86vm1:arm64 (1:1.1.4-1+b4) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../139-libdrm-amdgpu1_2.4.124-2_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.124-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../140-libedit2_3.1-20250104-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20250104-1) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../141-libz3-4_4.13.3-1_arm64.deb ... Unpacking libz3-4:arm64 (4.13.3-1) ... Selecting previously unselected package libllvm19:arm64. Preparing to unpack .../142-libllvm19_1%3a19.1.7-3_arm64.deb ... Unpacking libllvm19:arm64 (1:19.1.7-3) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../143-libsensors-config_1%3a3.6.2-2_all.deb ... Unpacking libsensors-config (1:3.6.2-2) ... Selecting previously unselected package libsensors5:arm64. Preparing to unpack .../144-libsensors5_1%3a3.6.2-2_arm64.deb ... Unpacking libsensors5:arm64 (1:3.6.2-2) ... Selecting previously unselected package libxcb-randr0:arm64. Preparing to unpack .../145-libxcb-randr0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-randr0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-sync1:arm64. Preparing to unpack .../146-libxcb-sync1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-sync1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxshmfence1:arm64. Preparing to unpack .../147-libxshmfence1_1.3.3-1_arm64.deb ... Unpacking libxshmfence1:arm64 (1.3.3-1) ... Selecting previously unselected package mesa-libgallium:arm64. Preparing to unpack .../148-mesa-libgallium_25.0.4-1_arm64.deb ... Unpacking mesa-libgallium:arm64 (25.0.4-1) ... Selecting previously unselected package libwayland-server0:arm64. Preparing to unpack .../149-libwayland-server0_1.23.1-3_arm64.deb ... Unpacking libwayland-server0:arm64 (1.23.1-3) ... Selecting previously unselected package libgbm1:arm64. Preparing to unpack .../150-libgbm1_25.0.4-1_arm64.deb ... Unpacking libgbm1:arm64 (25.0.4-1) ... Selecting previously unselected package libvulkan1:arm64. Preparing to unpack .../151-libvulkan1_1.4.309.0-1_arm64.deb ... Unpacking libvulkan1:arm64 (1.4.309.0-1) ... Selecting previously unselected package libgl1-mesa-dri:arm64. Preparing to unpack .../152-libgl1-mesa-dri_25.0.4-1_arm64.deb ... Unpacking libgl1-mesa-dri:arm64 (25.0.4-1) ... Selecting previously unselected package libglx-mesa0:arm64. Preparing to unpack .../153-libglx-mesa0_25.0.4-1_arm64.deb ... Unpacking libglx-mesa0:arm64 (25.0.4-1) ... Selecting previously unselected package libglx0:arm64. Preparing to unpack .../154-libglx0_1.7.0-1+b2_arm64.deb ... Unpacking libglx0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libgl1:arm64. Preparing to unpack .../155-libgl1_1.7.0-1+b2_arm64.deb ... Unpacking libgl1:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../156-libasound2-data_1.2.14-1_all.deb ... Unpacking libasound2-data (1.2.14-1) ... Selecting previously unselected package libasound2t64:arm64. Preparing to unpack .../157-libasound2t64_1.2.14-1_arm64.deb ... Unpacking libasound2t64:arm64 (1.2.14-1) ... Selecting previously unselected package libgif7:arm64. Preparing to unpack .../158-libgif7_5.2.2-1+b1_arm64.deb ... Unpacking libgif7:arm64 (5.2.2-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../159-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package libxtst6:arm64. Preparing to unpack .../160-libxtst6_2%3a1.2.5-1_arm64.deb ... Unpacking libxtst6:arm64 (2:1.2.5-1) ... Selecting previously unselected package openjdk-21-jre:arm64. Preparing to unpack .../161-openjdk-21-jre_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jre:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jre. Preparing to unpack .../162-default-jre_2%3a1.21-76_arm64.deb ... Unpacking default-jre (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk-headless:arm64. Preparing to unpack .../163-openjdk-21-jdk-headless_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jdk-headless:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../164-default-jdk-headless_2%3a1.21-76_arm64.deb ... Unpacking default-jdk-headless (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk:arm64. Preparing to unpack .../165-openjdk-21-jdk_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jdk:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jdk. Preparing to unpack .../166-default-jdk_2%3a1.21-76_arm64.deb ... Unpacking default-jdk (2:1.21-76) ... Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../167-libgpg-error0_1.51-4_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-4) ... Selecting previously unselected package libassuan9:arm64. Preparing to unpack .../168-libassuan9_3.0.2-2_arm64.deb ... Unpacking libassuan9:arm64 (3.0.2-2) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../169-libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../170-gpgconf_2.4.7-16_arm64.deb ... Unpacking gpgconf (2.4.7-16) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../171-libksba8_1.6.7-2+b1_arm64.deb ... Unpacking libksba8:arm64 (1.6.7-2+b1) ... Selecting previously unselected package libnpth0t64:arm64. Preparing to unpack .../172-libnpth0t64_1.8-3_arm64.deb ... Unpacking libnpth0t64:arm64 (1.8-3) ... Selecting previously unselected package gpg. Preparing to unpack .../173-gpg_2.4.7-16_arm64.deb ... Unpacking gpg (2.4.7-16) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../174-pinentry-curses_1.3.1-2_arm64.deb ... Unpacking pinentry-curses (1.3.1-2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../175-gpg-agent_2.4.7-16_arm64.deb ... Unpacking gpg-agent (2.4.7-16) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../176-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../177-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../178-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../179-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../180-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../181-libclass-xsaccessor-perl_1.19-4+b5_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b5) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../182-libb-hooks-op-check-perl_0.22-3+b2_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../183-libdynaloader-functions-perl_0.004-2_all.deb ... Unpacking libdynaloader-functions-perl (0.004-2) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../184-libdevel-callchecker-perl_0.009-2_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.009-2) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../185-libparams-classify-perl_0.015-2+b4_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b4) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../186-libmodule-runtime-perl_0.018-1_all.deb ... Unpacking libmodule-runtime-perl (0.018-1) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../187-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../188-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../189-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../190-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../191-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../192-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../193-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../194-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../195-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../196-liburi-perl_5.30-1_all.deb ... Unpacking liburi-perl (5.30-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../197-libhtml-parser-perl_3.83-1+b2_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.83-1+b2) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../198-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../199-libclone-perl_0.47-1+b1_arm64.deb ... Unpacking libclone-perl:arm64 (0.47-1+b1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../200-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../201-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../202-libhttp-message-perl_7.00-2_all.deb ... Unpacking libhttp-message-perl (7.00-2) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../203-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../204-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:arm64. Preparing to unpack .../205-perl-openssl-defaults_7+b2_arm64.deb ... Unpacking perl-openssl-defaults:arm64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:arm64. Preparing to unpack .../206-libnet-ssleay-perl_1.94-3_arm64.deb ... Unpacking libnet-ssleay-perl:arm64 (1.94-3) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../207-libio-socket-ssl-perl_2.089-1_all.deb ... Unpacking libio-socket-ssl-perl (2.089-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../208-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../209-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../210-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../211-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../212-libwww-perl_6.78-1_all.deb ... Unpacking libwww-perl (6.78-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../213-patchutils_0.4.2-1+b1_arm64.deb ... Unpacking patchutils (0.4.2-1+b1) ... Selecting previously unselected package gpgv. Preparing to unpack .../214-gpgv_2.4.7-16_arm64.deb ... Unpacking gpgv (2.4.7-16) ... Selecting previously unselected package sopv-gpgv. Preparing to unpack .../215-sopv-gpgv_0.1.4-1_all.deb ... Unpacking sopv-gpgv (0.1.4-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../216-wdiff_1.2.2-9_arm64.deb ... Unpacking wdiff (1.2.2-9) ... Selecting previously unselected package devscripts. Preparing to unpack .../217-devscripts_2.25.10_all.deb ... Unpacking devscripts (2.25.10) ... Selecting previously unselected package fastjar. Preparing to unpack .../218-fastjar_2%3a0.98-7+b1_arm64.deb ... Unpacking fastjar (2:0.98-7+b1) ... Selecting previously unselected package jarwrapper. Preparing to unpack .../219-jarwrapper_0.80_all.deb ... Unpacking jarwrapper (0.80) ... Selecting previously unselected package javahelper. Preparing to unpack .../220-javahelper_0.80_all.deb ... Unpacking javahelper (0.80) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../221-libhamcrest-java_2.2-2_all.deb ... Unpacking libhamcrest-java (2.2-2) ... Selecting previously unselected package junit4. Preparing to unpack .../222-junit4_4.13.2-5_all.deb ... Unpacking junit4 (4.13.2-5) ... Selecting previously unselected package libapiguardian-java. Preparing to unpack .../223-libapiguardian-java_1.1.2-1_all.deb ... Unpacking libapiguardian-java (1.1.2-1) ... Selecting previously unselected package libopentest4j-java. Preparing to unpack .../224-libopentest4j-java_1.2.0-4_all.deb ... Unpacking libopentest4j-java (1.2.0-4) ... Selecting previously unselected package libopentest4j-reporting-java. Preparing to unpack .../225-libopentest4j-reporting-java_0.1.0-M1-2_all.deb ... Unpacking libopentest4j-reporting-java (0.1.0-M1-2) ... Selecting previously unselected package libpicocli-java. Preparing to unpack .../226-libpicocli-java_4.6.2-2_all.deb ... Unpacking libpicocli-java (4.6.2-2) ... Selecting previously unselected package libunivocity-parsers-java. Preparing to unpack .../227-libunivocity-parsers-java_2.9.1-1_all.deb ... Unpacking libunivocity-parsers-java (2.9.1-1) ... Selecting previously unselected package junit5. Preparing to unpack .../228-junit5_5.10.3-1_all.deb ... Unpacking junit5 (5.10.3-1) ... Selecting previously unselected package libactivation-java. Preparing to unpack .../229-libactivation-java_1.2.0-2_all.deb ... Unpacking libactivation-java (1.2.0-2) ... Selecting previously unselected package libaopalliance-java. Preparing to unpack .../230-libaopalliance-java_20070526-7_all.deb ... Unpacking libaopalliance-java (20070526-7) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../231-libapache-pom-java_33-2_all.deb ... Unpacking libapache-pom-java (33-2) ... Selecting previously unselected package libasm-java. Preparing to unpack .../232-libasm-java_9.8-1_all.deb ... Unpacking libasm-java (9.8-1) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../233-libatinject-jsr330-api-java_1.0+ds1-6_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-6) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../234-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-lang3-java. Preparing to unpack .../235-libcommons-lang3-java_3.17.0-1_all.deb ... Unpacking libcommons-lang3-java (3.17.0-1) ... Selecting previously unselected package libfreemarker-java. Preparing to unpack .../236-libfreemarker-java_2.3.32-2.1_all.deb ... Unpacking libfreemarker-java (2.3.32-2.1) ... Selecting previously unselected package libgoogle-gson-java. Preparing to unpack .../237-libgoogle-gson-java_2.10.1-1_all.deb ... Unpacking libgoogle-gson-java (2.10.1-1) ... Selecting previously unselected package libjoptsimple-java. Preparing to unpack .../238-libjoptsimple-java_5.0.4-7_all.deb ... Unpacking libjoptsimple-java (5.0.4-7) ... Selecting previously unselected package libcommons-codec-java. Preparing to unpack .../239-libcommons-codec-java_1.18.0-1_all.deb ... Unpacking libcommons-codec-java (1.18.0-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../240-libcommons-logging-java_1.3.0-1_all.deb ... Unpacking libcommons-logging-java (1.3.0-1) ... Selecting previously unselected package libhttpcore-java. Preparing to unpack .../241-libhttpcore-java_4.4.16-1_all.deb ... Unpacking libhttpcore-java (4.4.16-1) ... Selecting previously unselected package libhttpclient-java. Preparing to unpack .../242-libhttpclient-java_4.5.14-1_all.deb ... Unpacking libhttpclient-java (4.5.14-1) ... Selecting previously unselected package liblightcouch-java. Preparing to unpack .../243-liblightcouch-java_0.2.0-1_all.deb ... Unpacking liblightcouch-java (0.2.0-1) ... Selecting previously unselected package libmongodb-java. Preparing to unpack .../244-libmongodb-java_3.6.3-2_all.deb ... Unpacking libmongodb-java (3.6.3-2) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../245-libslf4j-java_1.7.32-1_all.deb ... Unpacking libslf4j-java (1.7.32-1) ... Selecting previously unselected package liblog4j2-java. Preparing to unpack .../246-liblog4j2-java_2.19.0-2_all.deb ... Unpacking liblog4j2-java (2.19.0-2) ... Selecting previously unselected package libbarclay-java. Preparing to unpack .../247-libbarclay-java_5.0.0+dfsg-1_all.deb ... Unpacking libbarclay-java (5.0.0+dfsg-1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../248-libblas3_3.12.1-2_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-2) ... Selecting previously unselected package libbsh-java. Preparing to unpack .../249-libbsh-java_2.0b4-20_all.deb ... Unpacking libbsh-java (2.0b4-20) ... Selecting previously unselected package libcommons-io-java. Preparing to unpack .../250-libcommons-io-java_2.19.0-1_all.deb ... Unpacking libcommons-io-java (2.19.0-1) ... Selecting previously unselected package libmaven-shared-utils-java. Preparing to unpack .../251-libmaven-shared-utils-java_3.4.2-1_all.deb ... Unpacking libmaven-shared-utils-java (3.4.2-1) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../252-libcommons-cli-java_1.6.0-1_all.deb ... Unpacking libcommons-cli-java (1.6.0-1) ... Selecting previously unselected package libgeronimo-annotation-1.3-spec-java. Preparing to unpack .../253-libgeronimo-annotation-1.3-spec-java_1.3-1_all.deb ... Unpacking libgeronimo-annotation-1.3-spec-java (1.3-1) ... Selecting previously unselected package liberror-prone-java. Preparing to unpack .../254-liberror-prone-java_2.18.0-1_all.deb ... Unpacking liberror-prone-java (2.18.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../255-libjsr305-java_0.1~+svn49-12_all.deb ... Unpacking libjsr305-java (0.1~+svn49-12) ... Selecting previously unselected package libguava-java. Preparing to unpack .../256-libguava-java_32.0.1-1_all.deb ... Unpacking libguava-java (32.0.1-1) ... Selecting previously unselected package libguice-java. Preparing to unpack .../257-libguice-java_5.1.0-1_all.deb ... Unpacking libguice-java (5.1.0-1) ... Selecting previously unselected package libmaven-parent-java. Preparing to unpack .../258-libmaven-parent-java_43-2_all.deb ... Unpacking libmaven-parent-java (43-2) ... Selecting previously unselected package libplexus-utils2-java. Preparing to unpack .../259-libplexus-utils2-java_3.4.2-1_all.deb ... Unpacking libplexus-utils2-java (3.4.2-1) ... Selecting previously unselected package libwagon-provider-api-java. Preparing to unpack .../260-libwagon-provider-api-java_3.5.3-1_all.deb ... Unpacking libwagon-provider-api-java (3.5.3-1) ... Selecting previously unselected package libmaven-resolver-java. Preparing to unpack .../261-libmaven-resolver-java_1.9.22-1_all.deb ... Unpacking libmaven-resolver-java (1.9.22-1) ... Selecting previously unselected package libplexus-cipher-java. Preparing to unpack .../262-libplexus-cipher-java_2.0-1_all.deb ... Unpacking libplexus-cipher-java (2.0-1) ... Selecting previously unselected package libplexus-classworlds-java. Preparing to unpack .../263-libplexus-classworlds-java_2.7.0-1_all.deb ... Unpacking libplexus-classworlds-java (2.7.0-1) ... Selecting previously unselected package libplexus-component-annotations-java. Preparing to unpack .../264-libplexus-component-annotations-java_2.1.1-1_all.deb ... Unpacking libplexus-component-annotations-java (2.1.1-1) ... Selecting previously unselected package libplexus-interpolation-java. Preparing to unpack .../265-libplexus-interpolation-java_1.27-1_all.deb ... Unpacking libplexus-interpolation-java (1.27-1) ... Selecting previously unselected package libplexus-sec-dispatcher-java. Preparing to unpack .../266-libplexus-sec-dispatcher-java_2.0-3_all.deb ... Unpacking libplexus-sec-dispatcher-java (2.0-3) ... Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java. Preparing to unpack .../267-libgeronimo-interceptor-3.0-spec-java_1.0.1-5_all.deb ... Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Selecting previously unselected package libcdi-api-java. Preparing to unpack .../268-libcdi-api-java_1.2-4_all.deb ... Unpacking libcdi-api-java (1.2-4) ... Selecting previously unselected package libsisu-inject-java. Preparing to unpack .../269-libsisu-inject-java_0.3.5-1_all.deb ... Unpacking libsisu-inject-java (0.3.5-1) ... Selecting previously unselected package libsisu-plexus-java. Preparing to unpack .../270-libsisu-plexus-java_0.3.5-1_all.deb ... Unpacking libsisu-plexus-java (0.3.5-1) ... Selecting previously unselected package libmaven3-core-java. Preparing to unpack .../271-libmaven3-core-java_3.9.9-1_all.deb ... Unpacking libmaven3-core-java (3.9.9-1) ... Selecting previously unselected package libmaven-shared-io-java. Preparing to unpack .../272-libmaven-shared-io-java_3.0.0-4_all.deb ... Unpacking libmaven-shared-io-java (3.0.0-4) ... Selecting previously unselected package libmaven-file-management-java. Preparing to unpack .../273-libmaven-file-management-java_3.0.0-2_all.deb ... Unpacking libmaven-file-management-java (3.0.0-2) ... Selecting previously unselected package libbuild-helper-maven-plugin-java. Preparing to unpack .../274-libbuild-helper-maven-plugin-java_3.3.0-1_all.deb ... Unpacking libbuild-helper-maven-plugin-java (3.3.0-1) ... Selecting previously unselected package libbyte-buddy-java. Preparing to unpack .../275-libbyte-buddy-java_1.14.19-1_all.deb ... Unpacking libbyte-buddy-java (1.14.19-1) ... Selecting previously unselected package libcolt-free-java. Preparing to unpack .../276-libcolt-free-java_1.2.0+dfsg-8_all.deb ... Unpacking libcolt-free-java (1.2.0+dfsg-8) ... Selecting previously unselected package libcommons-collections3-java. Preparing to unpack .../277-libcommons-collections3-java_3.2.2-3_all.deb ... Unpacking libcommons-collections3-java (3.2.2-3) ... Selecting previously unselected package libcommons-beanutils-java. Preparing to unpack .../278-libcommons-beanutils-java_1.10.1-1_all.deb ... Unpacking libcommons-beanutils-java (1.10.1-1) ... Selecting previously unselected package libcommons-collections4-java. Preparing to unpack .../279-libcommons-collections4-java_4.4-2_all.deb ... Unpacking libcommons-collections4-java (4.4-2) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../280-libcommons-compress-java_1.27.1-2_all.deb ... Unpacking libcommons-compress-java (1.27.1-2) ... Selecting previously unselected package libcommons-lang-java. Preparing to unpack .../281-libcommons-lang-java_2.6-10_all.deb ... Unpacking libcommons-lang-java (2.6-10) ... Selecting previously unselected package libcommons-configuration-java. Preparing to unpack .../282-libcommons-configuration-java_1.10-7_all.deb ... Unpacking libcommons-configuration-java (1.10-7) ... Selecting previously unselected package libcommons-digester-java. Preparing to unpack .../283-libcommons-digester-java_1.8.1-7_all.deb ... Unpacking libcommons-digester-java (1.8.1-7) ... Selecting previously unselected package libcommons-exec-java. Preparing to unpack .../284-libcommons-exec-java_1.3-2_all.deb ... Unpacking libcommons-exec-java (1.3-2) ... Selecting previously unselected package libcommons-jexl2-java. Preparing to unpack .../285-libcommons-jexl2-java_2.1.1-6_all.deb ... Unpacking libcommons-jexl2-java (2.1.1-6) ... Selecting previously unselected package libcommons-math-java. Preparing to unpack .../286-libcommons-math-java_2.2-9_all.deb ... Unpacking libcommons-math-java (2.2-9) ... Selecting previously unselected package libcommons-math3-java. Preparing to unpack .../287-libcommons-math3-java_3.6.1-4_all.deb ... Unpacking libcommons-math3-java (3.6.1-4) ... Selecting previously unselected package libplexus-io-java. Preparing to unpack .../288-libplexus-io-java_3.3.1-2_all.deb ... Unpacking libplexus-io-java (3.3.1-2) ... Selecting previously unselected package libsnappy1v5:arm64. Preparing to unpack .../289-libsnappy1v5_1.2.2-1_arm64.deb ... Unpacking libsnappy1v5:arm64 (1.2.2-1) ... Selecting previously unselected package libsnappy-jni. Preparing to unpack .../290-libsnappy-jni_1.1.10.7-1_arm64.deb ... Unpacking libsnappy-jni (1.1.10.7-1) ... Selecting previously unselected package libsnappy-java. Preparing to unpack .../291-libsnappy-java_1.1.10.7-1_all.deb ... Unpacking libsnappy-java (1.1.10.7-1) ... Selecting previously unselected package libxz-java. Preparing to unpack .../292-libxz-java_1.9-1_all.deb ... Unpacking libxz-java (1.9-1) ... Selecting previously unselected package libplexus-archiver-java. Preparing to unpack .../293-libplexus-archiver-java_4.6.1-1_all.deb ... Unpacking libplexus-archiver-java (4.6.1-1) ... Selecting previously unselected package libmaven-archiver-java. Preparing to unpack .../294-libmaven-archiver-java_3.6.2-1_all.deb ... Unpacking libmaven-archiver-java (3.6.2-1) ... Selecting previously unselected package libmaven-jar-plugin-java. Preparing to unpack .../295-libmaven-jar-plugin-java_3.3.0-2_all.deb ... Unpacking libmaven-jar-plugin-java (3.3.0-2) ... Selecting previously unselected package libcommons-text-java. Preparing to unpack .../296-libcommons-text-java_1.13.1-1_all.deb ... Unpacking libcommons-text-java (1.13.1-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../297-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package libcommons-validator-java. Preparing to unpack .../298-libcommons-validator-java_1%3a1.9.0-1_all.deb ... Unpacking libcommons-validator-java (1:1.9.0-1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../299-libsasl2-modules-db_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../300-libsasl2-2_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../301-libldap2_2.6.9+dfsg-2_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-2) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../302-libnghttp2-14_1.64.0-1.1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../303-libnghttp3-9_1.8.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.8.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../304-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../305-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../306-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../307-libcurl4t64_8.13.0-5_arm64.deb ... Unpacking libcurl4t64:arm64 (8.13.0-5) ... Selecting previously unselected package libdistlib-java. Preparing to unpack .../308-libdistlib-java_1.0-5_all.deb ... Unpacking libdistlib-java (1.0-5) ... Selecting previously unselected package libjaxen-java. Preparing to unpack .../309-libjaxen-java_1.1.6-5_all.deb ... Unpacking libjaxen-java (1.1.6-5) ... Selecting previously unselected package libdom4j-java. Preparing to unpack .../310-libdom4j-java_2.1.4-1_all.deb ... Unpacking libdom4j-java (2.1.4-1) ... Selecting previously unselected package libdoxia-core-java. Preparing to unpack .../311-libdoxia-core-java_2.0.0-1_all.deb ... Unpacking libdoxia-core-java (2.0.0-1) ... Selecting previously unselected package libplexus-xml-java. Preparing to unpack .../312-libplexus-xml-java_3.0.1-2_all.deb ... Unpacking libplexus-xml-java (3.0.1-2) ... Selecting previously unselected package libdoxia-java. Preparing to unpack .../313-libdoxia-java_2.0.0-1_all.deb ... Unpacking libdoxia-java (2.0.0-1) ... Selecting previously unselected package libmaven-reporting-api-java. Preparing to unpack .../314-libmaven-reporting-api-java_4.0.0-1_all.deb ... Unpacking libmaven-reporting-api-java (4.0.0-1) ... Selecting previously unselected package libxbean-reflect-java. Preparing to unpack .../315-libxbean-reflect-java_4.5-9_all.deb ... Unpacking libxbean-reflect-java (4.5-9) ... Selecting previously unselected package libplexus-container-default-java. Preparing to unpack .../316-libplexus-container-default-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default-java (2.1.1-1) ... Selecting previously unselected package libplexus-i18n-java. Preparing to unpack .../317-libplexus-i18n-java_1.0-beta-10-6_all.deb ... Unpacking libplexus-i18n-java (1.0-beta-10-6) ... Selecting previously unselected package velocity. Preparing to unpack .../318-velocity_1.7-7_all.deb ... Unpacking velocity (1.7-7) ... Selecting previously unselected package libplexus-velocity-java. Preparing to unpack .../319-libplexus-velocity-java_1.2-4_all.deb ... Unpacking libplexus-velocity-java (1.2-4) ... Selecting previously unselected package liboro-java. Preparing to unpack .../320-liboro-java_2.0.8a-14_all.deb ... Unpacking liboro-java (2.0.8a-14) ... Selecting previously unselected package libvelocity-tools-java. Preparing to unpack .../321-libvelocity-tools-java_2.0-9_all.deb ... Unpacking libvelocity-tools-java (2.0-9) ... Selecting previously unselected package libdoxia-sitetools-java. Preparing to unpack .../322-libdoxia-sitetools-java_2.0.0-1_all.deb ... Unpacking libdoxia-sitetools-java (2.0.0-1) ... Selecting previously unselected package libfastutil-java. Preparing to unpack .../323-libfastutil-java_8.5.15+dfsg-1_all.deb ... Unpacking libfastutil-java (8.5.15+dfsg-1) ... Selecting previously unselected package libxpp3-java. Preparing to unpack .../324-libxpp3-java_1.1.4c-4_all.deb ... Unpacking libxpp3-java (1.1.4c-4) ... Selecting previously unselected package libxstream-java. Preparing to unpack .../325-libxstream-java_1.4.21-1_all.deb ... Unpacking libxstream-java (1.4.21-1) ... Selecting previously unselected package libjsap-java. Preparing to unpack .../326-libjsap-java_2.1-5_all.deb ... Unpacking libjsap-java (2.1-5) ... Selecting previously unselected package liblogback-java. Preparing to unpack .../327-liblogback-java_1%3a1.2.11-6_all.deb ... Unpacking liblogback-java (1:1.2.11-6) ... Selecting previously unselected package libdsiutils-java. Preparing to unpack .../328-libdsiutils-java_2.7.3+dfsg-1_all.deb ... Unpacking libdsiutils-java (2.7.3+dfsg-1) ... Selecting previously unselected package libobjenesis-java. Preparing to unpack .../329-libobjenesis-java_3.4-2_all.deb ... Unpacking libobjenesis-java (3.4-2) ... Selecting previously unselected package libeasymock-java. Preparing to unpack .../330-libeasymock-java_5.5.0-1_all.deb ... Unpacking libeasymock-java (5.5.0-1) ... Selecting previously unselected package libel-api-java. Preparing to unpack .../331-libel-api-java_3.0.0-3_all.deb ... Unpacking libel-api-java (3.0.0-3) ... Selecting previously unselected package libexec-maven-plugin-java. Preparing to unpack .../332-libexec-maven-plugin-java_3.1.0-2_all.deb ... Unpacking libexec-maven-plugin-java (3.1.0-2) ... Selecting previously unselected package libezmorph-java. Preparing to unpack .../333-libezmorph-java_1.0.6-4_all.deb ... Unpacking libezmorph-java (1.0.6-4) ... Selecting previously unselected package libgatk-native-bindings-java. Preparing to unpack .../334-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../335-libgfortran5_14.2.0-19_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-19) ... Selecting previously unselected package libxml-commons-external-java. Preparing to unpack .../336-libxml-commons-external-java_1.4.01-6_all.deb ... Unpacking libxml-commons-external-java (1.4.01-6) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Preparing to unpack .../337-libxml-commons-resolver1.1-java_1.2-11_all.deb ... Unpacking libxml-commons-resolver1.1-java (1.2-11) ... Selecting previously unselected package libxerces2-java. Preparing to unpack .../338-libxerces2-java_2.12.2-1_all.deb ... Unpacking libxerces2-java (2.12.2-1) ... Selecting previously unselected package libxom-java. Preparing to unpack .../339-libxom-java_1.3.9-1_all.deb ... Unpacking libxom-java (1.3.9-1) ... Selecting previously unselected package libjson-java. Preparing to unpack .../340-libjson-java_3.1.0+dfsg-2_all.deb ... Unpacking libjson-java (3.1.0+dfsg-2) ... Selecting previously unselected package libmbedcrypto16:arm64. Preparing to unpack .../341-libmbedcrypto16_3.6.3-1_arm64.deb ... Unpacking libmbedcrypto16:arm64 (3.6.3-1) ... Selecting previously unselected package libmbedx509-7:arm64. Preparing to unpack .../342-libmbedx509-7_3.6.3-1_arm64.deb ... Unpacking libmbedx509-7:arm64 (3.6.3-1) ... Selecting previously unselected package libmbedtls21:arm64. Preparing to unpack .../343-libmbedtls21_3.6.3-1_arm64.deb ... Unpacking libmbedtls21:arm64 (3.6.3-1) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../344-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:arm64. Preparing to unpack .../345-libncbi-vdb3_3.2.1+dfsg-2_arm64.deb ... Unpacking libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-ngs3:arm64. Preparing to unpack .../346-libncbi-ngs3_3.2.1+dfsg-4_arm64.deb ... Unpacking libncbi-ngs3:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package libngs-jni:arm64. Preparing to unpack .../347-libngs-jni_3.2.1+dfsg-4_arm64.deb ... Unpacking libngs-jni:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package libngs-java:arm64. Preparing to unpack .../348-libngs-java_3.2.1+dfsg-4_arm64.deb ... Unpacking libngs-java:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package librhino-java. Preparing to unpack .../349-librhino-java_1.7.15-1_all.deb ... Unpacking librhino-java (1.7.15-1) ... Selecting previously unselected package libhtsjdk-java. Preparing to unpack .../350-libhtsjdk-java_4.1.3+dfsg-2_all.deb ... Unpacking libhtsjdk-java (4.1.3+dfsg-2) ... Selecting previously unselected package libgkl-java. Preparing to unpack .../351-libgkl-java_0.8.11+dfsg-2_all.deb ... Unpacking libgkl-java (0.8.11+dfsg-2) ... Selecting previously unselected package libicu4j-java. Preparing to unpack .../352-libicu4j-java_73.2-1_all.deb ... Unpacking libicu4j-java (73.2-1) ... Selecting previously unselected package liblog4j1.2-java. Preparing to unpack .../353-liblog4j1.2-java_1.2.17-11_all.deb ... Unpacking liblog4j1.2-java (1.2.17-11) ... Selecting previously unselected package libicb-utils-java. Preparing to unpack .../354-libicb-utils-java_2.0.1+git20161002.afee1d9-5_all.deb ... Unpacking libicb-utils-java (2.0.1+git20161002.afee1d9-5) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../355-libice6_2%3a1.1.1-1_arm64.deb ... Unpacking libice6:arm64 (2:1.1.1-1) ... Selecting previously unselected package libicu76:arm64. Preparing to unpack .../356-libicu76_76.1-3_arm64.deb ... Unpacking libicu76:arm64 (76.1-3) ... Selecting previously unselected package libjansi-java. Preparing to unpack .../357-libjansi-java_2.4.1-2_all.deb ... Unpacking libjansi-java (2.4.1-2) ... Selecting previously unselected package libjavassist-java. Preparing to unpack .../358-libjavassist-java_1%3a3.27.0-1_all.deb ... Unpacking libjavassist-java (1:3.27.0-1) ... Selecting previously unselected package libjaxb-api-java. Preparing to unpack .../359-libjaxb-api-java_2.3.1-1_all.deb ... Unpacking libjaxb-api-java (2.3.1-1) ... Selecting previously unselected package libjboss-logging-java. Preparing to unpack .../360-libjboss-logging-java_3.5.3-1_all.deb ... Unpacking libjboss-logging-java (3.5.3-1) ... Selecting previously unselected package libjboss-vfs-java. Preparing to unpack .../361-libjboss-vfs-java_3.2.15.Final-3_all.deb ... Unpacking libjboss-vfs-java (3.2.15.Final-3) ... Selecting previously unselected package libjbzip2-java. Preparing to unpack .../362-libjbzip2-java_0.9.1-8_all.deb ... Unpacking libjbzip2-java (0.9.1-8) ... Selecting previously unselected package libjcommander-java. Preparing to unpack .../363-libjcommander-java_1.71-4_all.deb ... Unpacking libjcommander-java (1.71-4) ... Selecting previously unselected package libjsp-api-java. Preparing to unpack .../364-libjsp-api-java_2.3.4-3_all.deb ... Unpacking libjsp-api-java (2.3.4-3) ... Selecting previously unselected package libservlet-api-java. Preparing to unpack .../365-libservlet-api-java_4.0.1-2_all.deb ... Unpacking libservlet-api-java (4.0.1-2) ... Selecting previously unselected package libwebsocket-api-java. Preparing to unpack .../366-libwebsocket-api-java_1.1-2_all.deb ... Unpacking libwebsocket-api-java (1.1-2) ... Selecting previously unselected package libjetty9-java. Preparing to unpack .../367-libjetty9-java_9.4.57-1_all.deb ... Unpacking libjetty9-java (9.4.57-1) ... Selecting previously unselected package libjsoup-java. Preparing to unpack .../368-libjsoup-java_1.15.3-1_all.deb ... Unpacking libjsoup-java (1.15.3-1) ... Selecting previously unselected package libjtidy-java. Preparing to unpack .../369-libjtidy-java_7+svn20110807-6_all.deb ... Unpacking libjtidy-java (7+svn20110807-6) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../370-liblapack3_3.12.1-2_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-2) ... Selecting previously unselected package libmaven-antrun-plugin-java. Preparing to unpack .../371-libmaven-antrun-plugin-java_3.1.0-1_all.deb ... Unpacking libmaven-antrun-plugin-java (3.1.0-1) ... Selecting previously unselected package libmaven-common-artifact-filters-java. Preparing to unpack .../372-libmaven-common-artifact-filters-java_3.4.0-1_all.deb ... Unpacking libmaven-common-artifact-filters-java (3.4.0-1) ... Selecting previously unselected package libmaven-artifact-transfer-java. Preparing to unpack .../373-libmaven-artifact-transfer-java_0.13.1-2_all.deb ... Unpacking libmaven-artifact-transfer-java (0.13.1-2) ... Selecting previously unselected package libplexus-build-api-java. Preparing to unpack .../374-libplexus-build-api-java_0.0.7-4_all.deb ... Unpacking libplexus-build-api-java (0.0.7-4) ... Selecting previously unselected package libmaven-filtering-java. Preparing to unpack .../375-libmaven-filtering-java_3.4.0-1_all.deb ... Unpacking libmaven-filtering-java (3.4.0-1) ... Selecting previously unselected package libmaven-assembly-plugin-java. Preparing to unpack .../376-libmaven-assembly-plugin-java_3.4.2-2_all.deb ... Unpacking libmaven-assembly-plugin-java (3.4.2-2) ... Selecting previously unselected package libmaven-clean-plugin-java. Preparing to unpack .../377-libmaven-clean-plugin-java_3.2.0-2_all.deb ... Unpacking libmaven-clean-plugin-java (3.2.0-2) ... Selecting previously unselected package libmaven-shared-incremental-java. Preparing to unpack .../378-libmaven-shared-incremental-java_1.1-6_all.deb ... Unpacking libmaven-shared-incremental-java (1.1-6) ... Selecting previously unselected package libplexus-compiler-java. Preparing to unpack .../379-libplexus-compiler-java_2.13.0-1_all.deb ... Unpacking libplexus-compiler-java (2.13.0-1) ... Selecting previously unselected package libqdox2-java. Preparing to unpack .../380-libqdox2-java_2.0.3-1_all.deb ... Unpacking libqdox2-java (2.0.3-1) ... Selecting previously unselected package libplexus-languages-java. Preparing to unpack .../381-libplexus-languages-java_1.1.1-2_all.deb ... Unpacking libplexus-languages-java (1.1.1-2) ... Selecting previously unselected package libmaven-compiler-plugin-java. Preparing to unpack .../382-libmaven-compiler-plugin-java_3.13.0-1_all.deb ... Unpacking libmaven-compiler-plugin-java (3.13.0-1) ... Selecting previously unselected package libmaven-dependency-analyzer-java. Preparing to unpack .../383-libmaven-dependency-analyzer-java_1.15.1-1_all.deb ... Unpacking libmaven-dependency-analyzer-java (1.15.1-1) ... Selecting previously unselected package libmaven-dependency-tree-java. Preparing to unpack .../384-libmaven-dependency-tree-java_3.3.0-1_all.deb ... Unpacking libmaven-dependency-tree-java (3.3.0-1) ... Selecting previously unselected package libmaven-reporting-impl-java. Preparing to unpack .../385-libmaven-reporting-impl-java_4.0.0-1_all.deb ... Unpacking libmaven-reporting-impl-java (4.0.0-1) ... Selecting previously unselected package libmaven-dependency-plugin-java. Preparing to unpack .../386-libmaven-dependency-plugin-java_3.8.1-1_all.deb ... Unpacking libmaven-dependency-plugin-java (3.8.1-1) ... Selecting previously unselected package libmaven-invoker-java. Preparing to unpack .../387-libmaven-invoker-java_3.3.0-1_all.deb ... Unpacking libmaven-invoker-java (3.3.0-1) ... Selecting previously unselected package libplexus-interactivity-api-java. Preparing to unpack .../388-libplexus-interactivity-api-java_1.3-1_all.deb ... Unpacking libplexus-interactivity-api-java (1.3-1) ... Selecting previously unselected package libmaven-javadoc-plugin-java. Preparing to unpack .../389-libmaven-javadoc-plugin-java_3.10.1-2_all.deb ... Unpacking libmaven-javadoc-plugin-java (3.10.1-2) ... Selecting previously unselected package libplexus-ant-factory-java. Preparing to unpack .../390-libplexus-ant-factory-java_1.0~alpha2.1-5_all.deb ... Unpacking libplexus-ant-factory-java (1.0~alpha2.1-5) ... Selecting previously unselected package libplexus-container-default1.5-java. Preparing to unpack .../391-libplexus-container-default1.5-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default1.5-java (2.1.1-1) ... Selecting previously unselected package libplexus-bsh-factory-java. Preparing to unpack .../392-libplexus-bsh-factory-java_1.0~alpha7-5_all.deb ... Unpacking libplexus-bsh-factory-java (1.0~alpha7-5) ... Selecting previously unselected package libmaven-plugin-tools-java. Preparing to unpack .../393-libmaven-plugin-tools-java_3.10.2-2_all.deb ... Unpacking libmaven-plugin-tools-java (3.10.2-2) ... Selecting previously unselected package libmaven-reporting-exec-java. Preparing to unpack .../394-libmaven-reporting-exec-java_2.0.0-1_all.deb ... Unpacking libmaven-reporting-exec-java (2.0.0-1) ... Selecting previously unselected package libmaven-resources-plugin-java. Preparing to unpack .../395-libmaven-resources-plugin-java_3.3.1-1_all.deb ... Unpacking libmaven-resources-plugin-java (3.3.1-1) ... Selecting previously unselected package libmaven-site-plugin-java. Preparing to unpack .../396-libmaven-site-plugin-java_3.21.0-1_all.deb ... Unpacking libmaven-site-plugin-java (3.21.0-1) ... Selecting previously unselected package libmaven-source-plugin-java. Preparing to unpack .../397-libmaven-source-plugin-java_3.3.1-1_all.deb ... Unpacking libmaven-source-plugin-java (3.3.1-1) ... Selecting previously unselected package libpaper2:arm64. Preparing to unpack .../398-libpaper2_2.2.5-0.3+b2_arm64.deb ... Unpacking libpaper2:arm64 (2.2.5-0.3+b2) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../399-libpaper-utils_2.2.5-0.3+b2_arm64.deb ... Unpacking libpaper-utils (2.2.5-0.3+b2) ... Selecting previously unselected package libpicard-java. Preparing to unpack .../400-libpicard-java_3.3.0+dfsg-2_all.deb ... Unpacking libpicard-java (3.3.0+dfsg-2) ... Selecting previously unselected package libpj-java. Preparing to unpack .../401-libpj-java_0.0~20150107+dfsg-5_all.deb ... Unpacking libpj-java (0.0~20150107+dfsg-5) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../402-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../403-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libprotobuf32t64:arm64. Preparing to unpack .../404-libprotobuf32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-lite32t64:arm64. Preparing to unpack .../405-libprotobuf-lite32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf-lite32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-dev:arm64. Preparing to unpack .../406-libprotobuf-dev_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf-dev:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-java. Preparing to unpack .../407-libprotobuf-java_3.21.12-10_all.deb ... Unpacking libprotobuf-java (3.21.12-10) ... Selecting previously unselected package libprotoc32t64:arm64. Preparing to unpack .../408-libprotoc32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotoc32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libreflections-java. Preparing to unpack .../409-libreflections-java_0.10.2+dfsg-2_all.deb ... Unpacking libreflections-java (0.10.2+dfsg-2) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../410-libsm6_2%3a1.2.6-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.6-1) ... Selecting previously unselected package libsurefire-java. Preparing to unpack .../411-libsurefire-java_2.22.3-3_all.deb ... Unpacking libsurefire-java (2.22.3-3) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../412-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../413-libtirpc-common_1.3.6+ds-1_all.deb ... Unpacking libtirpc-common (1.3.6+ds-1) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../414-libtirpc3t64_1.3.6+ds-1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.6+ds-1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../415-libxft2_2.3.6-1+b4_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b4) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../416-libxss1_1%3a1.2.3-1+b3_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../417-libtk8.6_8.6.16-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.16-1) ... Selecting previously unselected package libwagon-file-java. Preparing to unpack .../418-libwagon-file-java_3.5.3-1_all.deb ... Unpacking libwagon-file-java (3.5.3-1) ... Selecting previously unselected package libwagon-http-java. Preparing to unpack .../419-libwagon-http-java_3.5.3-1_all.deb ... Unpacking libwagon-http-java (3.5.3-1) ... Selecting previously unselected package libxml2-utils. Preparing to unpack .../420-libxml2-utils_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2-utils (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../421-libxt6t64_1%3a1.2.1-1.2+b2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Selecting previously unselected package maven. Preparing to unpack .../422-maven_3.9.9-1_all.deb ... Unpacking maven (3.9.9-1) ... Selecting previously unselected package maven-repo-helper. Preparing to unpack .../423-maven-repo-helper_1.11_all.deb ... Unpacking maven-repo-helper (1.11) ... Selecting previously unselected package unzip. Preparing to unpack .../424-unzip_6.0-29_arm64.deb ... Unpacking unzip (6.0-29) ... Selecting previously unselected package maven-debian-helper. Preparing to unpack .../425-maven-debian-helper_2.6.7_all.deb ... Unpacking maven-debian-helper (2.6.7) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../426-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../427-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package protobuf-compiler. Preparing to unpack .../428-protobuf-compiler_3.21.12-10+b6_arm64.deb ... Unpacking protobuf-compiler (3.21.12-10+b6) ... Selecting previously unselected package zip. Preparing to unpack .../429-zip_3.0-15_arm64.deb ... Unpacking zip (3.0-15) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../430-xdg-utils_1.2.1-2_all.deb ... Unpacking xdg-utils (1.2.1-2) ... Selecting previously unselected package r-base-core. Preparing to unpack .../431-r-base-core_4.5.0-2_arm64.deb ... Unpacking r-base-core (4.5.0-2) ... Selecting previously unselected package r-cran-rjava. Preparing to unpack .../432-r-cran-rjava_1.0-11-2_arm64.deb ... Unpacking r-cran-rjava (1.0-11-2) ... Selecting previously unselected package testng. Preparing to unpack .../433-testng_6.9.12-4_all.deb ... Unpacking testng (6.9.12-4) ... Setting up libprotobuf-lite32t64:arm64 (3.21.12-10+b6) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up fastjar (2:0.98-7+b1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libjcommander-java (1.71-4) ... Setting up libfastutil-java (8.5.15+dfsg-1) ... Setting up libtext-charwidth-perl:arm64 (0.04-11+b4) ... Setting up wdiff (1.2.2-9) ... Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libprotobuf32t64:arm64 (3.21.12-10+b6) ... Setting up libfile-which-perl (1.27-2) ... Setting up systemd-sysv (257.5-2) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:arm64 (1.8-3) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up bsdextrautils (2.41-4) ... Setting up hicolor-icon-theme (0.18-2) ... Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... Setting up libgpg-error0:arm64 (1.51-4) ... Setting up libicu4j-java (73.2-1) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libobjenesis-java (3.4-2) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up liblogback-java (1:1.2.11-6) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:arm64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libtirpc-common (1.3.6+ds-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxcb-glx0:arm64 (1.17.0-2+b1) ... Setting up unzip (6.0-29) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libedit2:arm64 (3.1-20250104-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.8-1) ... Setting up x11-common (1:7.7+24) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.2-2) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libel-api-java (3.0.0-3) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up xkb-data (2.42-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2-1+b1) ... Setting up file (1:5.46-5) ... Setting up libjboss-logging-java (3.5.3-1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:arm64 (1.2.2-1) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 27 18:57:29 UTC 2025. Universal Time is now: Sun Apr 27 18:57:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.14-1) ... Setting up libjavassist-java (1:3.27.0-1) ... Setting up zip (3.0-15) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libasound2t64:arm64 (1.2.14-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libepoxy0:arm64 (1.5.10-2) ... Setting up libnspr4:arm64 (2:4.36-1) ... Setting up libxcb-sync1:arm64 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-6) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-16) ... Setting up libxpp3-java (1.1.4c-4) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:arm64 (1.16.2-2) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libproc2-0:arm64 (2:4.0.4-8) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.47-1.1) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-2) ... Setting up binfmt-support (2.2.2-7+b1) ... Running in chroot, ignoring request. 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:arm64 (0.22-3+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libpcsclite1:arm64 (2.3.3-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libsensors5:arm64 (1:3.6.2-2) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... 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:arm64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:arm64 (14.2.0-19) ... Setting up libvulkan1:arm64 (1.4.309.0-1) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libwebp7:arm64 (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:arm64 (5.2.2-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up libplexus-interactivity-api-java (1.3-1) ... Setting up libfreemarker-java (2.3.32-2.1) ... Setting up sensible-utils (0.0.25) ... Setting up libxshmfence1:arm64 (1.3.3-1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.56.1-2) ... Setting up libcommons-math-java (2.2-9) ... Setting up gpgv (2.4.7-16) ... Setting up libtiff6:arm64 (4.7.0-3) ... Setting up libxcb-randr0:arm64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.2-2) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libassuan9:arm64 (3.0.2-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-8) ... 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:arm64 (4.20.0-2) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.5) ... Setting up libcommons-math3-java (3.6.1-4) ... Setting up sgml-base (1.31+nmu1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libwayland-egl1:arm64 (1.23.1-3) ... Setting up libicu76:arm64 (76.1-3) ... Setting up libmbedcrypto16:arm64 (3.6.3-1) ... Setting up libpaper2:arm64 (2.2.5-0.3+b2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-7) ... Setting up libprotoc32t64:arm64 (3.21.12-10+b6) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up libfile-homedir-perl (1.006-2) ... Setting up libpj-java (0.0~20150107+dfsg-5) ... Setting up openssl (3.5.0-1) ... Setting up libdrm-common (2.4.124-2) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:arm64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-2) ... Setting up liburi-perl (5.30-1) ... Setting up dbus-bin (1.16.2-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libxkbcommon0:arm64 (1.7.0-2) ... Setting up libwayland-client0:arm64 (1.23.1-3) ... Setting up libnet-ssleay-perl:arm64 (1.94-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.1-2) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:arm64 (1:19.1.7-3) ... Setting up libwayland-server0:arm64 (1.23.1-3) ... Setting up libx11-xcb1:arm64 (2:1.8.12-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxstream-java (1.4.21-1) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libjetty9-java (9.4.57-1) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up protobuf-compiler (3.21.12-10+b6) ... Setting up libjboss-vfs-java (3.2.15.Final-3) ... Setting up libxrender1:arm64 (1:0.9.12-1) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:arm64 (2.3.8-2) ... Setting up libnss3:arm64 (2:3.110-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libpaper-utils (2.2.5-0.3+b2) ... Setting up libxom-java (1.3.9-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libmaven-dependency-analyzer-java (1.15.1-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:arm64 (3.21.12-10+b6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1+b1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:arm64 (2.84.1-2) ... Setting up libmbedx509-7:arm64 (3.6.3-1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b4) ... Setting up testng (6.9.12-4) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b4) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libxrandr2:arm64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0051) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:arm64 (3.6.3-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:arm64 (2.4.124-2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:arm64 (1.23.1-3) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gpgconf (2.4.7-16) ... Setting up libpam-systemd:arm64 (257.5-2) ... Setting up libcommons-beanutils-java (1.10.1-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2.3) ... 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+really2.9.14-0.4) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up libsm6:arm64 (2:1.2.6-1) ... Setting up libreflections-java (0.10.2+dfsg-2) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libavahi-client3:arm64 (0.8-16) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.4.7-16) ... Created symlink '/etc/systemd/user/sockets.target.wants/keyboxd.socket' -> '/usr/lib/systemd/user/keyboxd.socket'. Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.124-2) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.18.4+ds-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up mesa-libgallium:arm64 (25.0.4-1) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-2.3) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.6-1+b4) ... Setting up gpg-agent (2.4.7-16) ... Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'. Setting up libatk1.0-0t64:arm64 (2.56.1-2) ... Setting up openjdk-21-jre-headless:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libtirpc3t64:arm64 (1.3.6+ds-1) ... Setting up libgbm1:arm64 (25.0.4-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.3-2) ... Setting up libcommons-io-java (2.19.0-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:arm64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:arm64 (1:1.2.3-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libpango-1.0-0:arm64 (1.56.3-1) ... Setting up libgl1-mesa-dri:arm64 (25.0.4-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Setting up libcloudproviders0:arm64 (0.3.6-2) ... Setting up python3 (3.13.3-1) ... Setting up sopv-gpgv (0.1.4-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up libcolord2:arm64 (1.4.7-3) ... Setting up libdconf1:arm64 (0.40.0-5) ... Setting up libmaven-filtering-java (3.4.0-1) ... Setting up dbus-user-session (1.16.2-2) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (48.0-1) ... 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 (0.018-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:arm64 (2.56.1-2) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up libmaven-dependency-tree-java (3.3.0-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:arm64 (1.18.4-1+b1) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... Setting up libncbi-ngs3:arm64 (3.2.1+dfsg-4) ... Setting up libatk-bridge2.0-0t64:arm64 (2.56.1-2) ... Setting up libngs-jni:arm64 (3.2.1+dfsg-4) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:arm64 (25.0.4-1) ... Setting up libglx0:arm64 (1.7.0-1+b2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:arm64 (8.13.0-5) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libmaven-invoker-java (3.3.0-1) ... Setting up debhelper (13.24.2) ... Setting up dconf-service (0.40.0-5) ... Setting up libgl1:arm64 (1.7.0-1+b2) ... Setting up r-base-core (4.5.0-2) ... Creating config file /etc/R/Renviron with new version Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:arm64 (3.2.1+dfsg-4) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libmaven-source-plugin-java (3.3.1-1) ... Setting up libgtk-3-common (3.24.49-3) ... Setting up libgtk-3-0t64:arm64 (3.24.49-3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.78-1) ... Setting up devscripts (2.25.10) ... 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 (1.13.1-1) ... 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 (2.41-7) ... Processing triggers for systemd (257.5-2) ... 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_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_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: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:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven (3.9.9-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:arm64 (21.0.7+6-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up ant-contrib (1.0~b3+svn177-12) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.21-76) ... Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-5) ... Setting up openjdk-21-jdk:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up libjsap-java (2.1-5) ... Setting up r-cran-rjava (1.0-11-2) ... 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 (3.10.2-2) ... 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+nmu1) ... 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 (20250419) ... 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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with javahelper dh_auto_clean bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibgoby-io-java jh_clean Duplicate specification "unlink|u" for option "u" debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' dh_clean rm -rf goby-distribution/test-data goby-distribution/test-results rm -rf test-results/ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo jh_linkjars dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1 [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16 [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15 [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Goby Framework [pom] [INFO] Goby I/O [jar] [INFO] Goby Full Distribution [jar] [INFO] [INFO] ----------------< org.campagnelab.goby:goby-framework >----------------- [INFO] Building Goby Framework 3.3.1 [1/3] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] from goby-io/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.17 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:3.1.2 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)' [INFO] [INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ goby-io --- [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ goby-io --- [INFO] Recompiling the module because of changed source code. [INFO] Compiling 260 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- antrun:3.1.0:run (default) @ goby-io --- [WARNING] Parameter 'tasks' is deprecated: Use target instead. For version 3.0.0, this parameter is only defined to break the build if you use it! [WARNING] Parameter tasks is deprecated, use target instead [INFO] Executing tasks [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2 [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-io --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-io --- [INFO] No sources to compile [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ goby-io --- [INFO] Tests are skipped. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1.jar [INFO] [INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-io >>> [INFO] [INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-io <<< [INFO] [INFO] [INFO] --- source:3.3.1:jar (attach-sources) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-sources.jar [INFO] [INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-io --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol [WARNING] @XmlRootElement [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist [WARNING] import DistLib.hypergeometric; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol [WARNING] Rengine rEngine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExactRCalculator [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Unmarshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class StatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.CommandLine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.DefaultExecutor; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.PumpStreamHandler; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol [WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class MethylStatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.PJProperties; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElementWrapper; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol [WARNING] @XmlRootElement(name = "info-output") [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol [WARNING] private void writeInfoOutput() throws JAXBException, IOException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:33: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:47: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol [WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol [WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol [WARNING] private Rengine rengine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol [WARNING] public Rengine getRengine() { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.REXP; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RVector; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol [WARNING] private static Result evaluateFisherExpression(final Rengine rengine, [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExact [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:35: error: cannot find symbol [WARNING] @XmlElement(name = "al") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:36: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "annotation-lengths") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:39: error: cannot find symbol [WARNING] @XmlElement(name = "tc") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:40: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "total-counts") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-javadoc.jar [INFO] [INFO] ---------------< org.campagnelab.goby:goby-distribution >--------------- [INFO] Building Goby Full Distribution 3.3.1 [3/3] [INFO] from goby-distribution/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ goby-distribution --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] Copying 72 resources from src/main/java to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ goby-distribution --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 525 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-distribution --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-distribution --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 120 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ goby-distribution --- [INFO] Tests are skipped. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1.jar [INFO] [INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-distribution >>> [INFO] [INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-distribution <<< [INFO] [INFO] [INFO] --- source:3.3.1:jar (attach-sources) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-sources.jar [INFO] [INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-distribution --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J). [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J) [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning: @return tag cannot be used in method with void return type. [WARNING] void flush(InputBitStream ibs) throws IOException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning: reference not found: org.campagnelab.goby.aligners.LastagAligner [WARNING] * @see org.campagnelab.goby.aligners.LastagAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:79: warning: reference not found: org.campagnelab.goby.aligners.LastAligner [WARNING] * @see org.campagnelab.goby.aligners.LastAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:87: warning: reference not found: org.campagnelab.goby.aligners.BWAAligner [WARNING] * @see org.campagnelab.goby.aligners.BWAAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:95: warning: reference not found: org.campagnelab.goby.aligners.GSnapAligner [WARNING] * @see org.campagnelab.goby.aligners.GSnapAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:131: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * @return the next {@link edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<' [WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol ?@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 [ 0.133 s] [INFO] Goby I/O ........................................... SUCCESS [ 40.749 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 43.490 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:24 min [INFO] Finished at: 2025-04-27T07:00:27-12:00 [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 07:01:01.252 INFO RLoggerMainLoopCallback - 07:01:01.257 INFO RLoggerMainLoopCallback - R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 07:01:01.257 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. 07:01:01.257 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. 07:01:01.258 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT qPhred=1 qPhred=2 qPhred=3 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 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] 07:01:02.380 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. 0 AAC 3 ACC 6 ATC 9 AGC 12 AAC 15 ACC 18 ATC 21 AGC 24 AAC 27 ACC 30 ATC 33 AGC 36 AAC 39 ACC 42 ATC 45 AGC 48 AAC 51 ACC 54 ATC 57 AGC 60 AAC 63 ACC 66 ATC 69 AGC 72 AAC 75 ACC 78 ATC 81 AGC07:01:09.707 WARN MessageChunksWriter - Using chunk-size=10000 07:01:09.708 WARN MessageChunksWriter - Using chunk-size=9 07:01:09.713 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 07:01:09.724 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 07:01:09.731 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 Number of bits/base 3.6590436 Creating base test directory: test-results/stats [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. 07:01:10.072 INFO BullardUpperQuartileNormalization - normalization denominator 49719.7 for sample B-7 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 48867.0 for sample B-3 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 99505.1 for sample A-3 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-12 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49588.6 for sample B-15 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 51097.2 for sample B-14 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49326.2 for sample B-11 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 94520.0 for sample A-17 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49916.5 for sample B-2 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 47358.4 for sample B-10 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 98586.8 for sample A-16 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 50703.6 for sample B-8 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 48735.8 for sample B-4 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-2 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 98521.2 for sample A-0 07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49326.2 for sample B-6 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97996.4 for sample A-9 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98062.0 for sample A-8 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98980.3 for sample A-5 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97537.3 for sample A-4 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 99964.2 for sample A-6 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98390.0 for sample A-7 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48211.1 for sample B-5 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-10 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 100030 for sample A-14 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 50769.2 for sample B-9 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97865.2 for sample A-1 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48735.8 for sample B-0 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48604.7 for sample B-12 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 49719.7 for sample B-13 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 93536.1 for sample A-19 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97799.6 for sample A-18 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 96750.1 for sample A-15 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48014.3 for sample B-1 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97012.5 for sample A-13 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98258.8 for sample A-11 07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 49588.6 for sample B-16 07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 49785.3 for sample B-17 07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 47292.8 for sample B-19 07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 48342.3 for sample B-18 Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T]07:01:10.230 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 07:01:10.309 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 07:01:10.309 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 07:01:10.345 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 07:01:10.346 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 07:01:10.563 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 07:01:10.629 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. 07:01:10.629 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 07:01:10.785 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 07:01:10.808 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 [1.0042223266471022, 0.5016882445373338, 0.006078705586435645, -0.9951369613424312, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00294094 original=0.00294094 truncated fdr=0.00375760 original=0.00375760 truncated fdr=0.00569307 original=0.00569307 truncated fdr=0.00833856 original=0.00833856 truncated fdr=0.0201744 original=0.0201744 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0523700 original=0.0523700 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0733761 original=0.0733761 truncated fdr=0.0742187 original=0.0742187 truncated fdr=0.0847349 original=0.0847349 truncated fdr=0.151073 original=0.151073 truncated fdr=0.335641 original=0.335641 truncated fdr=0.391390 original=0.391390 truncated fdr=0.391390 original=0.391390 truncated fdr=0.443709 original=0.443709 truncated fdr=0.477756 original=0.477756 truncated fdr=0.479630 original=0.479630 truncated fdr=0.637850 original=0.637850 truncated fdr=0.977998 original=0.977998 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. ##fileformat=VCFv4.1 ##Goby=UNKNOWN ##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 1/1 ..T Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 07:01:34.553 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 07:01:34.557 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 07:01:34.564 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 07:01:34.567 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 07:01:34.578 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 07:01:34.585 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 07:01:34.592 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 07:01:34.595 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 07:01:34.598 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 07:01:34.609 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 07:01:34.919 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 07:01:34.930 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 07:01:34.933 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 07:01:34.939 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 07:01:34.942 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 07:01:34.953 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 07:01:34.955 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 07:01:34.958 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 07:01:34.968 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 07:01:34.971 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 07:01:35.166 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 07:01:35.176 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 07:01:35.179 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 07:01:35.185 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 07:01:35.192 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 07:01:35.194 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 07:01:35.201 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 07:01:35.203 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 07:01:35.213 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 07:01:35.216 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 07:01:35.377 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 07:01:35.384 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 07:01:35.386 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 07:01:35.392 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 07:01:35.394 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 07:01:35.413 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 07:01:35.415 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 07:01:35.418 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 07:01:35.424 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 07:01:35.426 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 07:01:35.670 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 07:01:35.680 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 07:01:35.682 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 07:01:35.685 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 07:01:35.686 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 07:01:35.693 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 07:01:35.695 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 07:01:35.698 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 07:01:35.700 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 07:01:35.702 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 07:01:35.803 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 07:01:35.805 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 07:01:35.806 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 07:01:35.817 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 07:01:35.827 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 07:01:35.830 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 07:01:35.831 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 07:01:35.833 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 07:01:35.835 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 07:01:35.841 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 07:01:35.928 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 07:01:35.930 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 07:01:35.933 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 07:01:35.935 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 07:01:35.936 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 07:01:35.938 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 07:01:35.948 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 07:01:35.950 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 07:01:35.960 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 07:01:35.962 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 07:01:36.091 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 07:01:36.101 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 07:01:36.102 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 07:01:36.104 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 07:01:36.106 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 07:01:36.115 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 07:01:36.117 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 07:01:36.119 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 07:01:36.120 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 07:01:36.122 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 07:01:36.246 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 07:01:36.252 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 07:01:36.254 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 07:01:36.264 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 07:01:36.265 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 07:01:36.267 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 07:01:36.269 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 07:01:36.270 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 07:01:36.280 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 07:01:36.282 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 07:01:36.361 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 07:01:36.363 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 07:01:36.364 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 07:01:36.366 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 07:01:36.367 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 07:01:36.369 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 07:01:36.370 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 07:01:36.373 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 07:01:36.374 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 07:01:36.376 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 07:01:36.504 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 07:01:36.506 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 07:01:36.512 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 07:01:36.513 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 07:01:36.515 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 07:01:36.521 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 07:01:36.522 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 07:01:36.528 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 07:01:36.530 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 07:01:36.536 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 07:01:36.690 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 07:01:36.691 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 07:01:36.701 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 07:01:36.702 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 07:01:36.704 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 07:01:36.706 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 07:01:36.715 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 07:01:36.717 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 07:01:36.719 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 07:01:36.721 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + /T q=40 s=0 info: - /T q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /C q=30 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /N q=30 s=0 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + /T q=40 s=1 info: + /T q=10 s=1 info: + /T q=20 s=1 info: + /T q=30 s=1 info: + /N q=40 s=1 info: + /N q=40 s=1 list: pos=-1 #bases: 33 #indels: 0 filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1} Scanning target file.. Target file had 1 entries. Wrote 1 target ids to alignment header. Setting quality threshold to 0.05 Total logical entries written: 2 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 3 Number of targets: 3 Removed by quality filter: 0 Not best score: 1 Number of alignments written: 2 query_index: 0 target_index: 0 position: 14977972 score: 780.0 matching_reverse_strand: false multiplicity: 1 number_of_mismatches: 1 number_of_indels: 0 query_length: 142 query_aligned_length: 134 target_aligned_length: 134 sequence_variations { to: "T" from: "A" position: 6 to_quality: "/" read_index: 14 } fragment_index: 0 query_index_occurrences: 2 ambiguity: 1 TTC[27]->CGT[27] / qual=1:2:3 A[15]->G[20] / qual=20 A[15]->G[20] / qual=20 Processing test-data/sample-qual-scores/30reads.fa Processed 0 read entries. Min quality score: 2147483647 Max quality score: -2147483648 Avg quality score: 0 Probable quality encoding scheme: fasta Processing test-data/sample-qual-scores/30reads.fq Processed 30 read entries. Min quality score: 69 Max quality score: 98 Avg quality score: 94 Probable quality encoding scheme: Illumina/Solexa field CHROM value: 0 field POS value: 145497099 field ID value: . field REF value: A field ALT value: G field QUAL value: 17.1 field FILTER value: . field INFO[DP] value: 2 field INFO[DP4] value: 0,0,2,0 field INFO[MQ] value: 25 field INFO[FQ] value: -30.8 field INFO[AF1] value: 0.9999 field INFO[CI95] value: 0.5,1 field INFO[PV4] value: field INFO[INDEL] value: INDEL field INFO[PC2] value: 3,3 field INFO[PCHI2] value: 0.752 field INFO[QCHI2] value: 1 field INFO[RP] value: field FORMAT[GT] value: field FORMAT[GQ] value: field FORMAT[GL] value: field FORMAT[DP] value: field FORMAT[SP] value: field FORMAT[PL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 field CHROM gfi:0 value: 0 field POS gfi:1 value: 145497099 field ID gfi:2 value: . field REF gfi:3 value: A field ALT gfi:4 value: G field QUAL gfi:5 value: 17.1 field FILTER gfi:6 value: . field FORMAT[GT] gfi:7 value: field FORMAT[GQ] gfi:8 value: field FORMAT[GL] gfi:9 value: field FORMAT[DP] gfi:10 value: field FORMAT[SP] gfi:11 value: field FORMAT[PL] gfi:12 value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 Total logical entries written: 1 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 45 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 Appending count: 16576 length: 10 Appending count: 35371 length: 4 Appending count: 23073 length: 1 Appending count: 22583 length: 2 Appending count: 17646 length: 5 Appending count: 19398 length: 1 Appending count: 12875 length: 9 Appending count: 39440 length: 1 Appending count: 46977 length: 7 Appending count: 39057 length: 10 Appending count: 7950 length: 9 Appending count: 1004 length: 8 Appending count: 14153 length: 2 Appending count: 2284 length: 6 Appending count: 5888 length: 1 Appending count: 36281 length: 7 Appending count: 45232 length: 3 Appending count: 4131 length: 6 Appending count: 28736 length: 2 Appending count: 6015 length: 6 Appending count: 26795 length: 10 Appending count: 9739 length: 3 Appending count: 49032 length: 9 Appending count: 9375 length: 3 Appending count: 8631 length: 9 Appending count: 21777 length: 7 Appending count: 38666 length: 9 Appending count: 38565 length: 10 Appending count: 30414 length: 6 Appending count: 27984 length: 5 position= 0 count= 16576 position= 1 count= 16576 position= 2 count= 16576 position= 3 count= 16576 position= 4 count= 16576 position= 5 count= 16576 position= 6 count= 16576 position= 7 count= 16576 position= 8 count= 16576 position= 9 count= 16576 position= 10 count= 35371 position= 11 count= 35371 position= 12 count= 35371 position= 13 count= 35371 position= 14 count= 23073 position= 15 count= 22583 position= 16 count= 22583 position= 17 count= 17646 position= 18 count= 17646 position= 19 count= 17646 position= 20 count= 17646 position= 21 count= 17646 position= 22 count= 19398 position= 23 count= 12875 position= 24 count= 12875 position= 25 count= 12875 position= 26 count= 12875 position= 27 count= 12875 position= 28 count= 12875 position= 29 count= 12875 position= 30 count= 12875 position= 31 count= 12875 position= 32 count= 39440 position= 33 count= 46977 position= 34 count= 46977 position= 35 count= 46977 position= 36 count= 46977 position= 37 count= 46977 position= 38 count= 46977 position= 39 count= 46977 position= 40 count= 39057 position= 41 count= 39057 position= 42 count= 39057 position= 43 count= 39057 position= 44 count= 39057 position= 45 count= 39057 position= 46 count= 39057 position= 47 count= 39057 position= 48 count= 39057 position= 49 count= 39057 position= 50 count= 7950 position= 51 count= 7950 position= 52 count= 7950 position= 53 count= 7950 position= 54 count= 7950 position= 55 count= 7950 position= 56 count= 7950 position= 57 count= 7950 position= 58 count= 7950 position= 59 count= 1004 position= 60 count= 1004 position= 61 count= 1004 position= 62 count= 1004 position= 63 count= 1004 position= 64 count= 1004 position= 65 count= 1004 position= 66 count= 1004 position= 67 count= 14153 position= 68 count= 14153 position= 69 count= 2284 position= 70 count= 2284 position= 71 count= 2284 position= 72 count= 2284 position= 73 count= 2284 position= 74 count= 2284 position= 75 count= 5888 position= 76 count= 36281 position= 77 count= 36281 position= 78 count= 36281 position= 79 count= 36281 position= 80 count= 36281 position= 81 count= 36281 position= 82 count= 36281 position= 83 count= 45232 position= 84 count= 45232 position= 85 count= 45232 position= 86 count= 4131 position= 87 count= 4131 position= 88 count= 4131 position= 89 count= 4131 position= 90 count= 4131 position= 91 count= 4131 position= 92 count= 28736 position= 93 count= 28736 position= 94 count= 6015 position= 95 count= 6015 position= 96 count= 6015 position= 97 count= 6015 position= 98 count= 6015 position= 99 count= 6015 position= 100 count= 26795 position= 101 count= 26795 position= 102 count= 26795 position= 103 count= 26795 position= 104 count= 26795 position= 105 count= 26795 position= 106 count= 26795 position= 107 count= 26795 position= 108 count= 26795 position= 109 count= 26795 position= 110 count= 9739 position= 111 count= 9739 position= 112 count= 9739 position= 113 count= 49032 position= 114 count= 49032 position= 115 count= 49032 position= 116 count= 49032 position= 117 count= 49032 position= 118 count= 49032 position= 119 count= 49032 position= 120 count= 49032 position= 121 count= 49032 position= 122 count= 9375 position= 123 count= 9375 position= 124 count= 9375 position= 125 count= 8631 position= 126 count= 8631 position= 127 count= 8631 position= 128 count= 8631 position= 129 count= 8631 position= 130 count= 8631 position= 131 count= 8631 position= 132 count= 8631 position= 133 count= 8631 position= 134 count= 21777 position= 135 count= 21777 position= 136 count= 21777 position= 137 count= 21777 position= 138 count= 21777 position= 139 count= 21777 position= 140 count= 21777 position= 141 count= 38666 position= 142 count= 38666 position= 143 count= 38666 position= 144 count= 38666 position= 145 count= 38666 position= 146 count= 38666 position= 147 count= 38666 position= 148 count= 38666 position= 149 count= 38666 position= 150 count= 38565 position= 151 count= 38565 position= 152 count= 38565 position= 153 count= 38565 position= 154 count= 38565 position= 155 count= 38565 position= 156 count= 38565 position= 157 count= 38565 position= 158 count= 38565 position= 159 count= 38565 position= 160 count= 30414 position= 161 count= 30414 position= 162 count= 30414 position= 163 count= 30414 position= 164 count= 30414 position= 165 count= 30414 position= 166 count= 27984 position= 167 count= 27984 position= 168 count= 27984 position= 169 count= 27984 position= 170 count= 27984 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 07:01:39.310 WARN WiggleWindow - Not writing 101 7 07:01:39.310 WARN WiggleWindow - Not writing 111 7 07:01:39.310 WARN WiggleWindow - Not writing 131 8 07:01:39.310 WARN WiggleWindow - Not writing 141 8 07:01:39.310 WARN WiggleWindow - Not writing 151 8 appending (count=0,length=1) appending (count=4,length=3) appending (count=1,length=3) appending (count=0,length=2) appending (count=3,length=1) appending (count=1,length=1) appending (count=0,length=1) appending (count=4,length=3) appending (count=0,length=5) appending (count=3,length=1) appending (count=0,length=2) appending (count=2,length=1) appending (count=0,length=2) appending (count=3,length=1) appending (count=2,length=1) appending (count=0,length=1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) loading transition for reader[0] position=1 length=3 count=3 (0,1)(1,4) loading transition for reader[0] position=4 length=2 count=0 (0,1)(1,4)(4,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 (0,0) loading transition for reader[0] position=1 length=1 count=1 (0,0)(1,1) loading transition for reader[0] position=2 length=4 count=0 (0,0)(1,1)(2,0) loading transition for reader[1] position=4 length=10 count=1 (0,0)(1,1)(2,0)(4,1) loading transition for reader[0] position=6 length=2 count=1 (0,0)(1,1)(2,0)(4,1)(6,2) loading transition for reader[0] position=8 length=1 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1) loading transition for reader[0] position=9 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) loading transition for reader[0] position=10 length=2 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) loading transition for reader[0] position=12 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) loading transition for reader[0] position=13 length=3 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) loading transition for reader[0] position=16 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 loading transition for reader[0] position=1 length=1 count=1 loading transition for reader[0] position=2 length=4 count=0 loading transition for reader[1] position=4 length=10 count=1 loading transition for reader[0] position=6 length=2 count=1 loading transition for reader[0] position=8 length=1 count=0 loading transition for reader[0] position=9 length=1 count=1 loading transition for reader[0] position=10 length=2 count=0 loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 loading transition for reader[0] position=0 length=1 count=0 (0,0) loading transition for reader[0] position=1 length=3 count=1 (0,0)(1,1) appending (count=10,length=4) appending (count=1,length=0) appending (count=2,length=8) Hello appending (count=10,length=4) 07:01:39.366 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 07:01:39.373 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 07:01:39.381 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 07:01:39.384 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 07:01:39.388 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 07:01:39.394 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.401 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.412 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.416 WARN MessageChunksWriter - Using chunk-size=1000 0 23 Setting quality threshold to 0.02 entry:query_index: 0 target_index: 0 position: 5 score: 5.0 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 read_index: 10 } entry:query_index: 1 target_index: 0 position: 5 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 to_quality: "((((" read_index: 10 } entry: query_index: 0 target_index: 0 position: 0 matching_reverse_strand: false query_length: 10 query_aligned_length: 10 sequence_variations { to: "AAA" from: "---" position: 3 read_index: 3 } processing entry on target 0 at position 0 processing entry on target 0 at position 5 processing entry on target 1 at position 0 processing entry on target 1 at position 5 processing entry on target 4 at position 0 processing entry on target 4 at position 5 entry:query_index: 0 target_index: 0 position: 10 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "AAA" from: "---" position: 20 read_index: 20 } entry:query_index: 1 target_index: 0 position: 1 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "T" from: "A" position: 20 read_index: 20 } 07:01:39.454 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 07:01:39.543 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.545 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.546 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.556 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.557 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.558 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.569 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.570 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.573 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 07:01:39.583 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.586 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.587 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.601 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.603 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.604 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.607 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 07:01:39.609 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 07:01:39.611 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 07:01:39.615 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.616 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.617 WARN MessageChunksWriter - Using chunk-size=1000 Processing queryIndex=8 with description '8 perfect start of ref' Processing queryIndex=9 with description '9 perfect start of ref reverse strand' Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' Processing queryIndex=0 with description '0 perfect match' Processing queryIndex=1 with description '1 perfect match on reverse strand' Processing queryIndex=2 with description '2 mutation' Processing queryIndex=3 with description '3 mutation on reverse strand' Processing queryIndex=4 with description '4 insertion' Processing queryIndex=6 with description '6 deletion' Processing queryIndex=7 with description '7 deletion on reverse strand' Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' Processing queryIndex=5 with description '5 insertion on reverse strand' Processing queryIndex=10 with description '10 perfect end of ref' Processing queryIndex=11 with description '11 perfect end of ref reverse strand' 07:01:39.646 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 07:01:39.651 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 07:01:39.657 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 07:01:39.661 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 07:01:39.665 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 07:01:39.669 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 07:01:39.673 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 07:01:39.680 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.683 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.688 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.693 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.696 WARN MessageChunksWriter - Using chunk-size=1 07:01:39.702 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.712 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 07:01:39.718 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.728 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries 07:01:39.732 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.733 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.745 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.747 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.761 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.762 WARN MessageChunksWriter - Using chunk-size=1000 0 2 07:01:39.776 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.778 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 07:01:39.793 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.794 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.808 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.809 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.823 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.824 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 5 entries [main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TAAAACCTAAAAAAAAAAAAAAACCCC expected =TAAAA--TAAAAAAAAAAAAAAACCCC recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT 07:01:39.860 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.926 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.927 WARN MessageChunksWriter - Using chunk-size=1000 07:01:39.992 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:40.049 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.051 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.067 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. 07:01:40.110 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. 07:01:40.110 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 07:01:40.110 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 5ms; used/avail/free/total/max mem: 895.63M/7.51G/178.11M/1.07G/8.40G 07:01:40.121 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 07:01:40.175 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. 07:01:40.186 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. 07:01:40.244 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. 07:01:40.244 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. 07:01:40.244 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. 07:01:40.244 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 07:01:40.244 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. 07:01:40.244 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: 945.96M/7.46G/127.78M/1.07G/8.40G 07:01:40.247 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. 07:01:40.261 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. 07:01:40.312 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.354 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.356 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.387 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:40.411 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.413 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: 1.04G/7.37G/37.60M/1.07G/8.40G 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 07:01:40.613 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.661 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.662 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.714 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:40.763 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.764 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.767 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. 07:01:40.818 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. 07:01:40.818 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 07:01:40.818 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: 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: 1ms; used/avail/free/total/max mem: 436.14M/7.97G/645.99M/1.08G/8.40G 07:01:40.822 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 07:01:40.838 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.914 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.920 WARN MessageChunksWriter - Using chunk-size=1000 07:01:40.962 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.009 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.010 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.021 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. 07:01:41.022 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. 07:01:41.025 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. 07:01:41.025 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. 07:01:41.025 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. 07:01:41.026 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 07:01:41.026 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. 07:01:41.026 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: 80.86M/8.32G/103.69M/184.55M/8.40G 07:01:41.036 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. 07:01:41.038 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. 07:01:41.041 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.088 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.089 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.136 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.182 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.186 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) 07:01:41.188 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) 07:01:41.189 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. 07:01:41.201 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. 07:01:41.201 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. 07:01:41.201 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. 07:01:41.201 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 07:01:41.201 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. 07:01:41.201 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 108.12M/8.29G/76.43M/184.55M/8.40G Second pass: writing the merged alignment. 07:01:41.207 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. 07:01:41.209 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 07:01:41.216 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.265 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.266 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.313 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.363 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.365 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.367 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. 07:01:41.373 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. 07:01:41.373 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 07:01:41.373 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: 1ms; used/avail/free/total/max mem: 133.28M/8.27G/51.26M/184.55M/8.40G 07:01:41.375 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 07:01:41.387 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.430 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.431 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.516 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.554 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.555 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 89.94M/8.31G/94.61M/184.55M/8.40G 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 07:01:41.691 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.730 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.740 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.782 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 07:01:41.838 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.839 WARN MessageChunksWriter - Using chunk-size=1000 07:01:41.851 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. 07:01:41.854 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. 07:01:41.899 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. 07:01:41.899 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. 07:01:41.899 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. 07:01:41.899 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 07:01:41.899 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. 07:01:41.899 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: 72.43M/8.33G/112.12M/184.55M/8.40G 07:01:41.902 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. 07:01:41.925 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 1999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 0 target_index: 3999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 3999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 query_index: 0 target_index: 0 position: 0 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 query_index: 1 target_index: 0 position: 1 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 07:01:42.041 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 07:01:42.041 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 [ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits [ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 {1} {0}decoding: 4 {0} {0}decoding: 4 {0} {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0} {0} {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0} {0} {0}decoding: 3 decoding: 4 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 [ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits [ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} count keys [0, 3, 5, 11, 13] -1 0.0 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 0.0 overlapping count 15, 17 0.0 overlapping count 9, 18 2.0 overlapping count 3, 8 2.0 overlapping count 11, 12 0.0 overlapping count 9, 10 1.0 overlapping count 8, 9 0.0 overlapping count 8, 8 0.0 overlapping count 5, 6 0.0 overlapping count 3, 3 0.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 0.0 -1 0.0 0 0.0 1 0.0 2 0.0 3 2.0 4 2.0 5 3.0 6 3.0 7 3.0 8 3.0 9 3.0 10 3.0 11 2.0 12 2.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 2.0 overlapping count 2, 3 2.0 overlapping count 3, 8 4.0 overlapping count 11, 12 2.0 overlapping count 9, 10 3.0 overlapping count 8, 9 4.0 overlapping count 8, 8 3.0 overlapping count 5, 6 3.0 overlapping count 3, 3 2.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 1.0 Total logical entries written: 4 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Total logical entries written: 4 Total bytes written: 62 Average bytes/logical entry: 15.5 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 Annotations loaded Annotations loaded Annotations loaded Annotations loaded Annotations loaded [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 106.692 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 [ 0.115 s] [INFO] Goby I/O ........................................... SUCCESS [ 15.391 s] [INFO] Goby Full Distribution ............................. SUCCESS [02:29 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:45 min [INFO] Finished at: 2025-04-27T07:03:16-12:00 [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 [ 0.337 s] [INFO] Goby I/O ........................................... SUCCESS [ 0.055 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 0.037 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.597 s [INFO] Finished at: 2025-04-27T07:03:18-12:00 [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 27, 2025 7:03:24 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian > dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2 Apr 27, 2025 7:03:29 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian ERROR: goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian goby-io/pom.xml: dependency is not packaged in the Maven repository for Debian: org.itadaki:bzip2:debian -------- Some problems were found in this project, exiting... mh_unpatchpoms -plibgoby-io-java dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package 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: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} 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 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'. dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-11_all.deb'. dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/271630 and its subdirectories I: Current time: Sun Apr 27 07:03:40 -12 2025 I: pbuilder-time-stamp: 1745780620 Sun Apr 27 19:03:44 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun Apr 27 19:03:44 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun Apr 27 19:03:44 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sun Apr 27 19:03:44 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-7AAO6e' ==================================================================================== Sun May 31 01:26:45 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 libgoby-java unstable /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp 3.3.1+dfsg2-11" as arguments. Sun May 31 01:26:45 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-0SjGfWZy" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun May 31 01:26:46 UTC 2026 I: Downloading source for unstable/libgoby-java=3.3.1+dfsg2-11 Reading package lists... NOTICE: 'libgoby-java' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgoby-java.git Please use: git clone https://salsa.debian.org/med-team/libgoby-java.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 41.6 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (dsc) [3008 B] Get:2 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (tar) [41.6 MB] Get:3 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (diff) [29.4 kB] Fetched 41.6 MB in 0s (141 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libgoby-java' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgoby-java.git Please use: git clone https://salsa.debian.org/med-team/libgoby-java.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 41.6 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (dsc) [3008 B] Get:2 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (tar) [41.6 MB] Get:3 http://deb.debian.org/debian unstable/main libgoby-java 3.3.1+dfsg2-11 (diff) [29.4 kB] Fetched 41.6 MB in 0s (141 MB/s) Download complete and in download only mode ============================================================================= Re-Building libgoby-java in unstable on arm64 on codethink03-arm64 now. Date: Sun May 31 02:26:46 BST 2026 Date UTC: Sun May 31 01:26:46 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/pbuilderrc_X7xR + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libgoby-java = debian-installer -o libgoby-java = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libgoby-java = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/pbuilderrc_X7xR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-11.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun May 31 15:26:46 +14 2026 I: pbuilder-time-stamp: 1780190806 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/3292973/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 31 01:26 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=c379785ceadf4065bf6c36170272c649 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3292973 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/pbuilderrc_X7xR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-11.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team 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 ... 19953 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} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gpg{a} gpg-agent{a} gpgconf{a} gpgv{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbarclay-java{a} libblas3{a} libbrotli1{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcolord2{a} libcolt-free-java{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdsiutils-java{a} libdynaloader-functions-perl{a} libeasymock-java{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastutil-java{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgbm1{a} libgcrypt20{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicb-utils-java{a} libice6{a} libicu4j-java{a} libicu76{a} libidn2-0{a} libimport-into-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libjansi-java{a} libjavassist-java{a} libjaxb-api-java{a} libjaxen-java{a} libjbig0{a} libjboss-logging-java{a} libjboss-vfs-java{a} libjbzip2-java{a} libjcommander-java{a} libjetty9-java{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjsap-java{a} libjson-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblightcouch-java{a} libllvm19{a} liblog4j1.2-java{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven-source-plugin-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libnpth0t64{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libpcsclite1{a} libpicard-java{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libpj-java{a} libpkgconf3{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} libreflections-java{a} librhino-java{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1t64{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} liburi-perl{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxom-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxss1{a} libxstream-java{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} mesa-libgallium{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sopv-gpgv{a} systemd{a} systemd-sysv{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpg-error-l10n libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjline3-java libjson-perl libkmod2 libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl libnss-systemd librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian linux-sysctl-defaults lynx lzip mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc publicsuffix python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended sopv-doc strace systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 459 newly installed, 0 to remove and 0 not upgraded. Need to get 373 MB of archives. After unpacking 1012 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 257.5-2 [1911 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libapparmor1 arm64 4.1.0-1 [42.9 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 systemd arm64 257.5-2 [2920 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 systemd-sysv arm64 257.5-2 [63.9 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 dbus-bin arm64 1.16.2-2 [78.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 dbus-daemon arm64 1.16.2-2 [152 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 dbus arm64 1.16.2-2 [70.7 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-2 [260 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.5.0-1 [1454 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20250419 [162 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libpam-systemd arm64 257.5-2 [275 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 43 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0051 [42.8 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.84.1-2 [1423 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b2 [756 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1.1 [274 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.7.0-3 [325 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [131 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 4.18.4+ds-2 [51.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 48.0-1 [504 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.110-1 [1292 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.3-1 [55.0 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.7+6-1 [40.6 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.56.1-2 [171 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 dbus-user-session arm64 1.16.2-2 [52.1 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libdconf1 arm64 0.40.0-5 [40.4 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dconf-service arm64 0.40.0-5 [30.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [27.3 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 87 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.56.1-2 [50.0 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libatspi2.0-0t64 arm64 2.56.1-2 [76.5 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libatk-bridge2.0-0t64 arm64 2.56.1-2 [64.8 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.3 [318 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.3 [387 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.4-1+b1 [130 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libcloudproviders0 arm64 0.3.6-2 [27.4 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libcolord2 arm64 1.4.7-3 [130 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-16 [112 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-16 [43.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-16 [46.7 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 129 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.3 [463 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.3-1 [213 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [52.9 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [33.7 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libwayland-client0 arm64 1.23.1-3 [26.1 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libwayland-cursor0 arm64 1.23.1-3 [11.7 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libwayland-egl1 arm64 1.23.1-3 [5952 B] Get: 146 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b4 [20.5 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.3-1 [39.3 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b4 [16.0 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 xkb-data all 2.42-1 [790 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libxkbcommon0 arm64 1.7.0-2 [106 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1+b3 [35.9 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libgtk-3-common all 3.24.49-3 [4908 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libgtk-3-0t64 arm64 3.24.49-3 [2565 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.124-2 [8288 B] Get: 158 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.124-2 [38.3 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.12-1 [247 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b4 [19.2 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.124-2 [21.8 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.7-3 [23.3 MB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.2-2 [36.4 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3.3-1 [11.1 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 mesa-libgallium arm64 25.0.4-1 [8031 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libwayland-server0 arm64 1.23.1-3 [33.7 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libgbm1 arm64 25.0.4-1 [43.6 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.4.309.0-1 [127 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 25.0.4-1 [45.3 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 25.0.4-1 [142 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.14-1 [21.1 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.14-1 [342 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.5-1 [25.7 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre arm64 21.0.7+6-1 [193 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.21-76 [1068 B] Get: 189 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk-headless arm64 21.0.7+6-1 [81.9 MB] Get: 190 http://deb.debian.org/debian unstable/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 191 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jdk arm64 21.0.7+6-1 [3557 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 default-jdk arm64 2:1.21-76 [1076 B] Get: 193 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.4.7-16 [121 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-3 [22.9 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.4.7-16 [577 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.3.1-2 [83.5 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.4.7-16 [248 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 203 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 206 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-2 [15.7 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 232 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.78-1 [183 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 gpgv arm64 2.4.7-16 [220 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 sopv-gpgv all 0.1.4-1 [11.3 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-9 [122 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.25.10 [1062 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.80 [9692 B] Get: 246 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.80 [80.4 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 250 http://deb.debian.org/debian unstable/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 251 http://deb.debian.org/debian unstable/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 junit5 all 5.10.3-1 [2459 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 257 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 258 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.8-1 [392 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 260 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libfreemarker-java all 2.3.32-2.1 [1525 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libjoptsimple-java all 5.0.4-7 [73.7 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.18.0-1 [304 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 268 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.19.0-1 [524 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libguice-java all 5.1.0-1 [932 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 285 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 291 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 294 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libbyte-buddy-java all 1.14.19-1 [4756 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.10.1-1 [231 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libcommons-configuration-java all 1.10-7 [348 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 libcommons-math-java all 2.2-9 [933 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.2-1 [28.3 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.7-1 [6476 B] Get: 317 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libcommons-text-java all 1.13.1-1 [228 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-2 [179 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.13.0-5 [349 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libdistlib-java all 1.0-5 [72.5 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 libdoxia-java all 2.0.0-1 [113 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 341 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 velocity all 1.7-7 [431 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 346 http://deb.debian.org/debian unstable/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 350 http://deb.debian.org/debian unstable/main arm64 libxpp3-java all 1.1.4c-4 [294 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 libxstream-java all 1.4.21-1 [567 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 libjsap-java all 2.1-5 [102 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 liblogback-java all 1:1.2.11-6 [701 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 libobjenesis-java all 3.4-2 [41.3 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 libeasymock-java all 5.5.0-1 [134 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 361 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 libxom-java all 1.3.9-1 [174 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto16 arm64 3.6.3-1 [343 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 libmbedx509-7 arm64 3.6.3-1 [148 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 libmbedtls21 arm64 3.6.3-1 [224 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1096 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 libncbi-ngs3 arm64 3.2.1+dfsg-4 [145 kB] Get: 373 http://deb.debian.org/debian unstable/main arm64 libngs-jni arm64 3.2.1+dfsg-4 [27.7 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 libngs-java arm64 3.2.1+dfsg-4 [114 kB] Get: 375 http://deb.debian.org/debian unstable/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 libicu4j-java all 73.2-1 [16.4 MB] Get: 379 http://deb.debian.org/debian unstable/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-3 [9526 kB] Get: 383 http://deb.debian.org/debian unstable/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 384 http://deb.debian.org/debian unstable/main arm64 libjavassist-java all 1:3.27.0-1 [731 kB] Get: 385 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 386 http://deb.debian.org/debian unstable/main arm64 libjboss-logging-java all 3.5.3-1 [56.2 kB] Get: 387 http://deb.debian.org/debian unstable/main arm64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB] Get: 388 http://deb.debian.org/debian unstable/main arm64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get: 389 http://deb.debian.org/debian unstable/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 390 http://deb.debian.org/debian unstable/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 391 http://deb.debian.org/debian unstable/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 392 http://deb.debian.org/debian unstable/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 393 http://deb.debian.org/debian unstable/main arm64 libjetty9-java all 9.4.57-1 [2965 kB] Get: 394 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 395 http://deb.debian.org/debian unstable/main arm64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 396 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 397 http://deb.debian.org/debian unstable/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 398 http://deb.debian.org/debian unstable/main arm64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 399 http://deb.debian.org/debian unstable/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 400 http://deb.debian.org/debian unstable/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 401 http://deb.debian.org/debian unstable/main arm64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 402 http://deb.debian.org/debian unstable/main arm64 libmaven-assembly-plugin-java all 3.4.2-2 [242 kB] Get: 403 http://deb.debian.org/debian unstable/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 404 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 405 http://deb.debian.org/debian unstable/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 406 http://deb.debian.org/debian unstable/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 407 http://deb.debian.org/debian unstable/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 408 http://deb.debian.org/debian unstable/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 409 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-analyzer-java all 1.15.1-1 [38.5 kB] Get: 410 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-tree-java all 3.3.0-1 [35.0 kB] Get: 411 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-impl-java all 4.0.0-1 [17.6 kB] Get: 412 http://deb.debian.org/debian unstable/main arm64 libmaven-dependency-plugin-java all 3.8.1-1 [191 kB] Get: 413 http://deb.debian.org/debian unstable/main arm64 libmaven-invoker-java all 3.3.0-1 [29.1 kB] Get: 414 http://deb.debian.org/debian unstable/main arm64 libplexus-interactivity-api-java all 1.3-1 [11.6 kB] Get: 415 http://deb.debian.org/debian unstable/main arm64 libmaven-javadoc-plugin-java all 3.10.1-2 [451 kB] Get: 416 http://deb.debian.org/debian unstable/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB] Get: 417 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 418 http://deb.debian.org/debian unstable/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 419 http://deb.debian.org/debian unstable/main arm64 libmaven-plugin-tools-java all 3.10.2-2 [245 kB] Get: 420 http://deb.debian.org/debian unstable/main arm64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 421 http://deb.debian.org/debian unstable/main arm64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 422 http://deb.debian.org/debian unstable/main arm64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 423 http://deb.debian.org/debian unstable/main arm64 libmaven-source-plugin-java all 3.3.1-1 [27.7 kB] Get: 424 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b2 [16.6 kB] Get: 425 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b2 [16.4 kB] Get: 426 http://deb.debian.org/debian unstable/main arm64 libpicard-java all 3.3.0+dfsg-2 [1778 kB] Get: 427 http://deb.debian.org/debian unstable/main arm64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB] Get: 428 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 429 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 430 http://deb.debian.org/debian unstable/main arm64 libprotobuf32t64 arm64 3.21.12-10+b6 [859 kB] Get: 431 http://deb.debian.org/debian unstable/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b6 [250 kB] Get: 432 http://deb.debian.org/debian unstable/main arm64 libprotobuf-dev arm64 3.21.12-10+b6 [1263 kB] Get: 433 http://deb.debian.org/debian unstable/main arm64 libprotobuf-java all 3.21.12-10 [1268 kB] Get: 434 http://deb.debian.org/debian unstable/main arm64 libprotoc32t64 arm64 3.21.12-10+b6 [790 kB] Get: 435 http://deb.debian.org/debian unstable/main arm64 libreflections-java all 0.10.2+dfsg-2 [125 kB] Get: 436 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.6-1 [36.4 kB] Get: 437 http://deb.debian.org/debian unstable/main arm64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 438 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 439 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get: 440 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.6+ds-1 [79.1 kB] Get: 441 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 442 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 443 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 444 http://deb.debian.org/debian unstable/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 445 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 446 http://deb.debian.org/debian unstable/main arm64 libxml2-utils arm64 2.12.7+dfsg+really2.9.14-0.4 [98.3 kB] Get: 447 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 448 http://deb.debian.org/debian unstable/main arm64 maven all 3.9.9-1 [19.7 kB] Get: 449 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 450 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-29 [163 kB] Get: 451 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.7 [108 kB] Get: 452 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 453 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 454 http://deb.debian.org/debian unstable/main arm64 protobuf-compiler arm64 3.21.12-10+b6 [84.9 kB] Get: 455 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-15 [227 kB] Get: 456 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 457 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.5.0-2 [28.4 MB] Get: 458 http://deb.debian.org/debian unstable/main arm64 r-cran-rjava arm64 1.0-11-2 [712 kB] Get: 459 http://deb.debian.org/debian unstable/main arm64 testng all 6.9.12-4 [795 kB] Fetched 373 MB in 4s (91.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19953 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.5-2_arm64.deb ... Unpacking libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package libapparmor1:arm64. Preparing to unpack .../libapparmor1_4.1.0-1_arm64.deb ... Unpacking libapparmor1:arm64 (4.1.0-1) ... Setting up libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package systemd. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../systemd_257.5-2_arm64.deb ... Unpacking systemd (257.5-2) ... Setting up libapparmor1:arm64 (4.1.0-1) ... Setting up systemd (257.5-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20904 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.5-2_arm64.deb ... Unpacking systemd-sysv (257.5-2) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../01-libdbus-1-3_1.16.2-2_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.16.2-2) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.16.2-2_arm64.deb ... Unpacking dbus-bin (1.16.2-2) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../03-dbus-session-bus-common_1.16.2-2_all.deb ... Unpacking dbus-session-bus-common (1.16.2-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../04-libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../05-dbus-daemon_1.16.2-2_arm64.deb ... Unpacking dbus-daemon (1.16.2-2) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../06-dbus-system-bus-common_1.16.2-2_all.deb ... Unpacking dbus-system-bus-common (1.16.2-2) ... Selecting previously unselected package dbus. Preparing to unpack .../07-dbus_1.16.2-2_arm64.deb ... Unpacking dbus (1.16.2-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../09-binfmt-support_2.2.2-7+b1_arm64.deb ... Unpacking binfmt-support (2.2.2-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../10-libpython3.13-minimal_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../11-python3.13-minimal_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21354 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_arm64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.8-2_arm64.deb ... Unpacking libffi8:arm64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22366 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.3-1_arm64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-8_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-8) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-8_arm64.deb ... Unpacking procps (2:4.0.4-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.5.0-1_arm64.deb ... Unpacking openssl (3.5.0-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../007-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package libpam-systemd:arm64. Preparing to unpack .../012-libpam-systemd_257.5-2_arm64.deb ... Unpacking libpam-systemd:arm64 (257.5-2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../015-libtext-charwidth-perl_0.04-11+b4_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../016-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../017-ucf_3.0051_all.deb ... Moving old data out of the way Unpacking ucf (3.0051) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../018-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../019-libglib2.0-0t64_2.84.1-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.84.1-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../020-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../021-shared-mime-info_2.4-5+b2_arm64.deb ... Unpacking shared-mime-info (2.4-5+b2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../022-libjpeg62-turbo_1%3a2.1.5-3.1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../023-libpng16-16t64_1.6.47-1.1_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.47-1.1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../024-libdeflate0_1.23-2_arm64.deb ... Unpacking libdeflate0:arm64 (1.23-2) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../025-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../026-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../027-libsharpyuv0_1.5.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../028-libwebp7_1.5.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../029-libtiff6_4.7.0-3_arm64.deb ... Unpacking libtiff6:arm64 (4.7.0-3) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. Preparing to unpack .../030-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_arm64.deb ... Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../031-gtk-update-icon-cache_4.18.4+ds-2_arm64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.18.4+ds-2) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../032-hicolor-icon-theme_0.18-2_all.deb ... Unpacking hicolor-icon-theme (0.18-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../033-adwaita-icon-theme_48.0-1_all.deb ... Unpacking adwaita-icon-theme (48.0-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../034-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../035-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../036-liblcms2-2_2.16-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.16-2) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../037-libnspr4_2%3a4.36-1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.36-1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../038-libnss3_2%3a3.110-1_arm64.deb ... Unpacking libnss3:arm64 (2:3.110-1) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../039-libpcsclite1_2.3.3-1_arm64.deb ... Unpacking libpcsclite1:arm64 (2.3.3-1) ... Selecting previously unselected package openjdk-21-jre-headless:arm64. Preparing to unpack .../040-openjdk-21-jre-headless_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jre-headless:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../041-default-jre-headless_2%3a1.21-76_arm64.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../042-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package ant-contrib. Preparing to unpack .../043-ant-contrib_1.0~b3+svn177-12_all.deb ... Unpacking ant-contrib (1.0~b3+svn177-12) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../044-at-spi2-common_2.56.1-2_all.deb ... Unpacking at-spi2-common (2.56.1-2) ... Selecting previously unselected package m4. Preparing to unpack .../045-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../046-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../047-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../048-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../049-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package dbus-user-session. Preparing to unpack .../050-dbus-user-session_1.16.2-2_arm64.deb ... Unpacking dbus-user-session (1.16.2-2) ... Selecting previously unselected package libdconf1:arm64. Preparing to unpack .../051-libdconf1_0.40.0-5_arm64.deb ... Unpacking libdconf1:arm64 (0.40.0-5) ... Selecting previously unselected package dconf-service. Preparing to unpack .../052-dconf-service_0.40.0-5_arm64.deb ... Unpacking dconf-service (0.40.0-5) ... Selecting previously unselected package dconf-gsettings-backend:arm64. Preparing to unpack .../053-dconf-gsettings-backend_0.40.0-5_arm64.deb ... Unpacking dconf-gsettings-backend:arm64 (0.40.0-5) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../054-dctrl-tools_2.24-3+b1_arm64.deb ... Unpacking dctrl-tools (2.24-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../055-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../056-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../057-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../058-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../059-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../060-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../061-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../062-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../063-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package gettext. Preparing to unpack .../064-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../065-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../066-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../067-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libatk1.0-0t64:arm64. Preparing to unpack .../068-libatk1.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatk1.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../069-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../070-libxdmcp6_1%3a1.1.5-1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../071-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../072-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../073-libx11-6_2%3a1.8.12-1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.12-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../074-libxext6_2%3a1.3.4-1+b3_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../075-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libatspi2.0-0t64:arm64. Preparing to unpack .../076-libatspi2.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatspi2.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libatk-bridge2.0-0t64:arm64. Preparing to unpack .../077-libatk-bridge2.0-0t64_2.56.1-2_arm64.deb ... Unpacking libatk-bridge2.0-0t64:arm64 (2.56.1-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../078-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../079-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../080-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../081-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../082-fontconfig-config_2.15.0-2.3_arm64.deb ... Unpacking fontconfig-config (2.15.0-2.3) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../083-libfontconfig1_2.15.0-2.3_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-2.3) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../084-libpixman-1-0_0.44.0-3_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.44.0-3) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../085-libxcb-render0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../086-libxcb-shm0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../087-libxrender1_1%3a0.9.12-1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.12-1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../088-libcairo2_1.18.4-1+b1_arm64.deb ... Unpacking libcairo2:arm64 (1.18.4-1+b1) ... Selecting previously unselected package libcairo-gobject2:arm64. Preparing to unpack .../089-libcairo-gobject2_1.18.4-1+b1_arm64.deb ... Unpacking libcairo-gobject2:arm64 (1.18.4-1+b1) ... Selecting previously unselected package libcloudproviders0:arm64. Preparing to unpack .../090-libcloudproviders0_0.3.6-2_arm64.deb ... Unpacking libcloudproviders0:arm64 (0.3.6-2) ... Selecting previously unselected package libcolord2:arm64. Preparing to unpack .../091-libcolord2_1.4.7-3_arm64.deb ... Unpacking libcolord2:arm64 (1.4.7-3) ... Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../092-libavahi-common-data_0.8-16_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-16) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../093-libavahi-common3_0.8-16_arm64.deb ... Unpacking libavahi-common3:arm64 (0.8-16) ... Selecting previously unselected package libavahi-client3:arm64. Preparing to unpack .../094-libavahi-client3_0.8-16_arm64.deb ... Unpacking libavahi-client3:arm64 (0.8-16) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../095-libidn2-0_2.3.8-2_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-2) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../096-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../097-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../098-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../099-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../100-libcom-err2_1.47.2-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../101-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../102-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../103-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../104-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libcups2t64:arm64. Preparing to unpack .../105-libcups2t64_2.4.10-2+b1_arm64.deb ... Unpacking libcups2t64:arm64 (2.4.10-2+b1) ... Selecting previously unselected package libepoxy0:arm64. Preparing to unpack .../106-libepoxy0_1.5.10-2_arm64.deb ... Unpacking libepoxy0:arm64 (1.5.10-2) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../107-libfribidi0_1.0.16-1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.16-1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../108-libgraphite2-3_1.3.14-2+b1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../109-libharfbuzz0b_10.2.0-1+b1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.2.0-1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../110-fontconfig_2.15.0-2.3_arm64.deb ... Unpacking fontconfig (2.15.0-2.3) ... Selecting previously unselected package libthai-data. Preparing to unpack .../111-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../112-libdatrie1_0.2.13-3+b1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3+b1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../113-libthai0_0.1.29-2+b1_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../114-libpango-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../115-libpangoft2-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../116-libpangocairo-1.0-0_1.56.3-1_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1) ... Selecting previously unselected package libwayland-client0:arm64. Preparing to unpack .../117-libwayland-client0_1.23.1-3_arm64.deb ... Unpacking libwayland-client0:arm64 (1.23.1-3) ... Selecting previously unselected package libwayland-cursor0:arm64. Preparing to unpack .../118-libwayland-cursor0_1.23.1-3_arm64.deb ... Unpacking libwayland-cursor0:arm64 (1.23.1-3) ... Selecting previously unselected package libwayland-egl1:arm64. Preparing to unpack .../119-libwayland-egl1_1.23.1-3_arm64.deb ... Unpacking libwayland-egl1:arm64 (1.23.1-3) ... Selecting previously unselected package libxcomposite1:arm64. Preparing to unpack .../120-libxcomposite1_1%3a0.4.6-1_arm64.deb ... Unpacking libxcomposite1:arm64 (1:0.4.6-1) ... Selecting previously unselected package libxfixes3:arm64. Preparing to unpack .../121-libxfixes3_1%3a6.0.0-2+b4_arm64.deb ... Unpacking libxfixes3:arm64 (1:6.0.0-2+b4) ... Selecting previously unselected package libxcursor1:arm64. Preparing to unpack .../122-libxcursor1_1%3a1.2.3-1_arm64.deb ... Unpacking libxcursor1:arm64 (1:1.2.3-1) ... Selecting previously unselected package libxdamage1:arm64. Preparing to unpack .../123-libxdamage1_1%3a1.1.6-1+b2_arm64.deb ... Unpacking libxdamage1:arm64 (1:1.1.6-1+b2) ... Selecting previously unselected package libxinerama1:arm64. Preparing to unpack .../124-libxinerama1_2%3a1.1.4-3+b4_arm64.deb ... Unpacking libxinerama1:arm64 (2:1.1.4-3+b4) ... Selecting previously unselected package xkb-data. Preparing to unpack .../125-xkb-data_2.42-1_all.deb ... Unpacking xkb-data (2.42-1) ... Selecting previously unselected package libxkbcommon0:arm64. Preparing to unpack .../126-libxkbcommon0_1.7.0-2_arm64.deb ... Unpacking libxkbcommon0:arm64 (1.7.0-2) ... Selecting previously unselected package libxrandr2:arm64. Preparing to unpack .../127-libxrandr2_2%3a1.5.4-1+b3_arm64.deb ... Unpacking libxrandr2:arm64 (2:1.5.4-1+b3) ... Selecting previously unselected package libgtk-3-common. Preparing to unpack .../128-libgtk-3-common_3.24.49-3_all.deb ... Unpacking libgtk-3-common (3.24.49-3) ... Selecting previously unselected package libgtk-3-0t64:arm64. Preparing to unpack .../129-libgtk-3-0t64_3.24.49-3_arm64.deb ... Unpacking libgtk-3-0t64:arm64 (3.24.49-3) ... Selecting previously unselected package libglvnd0:arm64. Preparing to unpack .../130-libglvnd0_1.7.0-1+b2_arm64.deb ... Unpacking libglvnd0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../131-libdrm-common_2.4.124-2_all.deb ... Unpacking libdrm-common (2.4.124-2) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../132-libdrm2_2.4.124-2_arm64.deb ... Unpacking libdrm2:arm64 (2.4.124-2) ... Selecting previously unselected package libx11-xcb1:arm64. Preparing to unpack .../133-libx11-xcb1_2%3a1.8.12-1_arm64.deb ... Unpacking libx11-xcb1:arm64 (2:1.8.12-1) ... Selecting previously unselected package libxcb-dri3-0:arm64. Preparing to unpack .../134-libxcb-dri3-0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-glx0:arm64. Preparing to unpack .../135-libxcb-glx0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-glx0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-present0:arm64. Preparing to unpack .../136-libxcb-present0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-present0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-xfixes0:arm64. Preparing to unpack .../137-libxcb-xfixes0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxxf86vm1:arm64. Preparing to unpack .../138-libxxf86vm1_1%3a1.1.4-1+b4_arm64.deb ... Unpacking libxxf86vm1:arm64 (1:1.1.4-1+b4) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../139-libdrm-amdgpu1_2.4.124-2_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.124-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../140-libedit2_3.1-20250104-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20250104-1) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../141-libz3-4_4.13.3-1_arm64.deb ... Unpacking libz3-4:arm64 (4.13.3-1) ... Selecting previously unselected package libllvm19:arm64. Preparing to unpack .../142-libllvm19_1%3a19.1.7-3_arm64.deb ... Unpacking libllvm19:arm64 (1:19.1.7-3) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../143-libsensors-config_1%3a3.6.2-2_all.deb ... Unpacking libsensors-config (1:3.6.2-2) ... Selecting previously unselected package libsensors5:arm64. Preparing to unpack .../144-libsensors5_1%3a3.6.2-2_arm64.deb ... Unpacking libsensors5:arm64 (1:3.6.2-2) ... Selecting previously unselected package libxcb-randr0:arm64. Preparing to unpack .../145-libxcb-randr0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-randr0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-sync1:arm64. Preparing to unpack .../146-libxcb-sync1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-sync1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxshmfence1:arm64. Preparing to unpack .../147-libxshmfence1_1.3.3-1_arm64.deb ... Unpacking libxshmfence1:arm64 (1.3.3-1) ... Selecting previously unselected package mesa-libgallium:arm64. Preparing to unpack .../148-mesa-libgallium_25.0.4-1_arm64.deb ... Unpacking mesa-libgallium:arm64 (25.0.4-1) ... Selecting previously unselected package libwayland-server0:arm64. Preparing to unpack .../149-libwayland-server0_1.23.1-3_arm64.deb ... Unpacking libwayland-server0:arm64 (1.23.1-3) ... Selecting previously unselected package libgbm1:arm64. Preparing to unpack .../150-libgbm1_25.0.4-1_arm64.deb ... Unpacking libgbm1:arm64 (25.0.4-1) ... Selecting previously unselected package libvulkan1:arm64. Preparing to unpack .../151-libvulkan1_1.4.309.0-1_arm64.deb ... Unpacking libvulkan1:arm64 (1.4.309.0-1) ... Selecting previously unselected package libgl1-mesa-dri:arm64. Preparing to unpack .../152-libgl1-mesa-dri_25.0.4-1_arm64.deb ... Unpacking libgl1-mesa-dri:arm64 (25.0.4-1) ... Selecting previously unselected package libglx-mesa0:arm64. Preparing to unpack .../153-libglx-mesa0_25.0.4-1_arm64.deb ... Unpacking libglx-mesa0:arm64 (25.0.4-1) ... Selecting previously unselected package libglx0:arm64. Preparing to unpack .../154-libglx0_1.7.0-1+b2_arm64.deb ... Unpacking libglx0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libgl1:arm64. Preparing to unpack .../155-libgl1_1.7.0-1+b2_arm64.deb ... Unpacking libgl1:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../156-libasound2-data_1.2.14-1_all.deb ... Unpacking libasound2-data (1.2.14-1) ... Selecting previously unselected package libasound2t64:arm64. Preparing to unpack .../157-libasound2t64_1.2.14-1_arm64.deb ... Unpacking libasound2t64:arm64 (1.2.14-1) ... Selecting previously unselected package libgif7:arm64. Preparing to unpack .../158-libgif7_5.2.2-1+b1_arm64.deb ... Unpacking libgif7:arm64 (5.2.2-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../159-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package libxtst6:arm64. Preparing to unpack .../160-libxtst6_2%3a1.2.5-1_arm64.deb ... Unpacking libxtst6:arm64 (2:1.2.5-1) ... Selecting previously unselected package openjdk-21-jre:arm64. Preparing to unpack .../161-openjdk-21-jre_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jre:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jre. Preparing to unpack .../162-default-jre_2%3a1.21-76_arm64.deb ... Unpacking default-jre (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk-headless:arm64. Preparing to unpack .../163-openjdk-21-jdk-headless_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jdk-headless:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../164-default-jdk-headless_2%3a1.21-76_arm64.deb ... Unpacking default-jdk-headless (2:1.21-76) ... Selecting previously unselected package openjdk-21-jdk:arm64. Preparing to unpack .../165-openjdk-21-jdk_21.0.7+6-1_arm64.deb ... Unpacking openjdk-21-jdk:arm64 (21.0.7+6-1) ... Selecting previously unselected package default-jdk. Preparing to unpack .../166-default-jdk_2%3a1.21-76_arm64.deb ... Unpacking default-jdk (2:1.21-76) ... Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../167-libgpg-error0_1.51-4_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-4) ... Selecting previously unselected package libassuan9:arm64. Preparing to unpack .../168-libassuan9_3.0.2-2_arm64.deb ... Unpacking libassuan9:arm64 (3.0.2-2) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../169-libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../170-gpgconf_2.4.7-16_arm64.deb ... Unpacking gpgconf (2.4.7-16) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../171-libksba8_1.6.7-2+b1_arm64.deb ... Unpacking libksba8:arm64 (1.6.7-2+b1) ... Selecting previously unselected package libnpth0t64:arm64. Preparing to unpack .../172-libnpth0t64_1.8-3_arm64.deb ... Unpacking libnpth0t64:arm64 (1.8-3) ... Selecting previously unselected package gpg. Preparing to unpack .../173-gpg_2.4.7-16_arm64.deb ... Unpacking gpg (2.4.7-16) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../174-pinentry-curses_1.3.1-2_arm64.deb ... Unpacking pinentry-curses (1.3.1-2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../175-gpg-agent_2.4.7-16_arm64.deb ... Unpacking gpg-agent (2.4.7-16) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../176-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../177-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../178-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../179-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../180-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../181-libclass-xsaccessor-perl_1.19-4+b5_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b5) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../182-libb-hooks-op-check-perl_0.22-3+b2_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../183-libdynaloader-functions-perl_0.004-2_all.deb ... Unpacking libdynaloader-functions-perl (0.004-2) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../184-libdevel-callchecker-perl_0.009-2_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.009-2) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../185-libparams-classify-perl_0.015-2+b4_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b4) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../186-libmodule-runtime-perl_0.018-1_all.deb ... Unpacking libmodule-runtime-perl (0.018-1) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../187-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../188-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../189-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../190-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../191-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../192-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../193-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../194-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../195-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../196-liburi-perl_5.30-1_all.deb ... Unpacking liburi-perl (5.30-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../197-libhtml-parser-perl_3.83-1+b2_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.83-1+b2) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../198-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../199-libclone-perl_0.47-1+b1_arm64.deb ... Unpacking libclone-perl:arm64 (0.47-1+b1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../200-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../201-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../202-libhttp-message-perl_7.00-2_all.deb ... Unpacking libhttp-message-perl (7.00-2) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../203-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../204-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:arm64. Preparing to unpack .../205-perl-openssl-defaults_7+b2_arm64.deb ... Unpacking perl-openssl-defaults:arm64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:arm64. Preparing to unpack .../206-libnet-ssleay-perl_1.94-3_arm64.deb ... Unpacking libnet-ssleay-perl:arm64 (1.94-3) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../207-libio-socket-ssl-perl_2.089-1_all.deb ... Unpacking libio-socket-ssl-perl (2.089-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../208-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../209-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../210-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../211-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../212-libwww-perl_6.78-1_all.deb ... Unpacking libwww-perl (6.78-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../213-patchutils_0.4.2-1+b1_arm64.deb ... Unpacking patchutils (0.4.2-1+b1) ... Selecting previously unselected package gpgv. Preparing to unpack .../214-gpgv_2.4.7-16_arm64.deb ... Unpacking gpgv (2.4.7-16) ... Selecting previously unselected package sopv-gpgv. Preparing to unpack .../215-sopv-gpgv_0.1.4-1_all.deb ... Unpacking sopv-gpgv (0.1.4-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../216-wdiff_1.2.2-9_arm64.deb ... Unpacking wdiff (1.2.2-9) ... Selecting previously unselected package devscripts. Preparing to unpack .../217-devscripts_2.25.10_all.deb ... Unpacking devscripts (2.25.10) ... Selecting previously unselected package fastjar. Preparing to unpack .../218-fastjar_2%3a0.98-7+b1_arm64.deb ... Unpacking fastjar (2:0.98-7+b1) ... Selecting previously unselected package jarwrapper. Preparing to unpack .../219-jarwrapper_0.80_all.deb ... Unpacking jarwrapper (0.80) ... Selecting previously unselected package javahelper. Preparing to unpack .../220-javahelper_0.80_all.deb ... Unpacking javahelper (0.80) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../221-libhamcrest-java_2.2-2_all.deb ... Unpacking libhamcrest-java (2.2-2) ... Selecting previously unselected package junit4. Preparing to unpack .../222-junit4_4.13.2-5_all.deb ... Unpacking junit4 (4.13.2-5) ... Selecting previously unselected package libapiguardian-java. Preparing to unpack .../223-libapiguardian-java_1.1.2-1_all.deb ... Unpacking libapiguardian-java (1.1.2-1) ... Selecting previously unselected package libopentest4j-java. Preparing to unpack .../224-libopentest4j-java_1.2.0-4_all.deb ... Unpacking libopentest4j-java (1.2.0-4) ... Selecting previously unselected package libopentest4j-reporting-java. Preparing to unpack .../225-libopentest4j-reporting-java_0.1.0-M1-2_all.deb ... Unpacking libopentest4j-reporting-java (0.1.0-M1-2) ... Selecting previously unselected package libpicocli-java. Preparing to unpack .../226-libpicocli-java_4.6.2-2_all.deb ... Unpacking libpicocli-java (4.6.2-2) ... Selecting previously unselected package libunivocity-parsers-java. Preparing to unpack .../227-libunivocity-parsers-java_2.9.1-1_all.deb ... Unpacking libunivocity-parsers-java (2.9.1-1) ... Selecting previously unselected package junit5. Preparing to unpack .../228-junit5_5.10.3-1_all.deb ... Unpacking junit5 (5.10.3-1) ... Selecting previously unselected package libactivation-java. Preparing to unpack .../229-libactivation-java_1.2.0-2_all.deb ... Unpacking libactivation-java (1.2.0-2) ... Selecting previously unselected package libaopalliance-java. Preparing to unpack .../230-libaopalliance-java_20070526-7_all.deb ... Unpacking libaopalliance-java (20070526-7) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../231-libapache-pom-java_33-2_all.deb ... Unpacking libapache-pom-java (33-2) ... Selecting previously unselected package libasm-java. Preparing to unpack .../232-libasm-java_9.8-1_all.deb ... Unpacking libasm-java (9.8-1) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../233-libatinject-jsr330-api-java_1.0+ds1-6_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-6) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../234-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-lang3-java. Preparing to unpack .../235-libcommons-lang3-java_3.17.0-1_all.deb ... Unpacking libcommons-lang3-java (3.17.0-1) ... Selecting previously unselected package libfreemarker-java. Preparing to unpack .../236-libfreemarker-java_2.3.32-2.1_all.deb ... Unpacking libfreemarker-java (2.3.32-2.1) ... Selecting previously unselected package libgoogle-gson-java. Preparing to unpack .../237-libgoogle-gson-java_2.10.1-1_all.deb ... Unpacking libgoogle-gson-java (2.10.1-1) ... Selecting previously unselected package libjoptsimple-java. Preparing to unpack .../238-libjoptsimple-java_5.0.4-7_all.deb ... Unpacking libjoptsimple-java (5.0.4-7) ... Selecting previously unselected package libcommons-codec-java. Preparing to unpack .../239-libcommons-codec-java_1.18.0-1_all.deb ... Unpacking libcommons-codec-java (1.18.0-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../240-libcommons-logging-java_1.3.0-1_all.deb ... Unpacking libcommons-logging-java (1.3.0-1) ... Selecting previously unselected package libhttpcore-java. Preparing to unpack .../241-libhttpcore-java_4.4.16-1_all.deb ... Unpacking libhttpcore-java (4.4.16-1) ... Selecting previously unselected package libhttpclient-java. Preparing to unpack .../242-libhttpclient-java_4.5.14-1_all.deb ... Unpacking libhttpclient-java (4.5.14-1) ... Selecting previously unselected package liblightcouch-java. Preparing to unpack .../243-liblightcouch-java_0.2.0-1_all.deb ... Unpacking liblightcouch-java (0.2.0-1) ... Selecting previously unselected package libmongodb-java. Preparing to unpack .../244-libmongodb-java_3.6.3-2_all.deb ... Unpacking libmongodb-java (3.6.3-2) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../245-libslf4j-java_1.7.32-1_all.deb ... Unpacking libslf4j-java (1.7.32-1) ... Selecting previously unselected package liblog4j2-java. Preparing to unpack .../246-liblog4j2-java_2.19.0-2_all.deb ... Unpacking liblog4j2-java (2.19.0-2) ... Selecting previously unselected package libbarclay-java. Preparing to unpack .../247-libbarclay-java_5.0.0+dfsg-1_all.deb ... Unpacking libbarclay-java (5.0.0+dfsg-1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../248-libblas3_3.12.1-2_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-2) ... Selecting previously unselected package libbsh-java. Preparing to unpack .../249-libbsh-java_2.0b4-20_all.deb ... Unpacking libbsh-java (2.0b4-20) ... Selecting previously unselected package libcommons-io-java. Preparing to unpack .../250-libcommons-io-java_2.19.0-1_all.deb ... Unpacking libcommons-io-java (2.19.0-1) ... Selecting previously unselected package libmaven-shared-utils-java. Preparing to unpack .../251-libmaven-shared-utils-java_3.4.2-1_all.deb ... Unpacking libmaven-shared-utils-java (3.4.2-1) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../252-libcommons-cli-java_1.6.0-1_all.deb ... Unpacking libcommons-cli-java (1.6.0-1) ... Selecting previously unselected package libgeronimo-annotation-1.3-spec-java. Preparing to unpack .../253-libgeronimo-annotation-1.3-spec-java_1.3-1_all.deb ... Unpacking libgeronimo-annotation-1.3-spec-java (1.3-1) ... Selecting previously unselected package liberror-prone-java. Preparing to unpack .../254-liberror-prone-java_2.18.0-1_all.deb ... Unpacking liberror-prone-java (2.18.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../255-libjsr305-java_0.1~+svn49-12_all.deb ... Unpacking libjsr305-java (0.1~+svn49-12) ... Selecting previously unselected package libguava-java. Preparing to unpack .../256-libguava-java_32.0.1-1_all.deb ... Unpacking libguava-java (32.0.1-1) ... Selecting previously unselected package libguice-java. Preparing to unpack .../257-libguice-java_5.1.0-1_all.deb ... Unpacking libguice-java (5.1.0-1) ... Selecting previously unselected package libmaven-parent-java. Preparing to unpack .../258-libmaven-parent-java_43-2_all.deb ... Unpacking libmaven-parent-java (43-2) ... Selecting previously unselected package libplexus-utils2-java. Preparing to unpack .../259-libplexus-utils2-java_3.4.2-1_all.deb ... Unpacking libplexus-utils2-java (3.4.2-1) ... Selecting previously unselected package libwagon-provider-api-java. Preparing to unpack .../260-libwagon-provider-api-java_3.5.3-1_all.deb ... Unpacking libwagon-provider-api-java (3.5.3-1) ... Selecting previously unselected package libmaven-resolver-java. Preparing to unpack .../261-libmaven-resolver-java_1.9.22-1_all.deb ... Unpacking libmaven-resolver-java (1.9.22-1) ... Selecting previously unselected package libplexus-cipher-java. Preparing to unpack .../262-libplexus-cipher-java_2.0-1_all.deb ... Unpacking libplexus-cipher-java (2.0-1) ... Selecting previously unselected package libplexus-classworlds-java. Preparing to unpack .../263-libplexus-classworlds-java_2.7.0-1_all.deb ... Unpacking libplexus-classworlds-java (2.7.0-1) ... Selecting previously unselected package libplexus-component-annotations-java. Preparing to unpack .../264-libplexus-component-annotations-java_2.1.1-1_all.deb ... Unpacking libplexus-component-annotations-java (2.1.1-1) ... Selecting previously unselected package libplexus-interpolation-java. Preparing to unpack .../265-libplexus-interpolation-java_1.27-1_all.deb ... Unpacking libplexus-interpolation-java (1.27-1) ... Selecting previously unselected package libplexus-sec-dispatcher-java. Preparing to unpack .../266-libplexus-sec-dispatcher-java_2.0-3_all.deb ... Unpacking libplexus-sec-dispatcher-java (2.0-3) ... Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java. Preparing to unpack .../267-libgeronimo-interceptor-3.0-spec-java_1.0.1-5_all.deb ... Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Selecting previously unselected package libcdi-api-java. Preparing to unpack .../268-libcdi-api-java_1.2-4_all.deb ... Unpacking libcdi-api-java (1.2-4) ... Selecting previously unselected package libsisu-inject-java. Preparing to unpack .../269-libsisu-inject-java_0.3.5-1_all.deb ... Unpacking libsisu-inject-java (0.3.5-1) ... Selecting previously unselected package libsisu-plexus-java. Preparing to unpack .../270-libsisu-plexus-java_0.3.5-1_all.deb ... Unpacking libsisu-plexus-java (0.3.5-1) ... Selecting previously unselected package libmaven3-core-java. Preparing to unpack .../271-libmaven3-core-java_3.9.9-1_all.deb ... Unpacking libmaven3-core-java (3.9.9-1) ... Selecting previously unselected package libmaven-shared-io-java. Preparing to unpack .../272-libmaven-shared-io-java_3.0.0-4_all.deb ... Unpacking libmaven-shared-io-java (3.0.0-4) ... Selecting previously unselected package libmaven-file-management-java. Preparing to unpack .../273-libmaven-file-management-java_3.0.0-2_all.deb ... Unpacking libmaven-file-management-java (3.0.0-2) ... Selecting previously unselected package libbuild-helper-maven-plugin-java. Preparing to unpack .../274-libbuild-helper-maven-plugin-java_3.3.0-1_all.deb ... Unpacking libbuild-helper-maven-plugin-java (3.3.0-1) ... Selecting previously unselected package libbyte-buddy-java. Preparing to unpack .../275-libbyte-buddy-java_1.14.19-1_all.deb ... Unpacking libbyte-buddy-java (1.14.19-1) ... Selecting previously unselected package libcolt-free-java. Preparing to unpack .../276-libcolt-free-java_1.2.0+dfsg-8_all.deb ... Unpacking libcolt-free-java (1.2.0+dfsg-8) ... Selecting previously unselected package libcommons-collections3-java. Preparing to unpack .../277-libcommons-collections3-java_3.2.2-3_all.deb ... Unpacking libcommons-collections3-java (3.2.2-3) ... Selecting previously unselected package libcommons-beanutils-java. Preparing to unpack .../278-libcommons-beanutils-java_1.10.1-1_all.deb ... Unpacking libcommons-beanutils-java (1.10.1-1) ... Selecting previously unselected package libcommons-collections4-java. Preparing to unpack .../279-libcommons-collections4-java_4.4-2_all.deb ... Unpacking libcommons-collections4-java (4.4-2) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../280-libcommons-compress-java_1.27.1-2_all.deb ... Unpacking libcommons-compress-java (1.27.1-2) ... Selecting previously unselected package libcommons-lang-java. Preparing to unpack .../281-libcommons-lang-java_2.6-10_all.deb ... Unpacking libcommons-lang-java (2.6-10) ... Selecting previously unselected package libcommons-configuration-java. Preparing to unpack .../282-libcommons-configuration-java_1.10-7_all.deb ... Unpacking libcommons-configuration-java (1.10-7) ... Selecting previously unselected package libcommons-digester-java. Preparing to unpack .../283-libcommons-digester-java_1.8.1-7_all.deb ... Unpacking libcommons-digester-java (1.8.1-7) ... Selecting previously unselected package libcommons-exec-java. Preparing to unpack .../284-libcommons-exec-java_1.3-2_all.deb ... Unpacking libcommons-exec-java (1.3-2) ... Selecting previously unselected package libcommons-jexl2-java. Preparing to unpack .../285-libcommons-jexl2-java_2.1.1-6_all.deb ... Unpacking libcommons-jexl2-java (2.1.1-6) ... Selecting previously unselected package libcommons-math-java. Preparing to unpack .../286-libcommons-math-java_2.2-9_all.deb ... Unpacking libcommons-math-java (2.2-9) ... Selecting previously unselected package libcommons-math3-java. Preparing to unpack .../287-libcommons-math3-java_3.6.1-4_all.deb ... Unpacking libcommons-math3-java (3.6.1-4) ... Selecting previously unselected package libplexus-io-java. Preparing to unpack .../288-libplexus-io-java_3.3.1-2_all.deb ... Unpacking libplexus-io-java (3.3.1-2) ... Selecting previously unselected package libsnappy1v5:arm64. Preparing to unpack .../289-libsnappy1v5_1.2.2-1_arm64.deb ... Unpacking libsnappy1v5:arm64 (1.2.2-1) ... Selecting previously unselected package libsnappy-jni. Preparing to unpack .../290-libsnappy-jni_1.1.10.7-1_arm64.deb ... Unpacking libsnappy-jni (1.1.10.7-1) ... Selecting previously unselected package libsnappy-java. Preparing to unpack .../291-libsnappy-java_1.1.10.7-1_all.deb ... Unpacking libsnappy-java (1.1.10.7-1) ... Selecting previously unselected package libxz-java. Preparing to unpack .../292-libxz-java_1.9-1_all.deb ... Unpacking libxz-java (1.9-1) ... Selecting previously unselected package libplexus-archiver-java. Preparing to unpack .../293-libplexus-archiver-java_4.6.1-1_all.deb ... Unpacking libplexus-archiver-java (4.6.1-1) ... Selecting previously unselected package libmaven-archiver-java. Preparing to unpack .../294-libmaven-archiver-java_3.6.2-1_all.deb ... Unpacking libmaven-archiver-java (3.6.2-1) ... Selecting previously unselected package libmaven-jar-plugin-java. Preparing to unpack .../295-libmaven-jar-plugin-java_3.3.0-2_all.deb ... Unpacking libmaven-jar-plugin-java (3.3.0-2) ... Selecting previously unselected package libcommons-text-java. Preparing to unpack .../296-libcommons-text-java_1.13.1-1_all.deb ... Unpacking libcommons-text-java (1.13.1-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../297-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package libcommons-validator-java. Preparing to unpack .../298-libcommons-validator-java_1%3a1.9.0-1_all.deb ... Unpacking libcommons-validator-java (1:1.9.0-1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../299-libsasl2-modules-db_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../300-libsasl2-2_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../301-libldap2_2.6.9+dfsg-2_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-2) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../302-libnghttp2-14_1.64.0-1.1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../303-libnghttp3-9_1.8.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.8.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../304-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../305-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../306-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../307-libcurl4t64_8.13.0-5_arm64.deb ... Unpacking libcurl4t64:arm64 (8.13.0-5) ... Selecting previously unselected package libdistlib-java. Preparing to unpack .../308-libdistlib-java_1.0-5_all.deb ... Unpacking libdistlib-java (1.0-5) ... Selecting previously unselected package libjaxen-java. Preparing to unpack .../309-libjaxen-java_1.1.6-5_all.deb ... Unpacking libjaxen-java (1.1.6-5) ... Selecting previously unselected package libdom4j-java. Preparing to unpack .../310-libdom4j-java_2.1.4-1_all.deb ... Unpacking libdom4j-java (2.1.4-1) ... Selecting previously unselected package libdoxia-core-java. Preparing to unpack .../311-libdoxia-core-java_2.0.0-1_all.deb ... Unpacking libdoxia-core-java (2.0.0-1) ... Selecting previously unselected package libplexus-xml-java. Preparing to unpack .../312-libplexus-xml-java_3.0.1-2_all.deb ... Unpacking libplexus-xml-java (3.0.1-2) ... Selecting previously unselected package libdoxia-java. Preparing to unpack .../313-libdoxia-java_2.0.0-1_all.deb ... Unpacking libdoxia-java (2.0.0-1) ... Selecting previously unselected package libmaven-reporting-api-java. Preparing to unpack .../314-libmaven-reporting-api-java_4.0.0-1_all.deb ... Unpacking libmaven-reporting-api-java (4.0.0-1) ... Selecting previously unselected package libxbean-reflect-java. Preparing to unpack .../315-libxbean-reflect-java_4.5-9_all.deb ... Unpacking libxbean-reflect-java (4.5-9) ... Selecting previously unselected package libplexus-container-default-java. Preparing to unpack .../316-libplexus-container-default-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default-java (2.1.1-1) ... Selecting previously unselected package libplexus-i18n-java. Preparing to unpack .../317-libplexus-i18n-java_1.0-beta-10-6_all.deb ... Unpacking libplexus-i18n-java (1.0-beta-10-6) ... Selecting previously unselected package velocity. Preparing to unpack .../318-velocity_1.7-7_all.deb ... Unpacking velocity (1.7-7) ... Selecting previously unselected package libplexus-velocity-java. Preparing to unpack .../319-libplexus-velocity-java_1.2-4_all.deb ... Unpacking libplexus-velocity-java (1.2-4) ... Selecting previously unselected package liboro-java. Preparing to unpack .../320-liboro-java_2.0.8a-14_all.deb ... Unpacking liboro-java (2.0.8a-14) ... Selecting previously unselected package libvelocity-tools-java. Preparing to unpack .../321-libvelocity-tools-java_2.0-9_all.deb ... Unpacking libvelocity-tools-java (2.0-9) ... Selecting previously unselected package libdoxia-sitetools-java. Preparing to unpack .../322-libdoxia-sitetools-java_2.0.0-1_all.deb ... Unpacking libdoxia-sitetools-java (2.0.0-1) ... Selecting previously unselected package libfastutil-java. Preparing to unpack .../323-libfastutil-java_8.5.15+dfsg-1_all.deb ... Unpacking libfastutil-java (8.5.15+dfsg-1) ... Selecting previously unselected package libxpp3-java. Preparing to unpack .../324-libxpp3-java_1.1.4c-4_all.deb ... Unpacking libxpp3-java (1.1.4c-4) ... Selecting previously unselected package libxstream-java. Preparing to unpack .../325-libxstream-java_1.4.21-1_all.deb ... Unpacking libxstream-java (1.4.21-1) ... Selecting previously unselected package libjsap-java. Preparing to unpack .../326-libjsap-java_2.1-5_all.deb ... Unpacking libjsap-java (2.1-5) ... Selecting previously unselected package liblogback-java. Preparing to unpack .../327-liblogback-java_1%3a1.2.11-6_all.deb ... Unpacking liblogback-java (1:1.2.11-6) ... Selecting previously unselected package libdsiutils-java. Preparing to unpack .../328-libdsiutils-java_2.7.3+dfsg-1_all.deb ... Unpacking libdsiutils-java (2.7.3+dfsg-1) ... Selecting previously unselected package libobjenesis-java. Preparing to unpack .../329-libobjenesis-java_3.4-2_all.deb ... Unpacking libobjenesis-java (3.4-2) ... Selecting previously unselected package libeasymock-java. Preparing to unpack .../330-libeasymock-java_5.5.0-1_all.deb ... Unpacking libeasymock-java (5.5.0-1) ... Selecting previously unselected package libel-api-java. Preparing to unpack .../331-libel-api-java_3.0.0-3_all.deb ... Unpacking libel-api-java (3.0.0-3) ... Selecting previously unselected package libexec-maven-plugin-java. Preparing to unpack .../332-libexec-maven-plugin-java_3.1.0-2_all.deb ... Unpacking libexec-maven-plugin-java (3.1.0-2) ... Selecting previously unselected package libezmorph-java. Preparing to unpack .../333-libezmorph-java_1.0.6-4_all.deb ... Unpacking libezmorph-java (1.0.6-4) ... Selecting previously unselected package libgatk-native-bindings-java. Preparing to unpack .../334-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../335-libgfortran5_14.2.0-19_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-19) ... Selecting previously unselected package libxml-commons-external-java. Preparing to unpack .../336-libxml-commons-external-java_1.4.01-6_all.deb ... Unpacking libxml-commons-external-java (1.4.01-6) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Preparing to unpack .../337-libxml-commons-resolver1.1-java_1.2-11_all.deb ... Unpacking libxml-commons-resolver1.1-java (1.2-11) ... Selecting previously unselected package libxerces2-java. Preparing to unpack .../338-libxerces2-java_2.12.2-1_all.deb ... Unpacking libxerces2-java (2.12.2-1) ... Selecting previously unselected package libxom-java. Preparing to unpack .../339-libxom-java_1.3.9-1_all.deb ... Unpacking libxom-java (1.3.9-1) ... Selecting previously unselected package libjson-java. Preparing to unpack .../340-libjson-java_3.1.0+dfsg-2_all.deb ... Unpacking libjson-java (3.1.0+dfsg-2) ... Selecting previously unselected package libmbedcrypto16:arm64. Preparing to unpack .../341-libmbedcrypto16_3.6.3-1_arm64.deb ... Unpacking libmbedcrypto16:arm64 (3.6.3-1) ... Selecting previously unselected package libmbedx509-7:arm64. Preparing to unpack .../342-libmbedx509-7_3.6.3-1_arm64.deb ... Unpacking libmbedx509-7:arm64 (3.6.3-1) ... Selecting previously unselected package libmbedtls21:arm64. Preparing to unpack .../343-libmbedtls21_3.6.3-1_arm64.deb ... Unpacking libmbedtls21:arm64 (3.6.3-1) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../344-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:arm64. Preparing to unpack .../345-libncbi-vdb3_3.2.1+dfsg-2_arm64.deb ... Unpacking libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-ngs3:arm64. Preparing to unpack .../346-libncbi-ngs3_3.2.1+dfsg-4_arm64.deb ... Unpacking libncbi-ngs3:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package libngs-jni:arm64. Preparing to unpack .../347-libngs-jni_3.2.1+dfsg-4_arm64.deb ... Unpacking libngs-jni:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package libngs-java:arm64. Preparing to unpack .../348-libngs-java_3.2.1+dfsg-4_arm64.deb ... Unpacking libngs-java:arm64 (3.2.1+dfsg-4) ... Selecting previously unselected package librhino-java. Preparing to unpack .../349-librhino-java_1.7.15-1_all.deb ... Unpacking librhino-java (1.7.15-1) ... Selecting previously unselected package libhtsjdk-java. Preparing to unpack .../350-libhtsjdk-java_4.1.3+dfsg-2_all.deb ... Unpacking libhtsjdk-java (4.1.3+dfsg-2) ... Selecting previously unselected package libgkl-java. Preparing to unpack .../351-libgkl-java_0.8.11+dfsg-2_all.deb ... Unpacking libgkl-java (0.8.11+dfsg-2) ... Selecting previously unselected package libicu4j-java. Preparing to unpack .../352-libicu4j-java_73.2-1_all.deb ... Unpacking libicu4j-java (73.2-1) ... Selecting previously unselected package liblog4j1.2-java. Preparing to unpack .../353-liblog4j1.2-java_1.2.17-11_all.deb ... Unpacking liblog4j1.2-java (1.2.17-11) ... Selecting previously unselected package libicb-utils-java. Preparing to unpack .../354-libicb-utils-java_2.0.1+git20161002.afee1d9-5_all.deb ... Unpacking libicb-utils-java (2.0.1+git20161002.afee1d9-5) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../355-libice6_2%3a1.1.1-1_arm64.deb ... Unpacking libice6:arm64 (2:1.1.1-1) ... Selecting previously unselected package libicu76:arm64. Preparing to unpack .../356-libicu76_76.1-3_arm64.deb ... Unpacking libicu76:arm64 (76.1-3) ... Selecting previously unselected package libjansi-java. Preparing to unpack .../357-libjansi-java_2.4.1-2_all.deb ... Unpacking libjansi-java (2.4.1-2) ... Selecting previously unselected package libjavassist-java. Preparing to unpack .../358-libjavassist-java_1%3a3.27.0-1_all.deb ... Unpacking libjavassist-java (1:3.27.0-1) ... Selecting previously unselected package libjaxb-api-java. Preparing to unpack .../359-libjaxb-api-java_2.3.1-1_all.deb ... Unpacking libjaxb-api-java (2.3.1-1) ... Selecting previously unselected package libjboss-logging-java. Preparing to unpack .../360-libjboss-logging-java_3.5.3-1_all.deb ... Unpacking libjboss-logging-java (3.5.3-1) ... Selecting previously unselected package libjboss-vfs-java. Preparing to unpack .../361-libjboss-vfs-java_3.2.15.Final-3_all.deb ... Unpacking libjboss-vfs-java (3.2.15.Final-3) ... Selecting previously unselected package libjbzip2-java. Preparing to unpack .../362-libjbzip2-java_0.9.1-8_all.deb ... Unpacking libjbzip2-java (0.9.1-8) ... Selecting previously unselected package libjcommander-java. Preparing to unpack .../363-libjcommander-java_1.71-4_all.deb ... Unpacking libjcommander-java (1.71-4) ... Selecting previously unselected package libjsp-api-java. Preparing to unpack .../364-libjsp-api-java_2.3.4-3_all.deb ... Unpacking libjsp-api-java (2.3.4-3) ... Selecting previously unselected package libservlet-api-java. Preparing to unpack .../365-libservlet-api-java_4.0.1-2_all.deb ... Unpacking libservlet-api-java (4.0.1-2) ... Selecting previously unselected package libwebsocket-api-java. Preparing to unpack .../366-libwebsocket-api-java_1.1-2_all.deb ... Unpacking libwebsocket-api-java (1.1-2) ... Selecting previously unselected package libjetty9-java. Preparing to unpack .../367-libjetty9-java_9.4.57-1_all.deb ... Unpacking libjetty9-java (9.4.57-1) ... Selecting previously unselected package libjsoup-java. Preparing to unpack .../368-libjsoup-java_1.15.3-1_all.deb ... Unpacking libjsoup-java (1.15.3-1) ... Selecting previously unselected package libjtidy-java. Preparing to unpack .../369-libjtidy-java_7+svn20110807-6_all.deb ... Unpacking libjtidy-java (7+svn20110807-6) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../370-liblapack3_3.12.1-2_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-2) ... Selecting previously unselected package libmaven-antrun-plugin-java. Preparing to unpack .../371-libmaven-antrun-plugin-java_3.1.0-1_all.deb ... Unpacking libmaven-antrun-plugin-java (3.1.0-1) ... Selecting previously unselected package libmaven-common-artifact-filters-java. Preparing to unpack .../372-libmaven-common-artifact-filters-java_3.4.0-1_all.deb ... Unpacking libmaven-common-artifact-filters-java (3.4.0-1) ... Selecting previously unselected package libmaven-artifact-transfer-java. Preparing to unpack .../373-libmaven-artifact-transfer-java_0.13.1-2_all.deb ... Unpacking libmaven-artifact-transfer-java (0.13.1-2) ... Selecting previously unselected package libplexus-build-api-java. Preparing to unpack .../374-libplexus-build-api-java_0.0.7-4_all.deb ... Unpacking libplexus-build-api-java (0.0.7-4) ... Selecting previously unselected package libmaven-filtering-java. Preparing to unpack .../375-libmaven-filtering-java_3.4.0-1_all.deb ... Unpacking libmaven-filtering-java (3.4.0-1) ... Selecting previously unselected package libmaven-assembly-plugin-java. Preparing to unpack .../376-libmaven-assembly-plugin-java_3.4.2-2_all.deb ... Unpacking libmaven-assembly-plugin-java (3.4.2-2) ... Selecting previously unselected package libmaven-clean-plugin-java. Preparing to unpack .../377-libmaven-clean-plugin-java_3.2.0-2_all.deb ... Unpacking libmaven-clean-plugin-java (3.2.0-2) ... Selecting previously unselected package libmaven-shared-incremental-java. Preparing to unpack .../378-libmaven-shared-incremental-java_1.1-6_all.deb ... Unpacking libmaven-shared-incremental-java (1.1-6) ... Selecting previously unselected package libplexus-compiler-java. Preparing to unpack .../379-libplexus-compiler-java_2.13.0-1_all.deb ... Unpacking libplexus-compiler-java (2.13.0-1) ... Selecting previously unselected package libqdox2-java. Preparing to unpack .../380-libqdox2-java_2.0.3-1_all.deb ... Unpacking libqdox2-java (2.0.3-1) ... Selecting previously unselected package libplexus-languages-java. Preparing to unpack .../381-libplexus-languages-java_1.1.1-2_all.deb ... Unpacking libplexus-languages-java (1.1.1-2) ... Selecting previously unselected package libmaven-compiler-plugin-java. Preparing to unpack .../382-libmaven-compiler-plugin-java_3.13.0-1_all.deb ... Unpacking libmaven-compiler-plugin-java (3.13.0-1) ... Selecting previously unselected package libmaven-dependency-analyzer-java. Preparing to unpack .../383-libmaven-dependency-analyzer-java_1.15.1-1_all.deb ... Unpacking libmaven-dependency-analyzer-java (1.15.1-1) ... Selecting previously unselected package libmaven-dependency-tree-java. Preparing to unpack .../384-libmaven-dependency-tree-java_3.3.0-1_all.deb ... Unpacking libmaven-dependency-tree-java (3.3.0-1) ... Selecting previously unselected package libmaven-reporting-impl-java. Preparing to unpack .../385-libmaven-reporting-impl-java_4.0.0-1_all.deb ... Unpacking libmaven-reporting-impl-java (4.0.0-1) ... Selecting previously unselected package libmaven-dependency-plugin-java. Preparing to unpack .../386-libmaven-dependency-plugin-java_3.8.1-1_all.deb ... Unpacking libmaven-dependency-plugin-java (3.8.1-1) ... Selecting previously unselected package libmaven-invoker-java. Preparing to unpack .../387-libmaven-invoker-java_3.3.0-1_all.deb ... Unpacking libmaven-invoker-java (3.3.0-1) ... Selecting previously unselected package libplexus-interactivity-api-java. Preparing to unpack .../388-libplexus-interactivity-api-java_1.3-1_all.deb ... Unpacking libplexus-interactivity-api-java (1.3-1) ... Selecting previously unselected package libmaven-javadoc-plugin-java. Preparing to unpack .../389-libmaven-javadoc-plugin-java_3.10.1-2_all.deb ... Unpacking libmaven-javadoc-plugin-java (3.10.1-2) ... Selecting previously unselected package libplexus-ant-factory-java. Preparing to unpack .../390-libplexus-ant-factory-java_1.0~alpha2.1-5_all.deb ... Unpacking libplexus-ant-factory-java (1.0~alpha2.1-5) ... Selecting previously unselected package libplexus-container-default1.5-java. Preparing to unpack .../391-libplexus-container-default1.5-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default1.5-java (2.1.1-1) ... Selecting previously unselected package libplexus-bsh-factory-java. Preparing to unpack .../392-libplexus-bsh-factory-java_1.0~alpha7-5_all.deb ... Unpacking libplexus-bsh-factory-java (1.0~alpha7-5) ... Selecting previously unselected package libmaven-plugin-tools-java. Preparing to unpack .../393-libmaven-plugin-tools-java_3.10.2-2_all.deb ... Unpacking libmaven-plugin-tools-java (3.10.2-2) ... Selecting previously unselected package libmaven-reporting-exec-java. Preparing to unpack .../394-libmaven-reporting-exec-java_2.0.0-1_all.deb ... Unpacking libmaven-reporting-exec-java (2.0.0-1) ... Selecting previously unselected package libmaven-resources-plugin-java. Preparing to unpack .../395-libmaven-resources-plugin-java_3.3.1-1_all.deb ... Unpacking libmaven-resources-plugin-java (3.3.1-1) ... Selecting previously unselected package libmaven-site-plugin-java. Preparing to unpack .../396-libmaven-site-plugin-java_3.21.0-1_all.deb ... Unpacking libmaven-site-plugin-java (3.21.0-1) ... Selecting previously unselected package libmaven-source-plugin-java. Preparing to unpack .../397-libmaven-source-plugin-java_3.3.1-1_all.deb ... Unpacking libmaven-source-plugin-java (3.3.1-1) ... Selecting previously unselected package libpaper2:arm64. Preparing to unpack .../398-libpaper2_2.2.5-0.3+b2_arm64.deb ... Unpacking libpaper2:arm64 (2.2.5-0.3+b2) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../399-libpaper-utils_2.2.5-0.3+b2_arm64.deb ... Unpacking libpaper-utils (2.2.5-0.3+b2) ... Selecting previously unselected package libpicard-java. Preparing to unpack .../400-libpicard-java_3.3.0+dfsg-2_all.deb ... Unpacking libpicard-java (3.3.0+dfsg-2) ... Selecting previously unselected package libpj-java. Preparing to unpack .../401-libpj-java_0.0~20150107+dfsg-5_all.deb ... Unpacking libpj-java (0.0~20150107+dfsg-5) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../402-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../403-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libprotobuf32t64:arm64. Preparing to unpack .../404-libprotobuf32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-lite32t64:arm64. Preparing to unpack .../405-libprotobuf-lite32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf-lite32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-dev:arm64. Preparing to unpack .../406-libprotobuf-dev_3.21.12-10+b6_arm64.deb ... Unpacking libprotobuf-dev:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libprotobuf-java. Preparing to unpack .../407-libprotobuf-java_3.21.12-10_all.deb ... Unpacking libprotobuf-java (3.21.12-10) ... Selecting previously unselected package libprotoc32t64:arm64. Preparing to unpack .../408-libprotoc32t64_3.21.12-10+b6_arm64.deb ... Unpacking libprotoc32t64:arm64 (3.21.12-10+b6) ... Selecting previously unselected package libreflections-java. Preparing to unpack .../409-libreflections-java_0.10.2+dfsg-2_all.deb ... Unpacking libreflections-java (0.10.2+dfsg-2) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../410-libsm6_2%3a1.2.6-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.6-1) ... Selecting previously unselected package libsurefire-java. Preparing to unpack .../411-libsurefire-java_2.22.3-3_all.deb ... Unpacking libsurefire-java (2.22.3-3) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../412-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../413-libtirpc-common_1.3.6+ds-1_all.deb ... Unpacking libtirpc-common (1.3.6+ds-1) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../414-libtirpc3t64_1.3.6+ds-1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.6+ds-1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../415-libxft2_2.3.6-1+b4_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b4) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../416-libxss1_1%3a1.2.3-1+b3_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../417-libtk8.6_8.6.16-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.16-1) ... Selecting previously unselected package libwagon-file-java. Preparing to unpack .../418-libwagon-file-java_3.5.3-1_all.deb ... Unpacking libwagon-file-java (3.5.3-1) ... Selecting previously unselected package libwagon-http-java. Preparing to unpack .../419-libwagon-http-java_3.5.3-1_all.deb ... Unpacking libwagon-http-java (3.5.3-1) ... Selecting previously unselected package libxml2-utils. Preparing to unpack .../420-libxml2-utils_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2-utils (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../421-libxt6t64_1%3a1.2.1-1.2+b2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Selecting previously unselected package maven. Preparing to unpack .../422-maven_3.9.9-1_all.deb ... Unpacking maven (3.9.9-1) ... Selecting previously unselected package maven-repo-helper. Preparing to unpack .../423-maven-repo-helper_1.11_all.deb ... Unpacking maven-repo-helper (1.11) ... Selecting previously unselected package unzip. Preparing to unpack .../424-unzip_6.0-29_arm64.deb ... Unpacking unzip (6.0-29) ... Selecting previously unselected package maven-debian-helper. Preparing to unpack .../425-maven-debian-helper_2.6.7_all.deb ... Unpacking maven-debian-helper (2.6.7) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../426-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../427-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package protobuf-compiler. Preparing to unpack .../428-protobuf-compiler_3.21.12-10+b6_arm64.deb ... Unpacking protobuf-compiler (3.21.12-10+b6) ... Selecting previously unselected package zip. Preparing to unpack .../429-zip_3.0-15_arm64.deb ... Unpacking zip (3.0-15) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../430-xdg-utils_1.2.1-2_all.deb ... Unpacking xdg-utils (1.2.1-2) ... Selecting previously unselected package r-base-core. Preparing to unpack .../431-r-base-core_4.5.0-2_arm64.deb ... Unpacking r-base-core (4.5.0-2) ... Selecting previously unselected package r-cran-rjava. Preparing to unpack .../432-r-cran-rjava_1.0-11-2_arm64.deb ... Unpacking r-cran-rjava (1.0-11-2) ... Selecting previously unselected package testng. Preparing to unpack .../433-testng_6.9.12-4_all.deb ... Unpacking testng (6.9.12-4) ... Setting up libprotobuf-lite32t64:arm64 (3.21.12-10+b6) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up fastjar (2:0.98-7+b1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libjcommander-java (1.71-4) ... Setting up libfastutil-java (8.5.15+dfsg-1) ... Setting up libtext-charwidth-perl:arm64 (0.04-11+b4) ... Setting up wdiff (1.2.2-9) ... Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libprotobuf32t64:arm64 (3.21.12-10+b6) ... Setting up libfile-which-perl (1.27-2) ... Setting up systemd-sysv (257.5-2) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libnpth0t64:arm64 (1.8-3) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up bsdextrautils (2.41-4) ... Setting up hicolor-icon-theme (0.18-2) ... Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... Setting up libgpg-error0:arm64 (1.51-4) ... Setting up libicu4j-java (73.2-1) ... Setting up java-common (0.76) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libobjenesis-java (3.4-2) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up liblogback-java (1:1.2.11-6) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:arm64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libtirpc-common (1.3.6+ds-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxcb-glx0:arm64 (1.17.0-2+b1) ... Setting up unzip (6.0-29) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libedit2:arm64 (3.1-20250104-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.8-1) ... Setting up x11-common (1:7.7+24) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.32-1) ... Setting up libsensors-config (1:3.6.2-2) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libel-api-java (3.0.0-3) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up xkb-data (2.42-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2-1+b1) ... Setting up file (1:5.46-5) ... Setting up libjboss-logging-java (3.5.3-1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up liboro-java (2.0.8a-14) ... Setting up libsnappy1v5:arm64 (1.2.2-1) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun May 31 01:27:43 UTC 2026. Universal Time is now: Sun May 31 01:27:43 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.14-1) ... Setting up libjavassist-java (1:3.27.0-1) ... Setting up zip (3.0-15) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libasound2t64:arm64 (1.2.14-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libepoxy0:arm64 (1.5.10-2) ... Setting up libnspr4:arm64 (2:4.36-1) ... Setting up libxcb-sync1:arm64 (1.17.0-2+b1) ... Setting up libjtidy-java (7+svn20110807-6) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-16) ... Setting up libxpp3-java (1.1.4c-4) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:arm64 (1.16.2-2) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libproc2-0:arm64 (2:4.0.4-8) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.47-1.1) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-2) ... Setting up binfmt-support (2.2.2-7+b1) ... Running in chroot, ignoring request. 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:arm64 (0.22-3+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libpcsclite1:arm64 (2.3.3-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libsensors5:arm64 (1:3.6.2-2) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... 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:arm64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:arm64 (14.2.0-19) ... Setting up libvulkan1:arm64 (1.4.309.0-1) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libwebp7:arm64 (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:arm64 (5.2.2-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up libplexus-interactivity-api-java (1.3-1) ... Setting up libfreemarker-java (2.3.32-2.1) ... Setting up sensible-utils (0.0.25) ... Setting up libxshmfence1:arm64 (1.3.3-1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.56.1-2) ... Setting up libcommons-math-java (2.2-9) ... Setting up gpgv (2.4.7-16) ... Setting up libtiff6:arm64 (4.7.0-3) ... Setting up libxcb-randr0:arm64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.2-2) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libassuan9:arm64 (3.0.2-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-8) ... 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:arm64 (4.20.0-2) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.5) ... Setting up libcommons-math3-java (3.6.1-4) ... Setting up sgml-base (1.31+nmu1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libwayland-egl1:arm64 (1.23.1-3) ... Setting up libicu76:arm64 (76.1-3) ... Setting up libmbedcrypto16:arm64 (3.6.3-1) ... Setting up libpaper2:arm64 (2.2.5-0.3+b2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-7) ... Setting up libprotoc32t64:arm64 (3.21.12-10+b6) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up libfile-homedir-perl (1.006-2) ... Setting up libpj-java (0.0~20150107+dfsg-5) ... Setting up openssl (3.5.0-1) ... Setting up libdrm-common (2.4.124-2) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:arm64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-2) ... Setting up liburi-perl (5.30-1) ... Setting up dbus-bin (1.16.2-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libxkbcommon0:arm64 (1.7.0-2) ... Setting up libwayland-client0:arm64 (1.23.1-3) ... Setting up libnet-ssleay-perl:arm64 (1.94-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.1-2) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:arm64 (1:19.1.7-3) ... Setting up libwayland-server0:arm64 (1.23.1-3) ... Setting up libx11-xcb1:arm64 (2:1.8.12-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxstream-java (1.4.21-1) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libjetty9-java (9.4.57-1) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up protobuf-compiler (3.21.12-10+b6) ... Setting up libjboss-vfs-java (3.2.15.Final-3) ... Setting up libxrender1:arm64 (1:0.9.12-1) ... Setting up jarwrapper (0.80) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:arm64 (2.3.8-2) ... Setting up libnss3:arm64 (2:3.110-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libpaper-utils (2.2.5-0.3+b2) ... Setting up libxom-java (1.3.9-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libmaven-dependency-analyzer-java (1.15.1-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:arm64 (3.21.12-10+b6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1+b1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:arm64 (2.84.1-2) ... Setting up libmbedx509-7:arm64 (3.6.3-1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b4) ... Setting up testng (6.9.12-4) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b4) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libxrandr2:arm64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0051) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:arm64 (3.6.3-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:arm64 (2.4.124-2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:arm64 (1.23.1-3) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gpgconf (2.4.7-16) ... Setting up libpam-systemd:arm64 (257.5-2) ... Setting up libcommons-beanutils-java (1.10.1-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2.3) ... 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+really2.9.14-0.4) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up libsm6:arm64 (2:1.2.6-1) ... Setting up libreflections-java (0.10.2+dfsg-2) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libavahi-client3:arm64 (0.8-16) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.4.7-16) ... Created symlink '/etc/systemd/user/sockets.target.wants/keyboxd.socket' -> '/usr/lib/systemd/user/keyboxd.socket'. Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.124-2) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.18.4+ds-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up mesa-libgallium:arm64 (25.0.4-1) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-2.3) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.6-1+b4) ... Setting up gpg-agent (2.4.7-16) ... Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'. Setting up libatk1.0-0t64:arm64 (2.56.1-2) ... Setting up openjdk-21-jre-headless:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libtirpc3t64:arm64 (1.3.6+ds-1) ... Setting up libgbm1:arm64 (25.0.4-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.3-2) ... Setting up libcommons-io-java (2.19.0-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up libxtst6:arm64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:arm64 (1:1.2.3-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libpango-1.0-0:arm64 (1.56.3-1) ... Setting up libgl1-mesa-dri:arm64 (25.0.4-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Setting up libcloudproviders0:arm64 (0.3.6-2) ... Setting up python3 (3.13.3-1) ... Setting up sopv-gpgv (0.1.4-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up libcolord2:arm64 (1.4.7-3) ... Setting up libdconf1:arm64 (0.40.0-5) ... Setting up libmaven-filtering-java (3.4.0-1) ... Setting up dbus-user-session (1.16.2-2) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (48.0-1) ... 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 (0.018-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:arm64 (2.56.1-2) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up libmaven-dependency-tree-java (3.3.0-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:arm64 (1.18.4-1+b1) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... Setting up libncbi-ngs3:arm64 (3.2.1+dfsg-4) ... Setting up libatk-bridge2.0-0t64:arm64 (2.56.1-2) ... Setting up libngs-jni:arm64 (3.2.1+dfsg-4) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:arm64 (25.0.4-1) ... Setting up libglx0:arm64 (1.7.0-1+b2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:arm64 (8.13.0-5) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libmaven-invoker-java (3.3.0-1) ... Setting up debhelper (13.24.2) ... Setting up dconf-service (0.40.0-5) ... Setting up libgl1:arm64 (1.7.0-1+b2) ... Setting up r-base-core (4.5.0-2) ... Creating config file /etc/R/Renviron with new version Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:arm64 (3.2.1+dfsg-4) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libmaven-source-plugin-java (3.3.1-1) ... Setting up libgtk-3-common (3.24.49-3) ... Setting up libgtk-3-0t64:arm64 (3.24.49-3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.78-1) ... Setting up devscripts (2.25.10) ... 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 (1.13.1-1) ... 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 (2.41-7) ... Processing triggers for systemd (257.5-2) ... 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_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_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: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:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven (3.9.9-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:arm64 (21.0.7+6-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up ant-contrib (1.0~b3+svn177-12) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.21-76) ... Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-5) ... Setting up openjdk-21-jdk:arm64 (21.0.7+6-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up libjsap-java (2.1-5) ... Setting up r-cran-rjava (1.0-11-2) ... 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 (3.10.2-2) ... 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+nmu1) ... 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 (20250419) ... 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: user script /srv/workspace/pbuilder/3292973/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with javahelper dh_auto_clean bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibgoby-io-java jh_clean Duplicate specification "unlink|u" for option "u" debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' dh_clean rm -rf goby-distribution/test-data goby-distribution/test-results rm -rf test-results/ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf dh_auto_configure mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo jh_linkjars dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1 [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16 [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15 [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Goby Framework [pom] [INFO] Goby I/O [jar] [INFO] Goby Full Distribution [jar] [INFO] [INFO] ----------------< org.campagnelab.goby:goby-framework >----------------- [INFO] Building Goby Framework 3.3.1 [1/3] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] from goby-io/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.17 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:3.1.2 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)' [INFO] [INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ goby-io --- [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ goby-io --- [INFO] Recompiling the module because of changed source code. [INFO] Compiling 260 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- antrun:3.1.0:run (default) @ goby-io --- [WARNING] Parameter 'tasks' is deprecated: Use target instead. For version 3.0.0, this parameter is only defined to break the build if you use it! [WARNING] Parameter tasks is deprecated, use target instead [INFO] Executing tasks [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2 [INFO] [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-io --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-io --- [INFO] No sources to compile [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ goby-io --- [INFO] Tests are skipped. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1.jar [INFO] [INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-io >>> [INFO] [INFO] --- build-helper:3.3.0:add-source (add-classes) @ goby-io --- [INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added. [INFO] [INFO] --- antrun:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- antrun:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-io <<< [INFO] [INFO] [INFO] --- source:3.3.1:jar (attach-sources) @ goby-io --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-sources.jar [INFO] [INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-io --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol [WARNING] @XmlRootElement [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist [WARNING] import DistLib.hypergeometric; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol [WARNING] Rengine rEngine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExactRCalculator [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Unmarshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class StatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.CommandLine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.DefaultExecutor; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.PumpStreamHandler; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol [WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class MethylStatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.PJProperties; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlElementWrapper; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol [WARNING] @XmlRootElement(name = "info-output") [WARNING] ^ [WARNING] symbol: class XmlRootElement [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol [WARNING] private void writeInfoOutput() throws JAXBException, IOException { [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist [WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: class XmlAccessorType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] location: class CompactAlignmentToAnnotationCountsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:33: error: cannot find symbol [WARNING] private ParallelTeam team; [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:47: error: cannot find symbol [WARNING] protected synchronized ParallelTeam getParallelTeam() { [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol [WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol [WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol [WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ [WARNING] symbol: class RMainLoopCallbacks [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol [WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol [WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol [WARNING] public void rFlushConsole(final Rengine rengine) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol [WARNING] public void rLoadHistory(final Rengine re, final String filename) { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol [WARNING] private Rengine rengine; [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol [WARNING] public Rengine getRengine() { [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.REXP; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RVector; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol [WARNING] private static Result evaluateFisherExpression(final Rengine rengine, [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class FisherExact [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:35: error: cannot find symbol [WARNING] @XmlElement(name = "al") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:36: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "annotation-lengths") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ [WARNING] symbol: variable XmlAccessType [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:39: error: cannot find symbol [WARNING] @XmlElement(name = "tc") [WARNING] ^ [WARNING] symbol: class XmlElement [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:40: error: cannot find symbol [WARNING] @XmlElementWrapper(name = "total-counts") [WARNING] ^ [WARNING] symbol: class XmlElementWrapper [WARNING] location: class InfoOutput [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-javadoc.jar [INFO] [INFO] ---------------< org.campagnelab.goby:goby-distribution >--------------- [INFO] Building Goby Full Distribution 3.3.1 [3/3] [INFO] from goby-distribution/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] Parameter 'additionalparam' is unknown for plugin 'maven-javadoc-plugin:3.10.1:jar (attach-javadocs)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ goby-distribution --- [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] Copying 72 resources from src/main/java to target/classes [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ goby-distribution --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 525 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[119,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java:[146,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ goby-distribution --- [INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ goby-distribution --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 120 source files with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ goby-distribution --- [INFO] Tests are skipped. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1.jar [INFO] [INFO] >>> source:3.3.1:jar (attach-sources) > generate-sources @ goby-distribution >>> [INFO] [INFO] <<< source:3.3.1:jar (attach-sources) < generate-sources @ goby-distribution <<< [INFO] [INFO] [INFO] --- source:3.3.1:jar (attach-sources) @ goby-distribution --- [INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-sources.jar [INFO] [INFO] --- javadoc:3.10.1:jar (attach-javadocs) @ goby-distribution --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<' [WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors). [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J). [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J) [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning: @return tag cannot be used in method with void return type. [WARNING] void flush(InputBitStream ibs) throws IOException; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS [WARNING] * the call, exactly {@link #BITS} excess bits will be present in the [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning: reference not found: org.campagnelab.goby.aligners.LastagAligner [WARNING] * @see org.campagnelab.goby.aligners.LastagAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:79: warning: reference not found: org.campagnelab.goby.aligners.LastAligner [WARNING] * @see org.campagnelab.goby.aligners.LastAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:87: warning: reference not found: org.campagnelab.goby.aligners.BWAAligner [WARNING] * @see org.campagnelab.goby.aligners.BWAAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:95: warning: reference not found: org.campagnelab.goby.aligners.GSnapAligner [WARNING] * @see org.campagnelab.goby.aligners.GSnapAligner [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:131: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * @return the next {@link edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore}. [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<' [WARNING] * positions p are startPosition <= p < endPosition [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<' [WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol ?@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 [ 0.087 s] [INFO] Goby I/O ........................................... SUCCESS [ 21.215 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 22.400 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 43.845 s [INFO] Finished at: 2026-05-31T15:29:04+14:00 [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 15:29:22.652 INFO RLoggerMainLoopCallback - 15:29:22.657 INFO RLoggerMainLoopCallback - R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 15:29:22.658 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. 15:29:22.658 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. 15:29:22.658 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT qPhred=1 qPhred=2 qPhred=3 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 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] 15:29:23.263 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. 0 AAC 3 ACC 6 ATC 9 AGC 12 AAC 15 ACC 18 ATC 21 AGC 24 AAC 27 ACC 30 ATC 33 AGC 36 AAC 39 ACC 42 ATC 45 AGC 48 AAC 51 ACC 54 ATC 57 AGC 60 AAC 63 ACC 66 ATC 69 AGC 72 AAC 75 ACC 78 ATC 81 AGC15:29:27.377 WARN MessageChunksWriter - Using chunk-size=10000 15:29:27.377 WARN MessageChunksWriter - Using chunk-size=9 15:29:27.382 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 15:29:27.385 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 15:29:27.391 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 Number of bits/base 3.6590436 Creating base test directory: test-results/stats [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. 15:29:27.522 INFO BullardUpperQuartileNormalization - normalization denominator 49233.3 for sample B-7 15:29:27.522 INFO BullardUpperQuartileNormalization - normalization denominator 49962.2 for sample B-3 15:29:27.522 INFO BullardUpperQuartileNormalization - normalization denominator 101912 for sample A-3 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 101448 for sample A-12 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 51353.7 for sample B-15 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 49034.5 for sample B-14 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 51420.0 for sample B-11 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 98201.5 for sample A-17 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 47908.0 for sample B-2 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 51022.4 for sample B-10 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 100852 for sample A-16 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 49233.3 for sample B-8 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 48570.7 for sample B-4 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 98797.9 for sample A-2 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 102840 for sample A-0 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 48703.2 for sample B-6 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 102045 for sample A-9 15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 98532.8 for sample A-8 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 99990.6 for sample A-5 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 98466.6 for sample A-4 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 99261.7 for sample A-6 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 101846 for sample A-7 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 47775.5 for sample B-5 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 99394.2 for sample A-10 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 98731.6 for sample A-14 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 51154.9 for sample B-9 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 100719 for sample A-1 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 50161.0 for sample B-0 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 49763.4 for sample B-12 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 49962.2 for sample B-13 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 98930.4 for sample A-19 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 101581 for sample A-18 15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 97538.9 for sample A-15 15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 51088.6 for sample B-1 15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 98797.9 for sample A-13 15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 98466.6 for sample A-11 15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 49697.1 for sample B-16 15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 50492.3 for sample B-17 15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 49498.3 for sample B-19 15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 49498.3 for sample B-18 Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T]15:29:27.590 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 15:29:27.625 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 15:29:27.626 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 15:29:27.639 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 15:29:27.639 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 15:29:27.781 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 15:29:27.835 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. 15:29:27.835 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 15:29:27.951 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 15:29:27.974 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 [1.00425679659177, 0.4969163859942799, 0.006128225262952388, -1.008924978833683, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00128842 original=0.00128842 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00284140 original=0.00284140 truncated fdr=0.00294094 original=0.00294094 truncated fdr=0.00375760 original=0.00375760 truncated fdr=0.00569307 original=0.00569307 truncated fdr=0.00833856 original=0.00833856 truncated fdr=0.0201744 original=0.0201744 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0379108 original=0.0379108 truncated fdr=0.0523700 original=0.0523700 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0622873 original=0.0622873 truncated fdr=0.0733761 original=0.0733761 truncated fdr=0.0742187 original=0.0742187 truncated fdr=0.0847349 original=0.0847349 truncated fdr=0.151073 original=0.151073 truncated fdr=0.335641 original=0.335641 truncated fdr=0.391390 original=0.391390 truncated fdr=0.391390 original=0.391390 truncated fdr=0.443709 original=0.443709 truncated fdr=0.477756 original=0.477756 truncated fdr=0.479630 original=0.479630 truncated fdr=0.637850 original=0.637850 truncated fdr=0.977998 original=0.977998 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 12 threads. ##fileformat=VCFv4.1 ##Goby=UNKNOWN ##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 1/1 ..T Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file-B-1.vcf Loading test-data/fdr-mode/file-B-2.vcf adjusting column: PCHI2 Combining test-data/fdr-mode/file-B-1.vcf Combining test-data/fdr-mode/file-B-2.vcf Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A Associating basename: basen3 to group: A Associating basename: basen4 to group: A Associating basename: basen5 to group: B Associating basename: basen6 to group: B Associating basename: basen7 to group: B Associating basename: basen8 to group: B Associating basename: basen9 to group: B Comparing A/B sample: basen0 group A sample: basen2 group A sample: basen4 group A sample: basen3 group A sample: basen1 group A sample: basen9 group B sample: basen6 group B sample: basen5 group B sample: basen7 group B sample: basen8 group B Using processor NONE Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences 15:29:41.560 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 15:29:41.566 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 15:29:41.571 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 15:29:41.576 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 15:29:41.580 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 15:29:41.586 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 15:29:41.591 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 15:29:41.595 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 15:29:41.600 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 15:29:41.604 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 15:29:41.715 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 15:29:41.718 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 15:29:41.720 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 15:29:41.722 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 15:29:41.724 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 15:29:41.727 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 15:29:41.729 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 15:29:41.731 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 15:29:41.733 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 15:29:41.735 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 15:29:41.815 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 15:29:41.817 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 15:29:41.819 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 15:29:41.821 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 15:29:41.824 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 15:29:41.826 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 15:29:41.828 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 15:29:41.830 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 15:29:41.832 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 15:29:41.835 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 15:29:41.956 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 15:29:41.959 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 15:29:41.962 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 15:29:41.965 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 15:29:41.968 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 15:29:41.971 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 15:29:41.974 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 15:29:41.976 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 15:29:41.979 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 15:29:41.982 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 15:29:42.058 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 15:29:42.060 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 15:29:42.062 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 15:29:42.064 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 15:29:42.065 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 15:29:42.067 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 15:29:42.069 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 15:29:42.071 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 15:29:42.073 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 15:29:42.075 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 15:29:42.137 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 15:29:42.139 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 15:29:42.140 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 15:29:42.142 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 15:29:42.143 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 15:29:42.145 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 15:29:42.147 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 15:29:42.148 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 15:29:42.150 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 15:29:42.152 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 15:29:42.209 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 15:29:42.211 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 15:29:42.212 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 15:29:42.213 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 15:29:42.215 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 15:29:42.216 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 15:29:42.218 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 15:29:42.220 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 15:29:42.221 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 15:29:42.223 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 15:29:42.278 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 15:29:42.279 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 15:29:42.280 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 15:29:42.282 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 15:29:42.283 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 15:29:42.285 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 15:29:42.286 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 15:29:42.288 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 15:29:42.289 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 15:29:42.291 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 15:29:42.346 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 15:29:42.347 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 15:29:42.349 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 15:29:42.350 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 15:29:42.352 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 15:29:42.354 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 15:29:42.355 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 15:29:42.357 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 15:29:42.358 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 15:29:42.360 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 15:29:42.448 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 15:29:42.449 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 15:29:42.451 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 15:29:42.452 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 15:29:42.454 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 15:29:42.455 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 15:29:42.457 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 15:29:42.459 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 15:29:42.460 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 15:29:42.462 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 15:29:42.516 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 15:29:42.518 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 15:29:42.519 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 15:29:42.520 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 15:29:42.521 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 15:29:42.523 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 15:29:42.524 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 15:29:42.525 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 15:29:42.526 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 15:29:42.528 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 15:29:42.590 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 15:29:42.591 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 15:29:42.592 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 15:29:42.593 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 15:29:42.595 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 15:29:42.596 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 15:29:42.597 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 15:29:42.598 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 15:29:42.599 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 15:29:42.601 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + ref: A s=0 info: + /T q=40 s=0 info: - /T q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /C q=30 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=40 s=0 info: + /C q=10 s=0 info: + /C q=20 s=0 info: + /N q=30 s=0 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + ref: A s=1 info: + /T q=40 s=1 info: + /T q=10 s=1 info: + /T q=20 s=1 info: + /T q=30 s=1 info: + /N q=40 s=1 info: + /N q=40 s=1 list: pos=-1 #bases: 33 #indels: 0 filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1} Scanning target file.. Target file had 1 entries. Wrote 1 target ids to alignment header. Setting quality threshold to 0.05 Total logical entries written: 2 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 3 Number of targets: 3 Removed by quality filter: 0 Not best score: 1 Number of alignments written: 2 query_index: 0 target_index: 0 position: 14977972 score: 780.0 matching_reverse_strand: false multiplicity: 1 number_of_mismatches: 1 number_of_indels: 0 query_length: 142 query_aligned_length: 134 target_aligned_length: 134 sequence_variations { to: "T" from: "A" position: 6 to_quality: "/" read_index: 14 } fragment_index: 0 query_index_occurrences: 2 ambiguity: 1 TTC[27]->CGT[27] / qual=1:2:3 A[15]->G[20] / qual=20 A[15]->G[20] / qual=20 Processing test-data/sample-qual-scores/30reads.fa Processed 0 read entries. Min quality score: 2147483647 Max quality score: -2147483648 Avg quality score: 0 Probable quality encoding scheme: fasta Processing test-data/sample-qual-scores/30reads.fq Processed 30 read entries. Min quality score: 69 Max quality score: 98 Avg quality score: 94 Probable quality encoding scheme: Illumina/Solexa field CHROM value: 0 field POS value: 145497099 field ID value: . field REF value: A field ALT value: G field QUAL value: 17.1 field FILTER value: . field INFO[DP] value: 2 field INFO[DP4] value: 0,0,2,0 field INFO[MQ] value: 25 field INFO[FQ] value: -30.8 field INFO[AF1] value: 0.9999 field INFO[CI95] value: 0.5,1 field INFO[PV4] value: field INFO[INDEL] value: INDEL field INFO[PC2] value: 3,3 field INFO[PCHI2] value: 0.752 field INFO[QCHI2] value: 1 field INFO[RP] value: field FORMAT[GT] value: field FORMAT[GQ] value: field FORMAT[GL] value: field FORMAT[DP] value: field FORMAT[SP] value: field FORMAT[PL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 field CHROM gfi:0 value: 0 field POS gfi:1 value: 145497099 field ID gfi:2 value: . field REF gfi:3 value: A field ALT gfi:4 value: G field QUAL gfi:5 value: 17.1 field FILTER gfi:6 value: . field FORMAT[GT] gfi:7 value: field FORMAT[GQ] gfi:8 value: field FORMAT[GL] gfi:9 value: field FORMAT[DP] gfi:10 value: field FORMAT[SP] gfi:11 value: field FORMAT[PL] gfi:12 value: field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 Total logical entries written: 1 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 0 Max query index: 0 Number of queries: 1 Number of targets: 45 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 Appending count: 19793 length: 6 Appending count: 36510 length: 7 Appending count: 44836 length: 10 Appending count: 12582 length: 7 Appending count: 24030 length: 4 Appending count: 36536 length: 9 Appending count: 48424 length: 2 Appending count: 12520 length: 6 Appending count: 47909 length: 8 Appending count: 3621 length: 8 Appending count: 7420 length: 9 Appending count: 27020 length: 1 Appending count: 9875 length: 2 Appending count: 10183 length: 6 Appending count: 8806 length: 8 Appending count: 13011 length: 3 Appending count: 42407 length: 4 Appending count: 1247 length: 10 Appending count: 21680 length: 6 Appending count: 13984 length: 1 Appending count: 3684 length: 3 Appending count: 21921 length: 9 Appending count: 22771 length: 7 Appending count: 3864 length: 1 Appending count: 2428 length: 8 Appending count: 31556 length: 2 Appending count: 32733 length: 9 Appending count: 754 length: 1 Appending count: 965 length: 8 Appending count: 33631 length: 9 position= 0 count= 19793 position= 1 count= 19793 position= 2 count= 19793 position= 3 count= 19793 position= 4 count= 19793 position= 5 count= 19793 position= 6 count= 36510 position= 7 count= 36510 position= 8 count= 36510 position= 9 count= 36510 position= 10 count= 36510 position= 11 count= 36510 position= 12 count= 36510 position= 13 count= 44836 position= 14 count= 44836 position= 15 count= 44836 position= 16 count= 44836 position= 17 count= 44836 position= 18 count= 44836 position= 19 count= 44836 position= 20 count= 44836 position= 21 count= 44836 position= 22 count= 44836 position= 23 count= 12582 position= 24 count= 12582 position= 25 count= 12582 position= 26 count= 12582 position= 27 count= 12582 position= 28 count= 12582 position= 29 count= 12582 position= 30 count= 24030 position= 31 count= 24030 position= 32 count= 24030 position= 33 count= 24030 position= 34 count= 36536 position= 35 count= 36536 position= 36 count= 36536 position= 37 count= 36536 position= 38 count= 36536 position= 39 count= 36536 position= 40 count= 36536 position= 41 count= 36536 position= 42 count= 36536 position= 43 count= 48424 position= 44 count= 48424 position= 45 count= 12520 position= 46 count= 12520 position= 47 count= 12520 position= 48 count= 12520 position= 49 count= 12520 position= 50 count= 12520 position= 51 count= 47909 position= 52 count= 47909 position= 53 count= 47909 position= 54 count= 47909 position= 55 count= 47909 position= 56 count= 47909 position= 57 count= 47909 position= 58 count= 47909 position= 59 count= 3621 position= 60 count= 3621 position= 61 count= 3621 position= 62 count= 3621 position= 63 count= 3621 position= 64 count= 3621 position= 65 count= 3621 position= 66 count= 3621 position= 67 count= 7420 position= 68 count= 7420 position= 69 count= 7420 position= 70 count= 7420 position= 71 count= 7420 position= 72 count= 7420 position= 73 count= 7420 position= 74 count= 7420 position= 75 count= 7420 position= 76 count= 27020 position= 77 count= 9875 position= 78 count= 9875 position= 79 count= 10183 position= 80 count= 10183 position= 81 count= 10183 position= 82 count= 10183 position= 83 count= 10183 position= 84 count= 10183 position= 85 count= 8806 position= 86 count= 8806 position= 87 count= 8806 position= 88 count= 8806 position= 89 count= 8806 position= 90 count= 8806 position= 91 count= 8806 position= 92 count= 8806 position= 93 count= 13011 position= 94 count= 13011 position= 95 count= 13011 position= 96 count= 42407 position= 97 count= 42407 position= 98 count= 42407 position= 99 count= 42407 position= 100 count= 1247 position= 101 count= 1247 position= 102 count= 1247 position= 103 count= 1247 position= 104 count= 1247 position= 105 count= 1247 position= 106 count= 1247 position= 107 count= 1247 position= 108 count= 1247 position= 109 count= 1247 position= 110 count= 21680 position= 111 count= 21680 position= 112 count= 21680 position= 113 count= 21680 position= 114 count= 21680 position= 115 count= 21680 position= 116 count= 13984 position= 117 count= 3684 position= 118 count= 3684 position= 119 count= 3684 position= 120 count= 21921 position= 121 count= 21921 position= 122 count= 21921 position= 123 count= 21921 position= 124 count= 21921 position= 125 count= 21921 position= 126 count= 21921 position= 127 count= 21921 position= 128 count= 21921 position= 129 count= 22771 position= 130 count= 22771 position= 131 count= 22771 position= 132 count= 22771 position= 133 count= 22771 position= 134 count= 22771 position= 135 count= 22771 position= 136 count= 3864 position= 137 count= 2428 position= 138 count= 2428 position= 139 count= 2428 position= 140 count= 2428 position= 141 count= 2428 position= 142 count= 2428 position= 143 count= 2428 position= 144 count= 2428 position= 145 count= 31556 position= 146 count= 31556 position= 147 count= 32733 position= 148 count= 32733 position= 149 count= 32733 position= 150 count= 32733 position= 151 count= 32733 position= 152 count= 32733 position= 153 count= 32733 position= 154 count= 32733 position= 155 count= 32733 position= 156 count= 754 position= 157 count= 965 position= 158 count= 965 position= 159 count= 965 position= 160 count= 965 position= 161 count= 965 position= 162 count= 965 position= 163 count= 965 position= 164 count= 965 position= 165 count= 33631 position= 166 count= 33631 position= 167 count= 33631 position= 168 count= 33631 position= 169 count= 33631 position= 170 count= 33631 position= 171 count= 33631 position= 172 count= 33631 position= 173 count= 33631 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 15:29:43.971 WARN WiggleWindow - Not writing 101 7 15:29:43.971 WARN WiggleWindow - Not writing 111 7 15:29:43.971 WARN WiggleWindow - Not writing 131 8 15:29:43.971 WARN WiggleWindow - Not writing 141 8 15:29:43.971 WARN WiggleWindow - Not writing 151 8 appending (count=0,length=1) appending (count=4,length=3) appending (count=1,length=3) appending (count=0,length=2) appending (count=3,length=1) appending (count=1,length=1) appending (count=0,length=1) appending (count=4,length=3) appending (count=0,length=5) appending (count=3,length=1) appending (count=0,length=2) appending (count=2,length=1) appending (count=0,length=2) appending (count=3,length=1) appending (count=2,length=1) appending (count=0,length=1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) loading transition for reader[0] position=1 length=3 count=3 (0,1)(1,4) loading transition for reader[0] position=4 length=2 count=0 (0,1)(1,4)(4,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 (0,0) loading transition for reader[0] position=1 length=1 count=1 (0,0)(1,1) loading transition for reader[0] position=2 length=4 count=0 (0,0)(1,1)(2,0) loading transition for reader[1] position=4 length=10 count=1 (0,0)(1,1)(2,0)(4,1) loading transition for reader[0] position=6 length=2 count=1 (0,0)(1,1)(2,0)(4,1)(6,2) loading transition for reader[0] position=8 length=1 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1) loading transition for reader[0] position=9 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) loading transition for reader[0] position=10 length=2 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) loading transition for reader[0] position=12 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) loading transition for reader[0] position=13 length=3 count=0 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) loading transition for reader[0] position=16 length=1 count=1 (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=4 count=0 loading transition for reader[0] position=1 length=1 count=1 loading transition for reader[0] position=2 length=4 count=0 loading transition for reader[1] position=4 length=10 count=1 loading transition for reader[0] position=6 length=2 count=1 loading transition for reader[0] position=8 length=1 count=0 loading transition for reader[0] position=9 length=1 count=1 loading transition for reader[0] position=10 length=2 count=0 loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 loading transition for reader[0] position=0 length=1 count=0 (0,0) loading transition for reader[0] position=1 length=3 count=1 (0,0)(1,1) appending (count=10,length=4) appending (count=1,length=0) appending (count=2,length=8) Hello appending (count=10,length=4) 15:29:43.991 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 15:29:43.998 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 15:29:44.006 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 15:29:44.010 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 15:29:44.014 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 15:29:44.020 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.025 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.037 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.039 WARN MessageChunksWriter - Using chunk-size=1000 0 23 Setting quality threshold to 0.02 entry:query_index: 0 target_index: 0 position: 5 score: 5.0 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 read_index: 10 } entry:query_index: 1 target_index: 0 position: 5 matching_reverse_strand: false query_length: 20 query_aligned_length: 20 target_aligned_length: 20 sequence_variations { to: "CTAG" from: "----" position: 10 to_quality: "((((" read_index: 10 } entry: query_index: 0 target_index: 0 position: 0 matching_reverse_strand: false query_length: 10 query_aligned_length: 10 sequence_variations { to: "AAA" from: "---" position: 3 read_index: 3 } processing entry on target 0 at position 0 processing entry on target 0 at position 5 processing entry on target 1 at position 0 processing entry on target 1 at position 5 processing entry on target 4 at position 0 processing entry on target 4 at position 5 entry:query_index: 0 target_index: 0 position: 10 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "AAA" from: "---" position: 20 read_index: 20 } entry:query_index: 1 target_index: 0 position: 1 matching_reverse_strand: false query_length: 50 query_aligned_length: 50 sequence_variations { to: "T" from: "A" position: 20 read_index: 20 } 15:29:44.066 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 15:29:44.137 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.138 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.140 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.148 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.149 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.150 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.158 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.159 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.161 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 15:29:44.169 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.171 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.172 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.182 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.184 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.185 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.187 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 15:29:44.189 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 15:29:44.190 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 15:29:44.194 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.195 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.197 WARN MessageChunksWriter - Using chunk-size=1000 Processing queryIndex=8 with description '8 perfect start of ref' Processing queryIndex=9 with description '9 perfect start of ref reverse strand' Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' Processing queryIndex=0 with description '0 perfect match' Processing queryIndex=1 with description '1 perfect match on reverse strand' Processing queryIndex=2 with description '2 mutation' Processing queryIndex=3 with description '3 mutation on reverse strand' Processing queryIndex=4 with description '4 insertion' Processing queryIndex=6 with description '6 deletion' Processing queryIndex=7 with description '7 deletion on reverse strand' Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' Processing queryIndex=5 with description '5 insertion on reverse strand' Processing queryIndex=10 with description '10 perfect end of ref' Processing queryIndex=11 with description '11 perfect end of ref reverse strand' 15:29:44.225 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 15:29:44.229 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 15:29:44.233 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 15:29:44.237 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 15:29:44.241 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 15:29:44.244 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 15:29:44.248 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 15:29:44.255 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.258 WARN MessageChunksWriter - Using chunk-size=1 15:29:44.263 WARN MessageChunksWriter - Using chunk-size=1 15:29:44.267 WARN MessageChunksWriter - Using chunk-size=1 15:29:44.271 WARN MessageChunksWriter - Using chunk-size=1 15:29:44.279 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.281 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 15:29:44.288 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.289 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries 15:29:44.293 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.295 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.300 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.302 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.307 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.309 WARN MessageChunksWriter - Using chunk-size=1000 0 2 15:29:44.314 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.316 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 15:29:44.321 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.323 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.328 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.330 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.335 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.336 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 5 entries [main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =TAAAACCTAAAAAAAAAAAAAAACCCC expected =TAAAA--TAAAAAAAAAAAAAAACCCC recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT 15:29:44.351 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.397 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.398 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.426 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:44.453 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.454 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.462 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. 15:29:44.485 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. 15:29:44.485 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 15:29:44.485 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: 3ms; used/avail/free/total/max mem: 1.36G/7.04G/425.69M/1.79G/8.40G 15:29:44.492 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 15:29:44.564 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. 15:29:44.568 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. 15:29:44.593 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. 15:29:44.594 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. 15:29:44.594 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. 15:29:44.594 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 15:29:44.594 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. 15:29:44.594 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: 411.40M/7.99G/1.38G/1.79G/8.40G 15:29:44.597 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. 15:29:44.608 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. 15:29:44.634 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.658 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.659 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.681 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:44.703 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.705 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: 503.67M/7.90G/1.28G/1.79G/8.40G 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 15:29:44.769 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.791 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.793 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.815 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:44.838 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.839 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.842 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. 15:29:44.848 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. 15:29:44.848 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 15:29:44.849 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 562.39M/7.84G/1.22G/1.79G/8.40G 15:29:44.851 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 15:29:44.856 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.879 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.880 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.902 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:44.924 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.925 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.927 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. 15:29:44.929 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. 15:29:44.931 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. 15:29:44.932 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. 15:29:44.932 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. 15:29:44.932 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 15:29:44.932 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. 15:29:44.932 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: 589.65M/7.81G/1.20G/1.79G/8.40G 15:29:44.934 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. 15:29:44.935 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. 15:29:44.938 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.960 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.962 WARN MessageChunksWriter - Using chunk-size=1000 15:29:44.983 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:45.005 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.007 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) 15:29:45.009 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) 15:29:45.010 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. 15:29:45.013 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. 15:29:45.013 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. 15:29:45.013 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. 15:29:45.013 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 15:29:45.013 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. 15:29:45.014 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: 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: 614.82M/7.79G/1.17G/1.79G/8.40G Second pass: writing the merged alignment. 15:29:45.016 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. 15:29:45.017 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 15:29:45.021 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.043 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.044 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.066 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:45.089 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.090 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.092 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. 15:29:45.094 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. 15:29:45.094 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 15:29:45.094 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: 1ms; used/avail/free/total/max mem: 639.99M/7.76G/1.15G/1.79G/8.40G 15:29:45.096 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 15:29:45.100 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.158 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.160 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.195 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:45.221 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.222 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: 698.71M/7.70G/1.09G/1.79G/8.40G 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 15:29:45.286 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.308 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.309 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.331 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 15:29:45.352 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.354 WARN MessageChunksWriter - Using chunk-size=1000 15:29:45.357 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. 15:29:45.360 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. 15:29:45.381 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. 15:29:45.381 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. 15:29:45.381 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. 15:29:45.381 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 15:29:45.381 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. 15:29:45.381 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: 788.88M/7.61G/997.89M/1.79G/8.40G 15:29:45.384 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. 15:29:45.395 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 1999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 0 target_index: 3999 position: 19991 score: 20020.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 1 target_index: 3999 position: 19992 score: 20021.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 query_index: 0 target_index: 0 position: 0 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 query_index: 1 target_index: 0 position: 1 query_position: 0 matching_reverse_strand: false query_length: 75 query_aligned_length: 75 target_aligned_length: 75 mapping_quality: 255 pair_flags: 0 fragment_index: 0 ambiguity: 1 15:29:45.481 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 15:29:45.482 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 [ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits [ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 {1} {0}decoding: 4 {0} {0}decoding: 4 {0} {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0} {0} {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0} {0} {0}decoding: 3 decoding: 4 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 [ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits [ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} count keys [0, 3, 5, 11, 13] -1 0.0 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 0.0 overlapping count 15, 17 0.0 overlapping count 9, 18 2.0 overlapping count 3, 8 2.0 overlapping count 11, 12 0.0 overlapping count 9, 10 1.0 overlapping count 8, 9 0.0 overlapping count 8, 8 0.0 overlapping count 5, 6 0.0 overlapping count 3, 3 0.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 0.0 -1 0.0 0 0.0 1 0.0 2 0.0 3 2.0 4 2.0 5 3.0 6 3.0 7 3.0 8 3.0 9 3.0 10 3.0 11 2.0 12 2.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 2.0 overlapping count 2, 3 2.0 overlapping count 3, 8 4.0 overlapping count 11, 12 2.0 overlapping count 9, 10 3.0 overlapping count 8, 9 4.0 overlapping count 8, 8 3.0 overlapping count 5, 6 3.0 overlapping count 3, 3 2.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 1.0 Total logical entries written: 4 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Total logical entries written: 4 Total bytes written: 62 Average bytes/logical entry: 15.5 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 Annotations loaded Annotations loaded Annotations loaded Annotations loaded Annotations loaded [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 83.885 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 [ 0.084 s] [INFO] Goby I/O ........................................... SUCCESS [ 7.859 s] [INFO] Goby Full Distribution ............................. SUCCESS [02:00 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:09 min [INFO] Finished at: 2026-05-31T15:31:15+14:00 [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 [ 0.332 s] [INFO] Goby I/O ........................................... SUCCESS [ 0.056 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 0.040 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.655 s [INFO] Finished at: 2026-05-31T15:31:17+14:00 [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 May 31, 2026 3:31:24 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 May 31, 2026 3:31:29 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 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'. dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-11_all.deb'. dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-11_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/B01_cleanup finished 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/3292973 and its subdirectories I: Current time: Sun May 31 15:31:40 +14 2026 I: pbuilder-time-stamp: 1780191100 + false + set +x Sun May 31 01:31:40 UTC 2026 I: Signing ./b2/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo as libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc Sun May 31 01:31:40 UTC 2026 I: Signed ./b2/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo as ./b2/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc Sun May 31 01:31:40 UTC 2026 - build #2 for libgoby-java/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Sun May 31 01:31:40 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-0SjGfWZy, removing. /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp: total 460 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 19:03 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 19:08 b2 -rw-r--r-- 1 jenkins jenkins 3008 May 14 2024 libgoby-java_3.3.1+dfsg2-11.dsc -rw------- 1 jenkins jenkins 451104 Apr 27 19:03 rbuildlog.0ltXdoE /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b1: total 3036 -rw-r--r-- 1 jenkins jenkins 446610 Apr 27 19:03 build.log -rw-r--r-- 1 jenkins jenkins 1575696 Apr 27 19:03 goby-java_3.3.1+dfsg2-11_all.deb -rw-r--r-- 1 jenkins jenkins 978952 Apr 27 19:03 libgoby-io-java_3.3.1+dfsg2-11_all.deb -rw-r--r-- 1 jenkins jenkins 29428 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 3008 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11.dsc -rw-r--r-- 1 jenkins jenkins 19044 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 19926 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1651 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_arm64.changes -rw-r--r-- 1 jenkins jenkins 1494 Apr 27 19:03 libgoby-java_3.3.1+dfsg2-11_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b2: total 3024 -rw-r--r-- 1 jenkins jenkins 448594 Apr 27 19:08 build.log -rw-r--r-- 1 jenkins jenkins 1575696 Apr 27 19:08 goby-java_3.3.1+dfsg2-11_all.deb -rw-r--r-- 1 jenkins jenkins 978952 Apr 27 19:08 libgoby-io-java_3.3.1+dfsg2-11_all.deb -rw-r--r-- 1 jenkins jenkins 29428 Apr 27 19:08 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 3008 Apr 27 19:08 libgoby-java_3.3.1+dfsg2-11.dsc -rw-r--r-- 1 jenkins jenkins 19044 Apr 27 19:08 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 19926 Apr 27 19:08 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1651 Apr 27 19:08 libgoby-java_3.3.1+dfsg2-11_arm64.changes -rw-r--r-- 1 jenkins jenkins 1494 Apr 27 19:08 libgoby-java_3.3.1+dfsg2-11_source.changes Sun Apr 27 19:08:41 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun Apr 27 19:08:42 UTC 2025 I: libgoby-java_3.3.1+dfsg2-11_arm64.changes: Format: 1.8 Date: Tue, 14 May 2024 18:17:12 +0200 Source: libgoby-java Binary: goby-java libgoby-io-java Architecture: all Version: 3.3.1+dfsg2-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: goby-java - next-generation sequencing data and results analysis tool libgoby-io-java - IO API for goby Changes: libgoby-java (3.3.1+dfsg2-11) unstable; urgency=medium . * Raising Standards version to 4.7.0 (no change) * Restricting autopkgtest architecture to amd64 and arm64, where sra-sdk packages are installable * Build-depending on pkgconf instead of obsolete pkg-config Checksums-Sha1: 8d6c264bb79c6a856462e629583538ec8b632b15 1575696 goby-java_3.3.1+dfsg2-11_all.deb ba8a87f95aa155b5cb3e4061e47f8eea597b32ec 978952 libgoby-io-java_3.3.1+dfsg2-11_all.deb fb5c325e27dea308ba091e58d69b70961e520baa 19044 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo Checksums-Sha256: 2fa45b31be92ce16796d6b626341f8d5558b316bb3d3cb1c1c34b8811f71f163 1575696 goby-java_3.3.1+dfsg2-11_all.deb 966fd3a4c6cf5de51d2eb89a40822d339904299f2f2d1212774c6d5ff34371f6 978952 libgoby-io-java_3.3.1+dfsg2-11_all.deb 7516451fdc9ce84b268f02e4c4a9aa126e0c6c9c8dfc5def39b162e642ab641b 19044 libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo Files: 7e8b2f21003504808ef0aae4d95df2e7 1575696 science optional goby-java_3.3.1+dfsg2-11_all.deb 95bf2d8dab731f27e265e656c7333bf7 978952 science optional libgoby-io-java_3.3.1+dfsg2-11_all.deb ba0ab143c2f0d3455ef5240590e7d3ce 19044 science optional libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-04-27 19:03:42.271803320 +0000 +++ b2/build.log 2025-04-27 19:08:41.645426666 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 27 06:55:28 -12 2025 -I: pbuilder-time-stamp: 1745780128 +I: Current time: Sun May 31 15:26:46 +14 2026 +I: pbuilder-time-stamp: 1780190806 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -40,52 +40,84 @@ 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/271630/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 31 01:26 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='7a7ac1dbbc154196a2a6c662048efd64' - 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='271630' - PS1='# ' - PS2='> ' + INVOCATION_ID=c379785ceadf4065bf6c36170272c649 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3292973 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.tP9jh8Dp/pbuilderrc_Bir9 --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.tP9jh8Dp/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/pbuilderrc_X7xR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-11.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/271630/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -660,7 +692,7 @@ Get: 457 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.5.0-2 [28.4 MB] Get: 458 http://deb.debian.org/debian unstable/main arm64 r-cran-rjava arm64 1.0-11-2 [712 kB] Get: 459 http://deb.debian.org/debian unstable/main arm64 testng all 6.9.12-4 [795 kB] -Fetched 373 MB in 3s (118 MB/s) +Fetched 373 MB in 4s (91.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19953 files and directories currently installed.) @@ -2161,8 +2193,8 @@ Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Apr 27 18:57:29 UTC 2025. -Universal Time is now: Sun Apr 27 18:57:29 UTC 2025. +Local time is now: Sun May 31 01:27:43 UTC 2026. +Universal Time is now: Sun May 31 01:27:43 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2755,7 +2787,11 @@ 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 +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -3633,14 +3669,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.133 s] -[INFO] Goby I/O ........................................... SUCCESS [ 40.749 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 43.490 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.087 s] +[INFO] Goby I/O ........................................... SUCCESS [ 21.215 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 22.400 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:24 min -[INFO] Finished at: 2025-04-27T07:00:27-12:00 +[INFO] Total time: 43.845 s +[INFO] Finished at: 2026-05-31T15:29:04+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' @@ -3799,24 +3835,24 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite -07:01:01.252 INFO RLoggerMainLoopCallback - +15:29:22.652 INFO RLoggerMainLoopCallback - -07:01:01.257 INFO RLoggerMainLoopCallback - R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" +15:29:22.657 INFO RLoggerMainLoopCallback - R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu -07:01:01.257 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. +15:29:22.658 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. -07:01:01.257 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. +15:29:22.658 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. -07:01:01.258 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or +15:29:22.658 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. @@ -3895,7 +3931,7 @@ 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] -07:01:02.380 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. +15:29:23.263 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. 0 AAC 3 ACC 6 @@ -3924,19 +3960,19 @@ AAC 75 ACC 78 ATC 81 -AGC07:01:09.707 WARN MessageChunksWriter - Using chunk-size=10000 -07:01:09.708 WARN MessageChunksWriter - Using chunk-size=9 -07:01:09.713 WARN MessageChunksWriter - Using chunk-size=9 +AGC15:29:27.377 WARN MessageChunksWriter - Using chunk-size=10000 +15:29:27.377 WARN MessageChunksWriter - Using chunk-size=9 +15:29:27.382 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 -07:01:09.724 WARN MessageChunksWriter - Using chunk-size=9 +15:29:27.385 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 -07:01:09.731 WARN MessageChunksWriter - Using chunk-size=9 +15:29:27.391 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 @@ -3966,57 +4002,57 @@ [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. -07:01:10.072 INFO BullardUpperQuartileNormalization - normalization denominator 49719.7 for sample B-7 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 48867.0 for sample B-3 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 99505.1 for sample A-3 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-12 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49588.6 for sample B-15 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 51097.2 for sample B-14 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49326.2 for sample B-11 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 94520.0 for sample A-17 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49916.5 for sample B-2 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 47358.4 for sample B-10 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 98586.8 for sample A-16 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 50703.6 for sample B-8 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 48735.8 for sample B-4 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-2 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 98521.2 for sample A-0 -07:01:10.073 INFO BullardUpperQuartileNormalization - normalization denominator 49326.2 for sample B-6 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97996.4 for sample A-9 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98062.0 for sample A-8 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98980.3 for sample A-5 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97537.3 for sample A-4 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 99964.2 for sample A-6 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98390.0 for sample A-7 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48211.1 for sample B-5 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 96422.2 for sample A-10 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 100030 for sample A-14 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 50769.2 for sample B-9 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97865.2 for sample A-1 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48735.8 for sample B-0 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48604.7 for sample B-12 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 49719.7 for sample B-13 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 93536.1 for sample A-19 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97799.6 for sample A-18 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 96750.1 for sample A-15 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 48014.3 for sample B-1 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 97012.5 for sample A-13 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 98258.8 for sample A-11 -07:01:10.074 INFO BullardUpperQuartileNormalization - normalization denominator 49588.6 for sample B-16 -07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 49785.3 for sample B-17 -07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 47292.8 for sample B-19 -07:01:10.075 INFO BullardUpperQuartileNormalization - normalization denominator 48342.3 for sample B-18 +15:29:27.522 INFO BullardUpperQuartileNormalization - normalization denominator 49233.3 for sample B-7 +15:29:27.522 INFO BullardUpperQuartileNormalization - normalization denominator 49962.2 for sample B-3 +15:29:27.522 INFO BullardUpperQuartileNormalization - normalization denominator 101912 for sample A-3 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 101448 for sample A-12 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 51353.7 for sample B-15 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 49034.5 for sample B-14 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 51420.0 for sample B-11 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 98201.5 for sample A-17 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 47908.0 for sample B-2 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 51022.4 for sample B-10 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 100852 for sample A-16 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 49233.3 for sample B-8 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 48570.7 for sample B-4 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 98797.9 for sample A-2 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 102840 for sample A-0 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 48703.2 for sample B-6 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 102045 for sample A-9 +15:29:27.523 INFO BullardUpperQuartileNormalization - normalization denominator 98532.8 for sample A-8 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 99990.6 for sample A-5 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 98466.6 for sample A-4 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 99261.7 for sample A-6 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 101846 for sample A-7 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 47775.5 for sample B-5 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 99394.2 for sample A-10 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 98731.6 for sample A-14 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 51154.9 for sample B-9 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 100719 for sample A-1 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 50161.0 for sample B-0 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 49763.4 for sample B-12 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 49962.2 for sample B-13 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 98930.4 for sample A-19 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 101581 for sample A-18 +15:29:27.524 INFO BullardUpperQuartileNormalization - normalization denominator 97538.9 for sample A-15 +15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 51088.6 for sample B-1 +15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 98797.9 for sample A-13 +15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 98466.6 for sample A-11 +15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 49697.1 for sample B-16 +15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 50492.3 for sample B-17 +15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 49498.3 for sample B-19 +15:29:27.525 INFO BullardUpperQuartileNormalization - normalization denominator 49498.3 for sample B-18 Creating base test directory: test-results/stats-writer -allele: A ref: [CC] alt: [T]07:01:10.230 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -07:01:10.309 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -07:01:10.309 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -07:01:10.345 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -07:01:10.346 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -07:01:10.563 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -07:01:10.629 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. -07:01:10.629 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -07:01:10.785 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -07:01:10.808 INFO FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed. +allele: A ref: [CC] alt: [T]15:29:27.590 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +15:29:27.625 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +15:29:27.626 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +15:29:27.639 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +15:29:27.639 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +15:29:27.781 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +15:29:27.835 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. +15:29:27.835 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +15:29:27.951 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +15:29:27.974 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] ] @@ -4070,7 +4106,7 @@ [ 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 [1.0042223266471022, 0.5016882445373338, 0.006078705586435645, -0.9951369613424312, 0.0, 0.0] ] +[ id-1 [1.00425679659177, 0.4969163859942799, 0.006128225262952388, -1.008924978833683, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 @@ -4175,34 +4211,34 @@ #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 -07:01:34.553 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. +15:29:41.560 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 -07:01:34.557 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. +15:29:41.566 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 -07:01:34.564 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. +15:29:41.571 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 -07:01:34.567 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. +15:29:41.576 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 -07:01:34.578 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. +15:29:41.580 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 -07:01:34.585 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. +15:29:41.586 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 -07:01:34.592 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. +15:29:41.591 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 -07:01:34.595 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. +15:29:41.595 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 -07:01:34.598 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. +15:29:41.600 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 -07:01:34.609 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. +15:29:41.604 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 @@ -4232,34 +4268,34 @@ #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 -07:01:34.919 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. +15:29:41.715 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 -07:01:34.930 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. +15:29:41.718 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 -07:01:34.933 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. +15:29:41.720 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 -07:01:34.939 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. +15:29:41.722 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 -07:01:34.942 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. +15:29:41.724 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 -07:01:34.953 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. +15:29:41.727 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 -07:01:34.955 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. +15:29:41.729 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 -07:01:34.958 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. +15:29:41.731 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 -07:01:34.968 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. +15:29:41.733 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 -07:01:34.971 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. +15:29:41.735 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 @@ -4289,34 +4325,34 @@ #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 -07:01:35.166 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. +15:29:41.815 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 -07:01:35.176 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. +15:29:41.817 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 -07:01:35.179 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. +15:29:41.819 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 -07:01:35.185 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. +15:29:41.821 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 -07:01:35.192 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. +15:29:41.824 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 -07:01:35.194 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. +15:29:41.826 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 -07:01:35.201 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. +15:29:41.828 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 -07:01:35.203 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. +15:29:41.830 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 -07:01:35.213 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. +15:29:41.832 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 -07:01:35.216 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. +15:29:41.835 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 @@ -4346,34 +4382,34 @@ #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 -07:01:35.377 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. +15:29:41.956 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 -07:01:35.384 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. +15:29:41.959 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 -07:01:35.386 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. +15:29:41.962 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 -07:01:35.392 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. +15:29:41.965 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 -07:01:35.394 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. +15:29:41.968 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 -07:01:35.413 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. +15:29:41.971 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 -07:01:35.415 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. +15:29:41.974 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 -07:01:35.418 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. +15:29:41.976 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 -07:01:35.424 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. +15:29:41.979 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 -07:01:35.426 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. +15:29:41.982 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 @@ -4403,34 +4439,34 @@ #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 -07:01:35.670 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. +15:29:42.058 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 -07:01:35.680 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. +15:29:42.060 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 -07:01:35.682 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. +15:29:42.062 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 -07:01:35.685 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. +15:29:42.064 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 -07:01:35.686 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. +15:29:42.065 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 -07:01:35.693 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. +15:29:42.067 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 -07:01:35.695 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. +15:29:42.069 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 -07:01:35.698 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. +15:29:42.071 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 -07:01:35.700 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. +15:29:42.073 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 -07:01:35.702 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. +15:29:42.075 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 @@ -4460,34 +4496,34 @@ #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 -07:01:35.803 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. +15:29:42.137 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 -07:01:35.805 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. +15:29:42.139 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 -07:01:35.806 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. +15:29:42.140 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 -07:01:35.817 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. +15:29:42.142 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 -07:01:35.827 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. +15:29:42.143 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 -07:01:35.830 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. +15:29:42.145 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 -07:01:35.831 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. +15:29:42.147 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 -07:01:35.833 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. +15:29:42.148 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 -07:01:35.835 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. +15:29:42.150 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 -07:01:35.841 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. +15:29:42.152 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 @@ -4517,34 +4553,34 @@ #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 -07:01:35.928 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. +15:29:42.209 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 -07:01:35.930 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. +15:29:42.211 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 -07:01:35.933 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. +15:29:42.212 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 -07:01:35.935 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. +15:29:42.213 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 -07:01:35.936 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. +15:29:42.215 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 -07:01:35.938 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. +15:29:42.216 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 -07:01:35.948 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. +15:29:42.218 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 -07:01:35.950 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. +15:29:42.220 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 -07:01:35.960 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. +15:29:42.221 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 -07:01:35.962 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. +15:29:42.223 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 @@ -4574,34 +4610,34 @@ #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 -07:01:36.091 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. +15:29:42.278 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 -07:01:36.101 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. +15:29:42.279 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 -07:01:36.102 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. +15:29:42.280 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 -07:01:36.104 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. +15:29:42.282 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 -07:01:36.106 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. +15:29:42.283 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 -07:01:36.115 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. +15:29:42.285 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 -07:01:36.117 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. +15:29:42.286 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 -07:01:36.119 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. +15:29:42.288 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 -07:01:36.120 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. +15:29:42.289 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 -07:01:36.122 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. +15:29:42.291 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 @@ -4631,34 +4667,34 @@ #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 -07:01:36.246 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. +15:29:42.346 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 -07:01:36.252 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. +15:29:42.347 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 -07:01:36.254 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. +15:29:42.349 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 -07:01:36.264 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. +15:29:42.350 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 -07:01:36.265 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. +15:29:42.352 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 -07:01:36.267 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. +15:29:42.354 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 -07:01:36.269 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. +15:29:42.355 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 -07:01:36.270 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. +15:29:42.357 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 -07:01:36.280 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. +15:29:42.358 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 -07:01:36.282 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. +15:29:42.360 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 @@ -4688,34 +4724,34 @@ #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 -07:01:36.361 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. +15:29:42.448 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 -07:01:36.363 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. +15:29:42.449 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 -07:01:36.364 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. +15:29:42.451 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 -07:01:36.366 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. +15:29:42.452 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 -07:01:36.367 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. +15:29:42.454 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 -07:01:36.369 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. +15:29:42.455 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 -07:01:36.370 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. +15:29:42.457 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 -07:01:36.373 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. +15:29:42.459 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 -07:01:36.374 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. +15:29:42.460 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 -07:01:36.376 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. +15:29:42.462 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 @@ -4745,34 +4781,34 @@ #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 -07:01:36.504 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. +15:29:42.516 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 -07:01:36.506 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. +15:29:42.518 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 -07:01:36.512 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. +15:29:42.519 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 -07:01:36.513 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. +15:29:42.520 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 -07:01:36.515 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. +15:29:42.521 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -07:01:36.521 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. +15:29:42.523 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -07:01:36.522 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. +15:29:42.524 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 -07:01:36.528 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. +15:29:42.525 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 -07:01:36.530 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. +15:29:42.526 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 -07:01:36.536 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. +15:29:42.528 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 @@ -4801,34 +4837,34 @@ [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 -07:01:36.690 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. +15:29:42.590 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 -07:01:36.691 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. +15:29:42.591 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 -07:01:36.701 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. +15:29:42.592 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 -07:01:36.702 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. +15:29:42.593 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 -07:01:36.704 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. +15:29:42.595 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 -07:01:36.706 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. +15:29:42.596 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 -07:01:36.715 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. +15:29:42.597 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 -07:01:36.717 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. +15:29:42.598 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 -07:01:36.719 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. +15:29:42.599 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 -07:01:36.721 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. +15:29:42.601 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 @@ -4988,207 +5024,210 @@ Number of targets: 45 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 -Appending count: 16576 length: 10 -Appending count: 35371 length: 4 -Appending count: 23073 length: 1 -Appending count: 22583 length: 2 -Appending count: 17646 length: 5 -Appending count: 19398 length: 1 -Appending count: 12875 length: 9 -Appending count: 39440 length: 1 -Appending count: 46977 length: 7 -Appending count: 39057 length: 10 -Appending count: 7950 length: 9 -Appending count: 1004 length: 8 -Appending count: 14153 length: 2 -Appending count: 2284 length: 6 -Appending count: 5888 length: 1 -Appending count: 36281 length: 7 -Appending count: 45232 length: 3 -Appending count: 4131 length: 6 -Appending count: 28736 length: 2 -Appending count: 6015 length: 6 -Appending count: 26795 length: 10 -Appending count: 9739 length: 3 -Appending count: 49032 length: 9 -Appending count: 9375 length: 3 -Appending count: 8631 length: 9 -Appending count: 21777 length: 7 -Appending count: 38666 length: 9 -Appending count: 38565 length: 10 -Appending count: 30414 length: 6 -Appending count: 27984 length: 5 - position= 0 count= 16576 - position= 1 count= 16576 - position= 2 count= 16576 - position= 3 count= 16576 - position= 4 count= 16576 - position= 5 count= 16576 - position= 6 count= 16576 - position= 7 count= 16576 - position= 8 count= 16576 - position= 9 count= 16576 - position= 10 count= 35371 - position= 11 count= 35371 - position= 12 count= 35371 - position= 13 count= 35371 - position= 14 count= 23073 - position= 15 count= 22583 - position= 16 count= 22583 - position= 17 count= 17646 - position= 18 count= 17646 - position= 19 count= 17646 - position= 20 count= 17646 - position= 21 count= 17646 - position= 22 count= 19398 - position= 23 count= 12875 - position= 24 count= 12875 - position= 25 count= 12875 - position= 26 count= 12875 - position= 27 count= 12875 - position= 28 count= 12875 - position= 29 count= 12875 - position= 30 count= 12875 - position= 31 count= 12875 - position= 32 count= 39440 - position= 33 count= 46977 - position= 34 count= 46977 - position= 35 count= 46977 - position= 36 count= 46977 - position= 37 count= 46977 - position= 38 count= 46977 - position= 39 count= 46977 - position= 40 count= 39057 - position= 41 count= 39057 - position= 42 count= 39057 - position= 43 count= 39057 - position= 44 count= 39057 - position= 45 count= 39057 - position= 46 count= 39057 - position= 47 count= 39057 - position= 48 count= 39057 - position= 49 count= 39057 - position= 50 count= 7950 - position= 51 count= 7950 - position= 52 count= 7950 - position= 53 count= 7950 - position= 54 count= 7950 - position= 55 count= 7950 - position= 56 count= 7950 - position= 57 count= 7950 - position= 58 count= 7950 - position= 59 count= 1004 - position= 60 count= 1004 - position= 61 count= 1004 - position= 62 count= 1004 - position= 63 count= 1004 - position= 64 count= 1004 - position= 65 count= 1004 - position= 66 count= 1004 - position= 67 count= 14153 - position= 68 count= 14153 - position= 69 count= 2284 - position= 70 count= 2284 - position= 71 count= 2284 - position= 72 count= 2284 - position= 73 count= 2284 - position= 74 count= 2284 - position= 75 count= 5888 - position= 76 count= 36281 - position= 77 count= 36281 - position= 78 count= 36281 - position= 79 count= 36281 - position= 80 count= 36281 - position= 81 count= 36281 - position= 82 count= 36281 - position= 83 count= 45232 - position= 84 count= 45232 - position= 85 count= 45232 - position= 86 count= 4131 - position= 87 count= 4131 - position= 88 count= 4131 - position= 89 count= 4131 - position= 90 count= 4131 - position= 91 count= 4131 - position= 92 count= 28736 - position= 93 count= 28736 - position= 94 count= 6015 - position= 95 count= 6015 - position= 96 count= 6015 - position= 97 count= 6015 - position= 98 count= 6015 - position= 99 count= 6015 - position= 100 count= 26795 - position= 101 count= 26795 - position= 102 count= 26795 - position= 103 count= 26795 - position= 104 count= 26795 - position= 105 count= 26795 - position= 106 count= 26795 - position= 107 count= 26795 - position= 108 count= 26795 - position= 109 count= 26795 - position= 110 count= 9739 - position= 111 count= 9739 - position= 112 count= 9739 - position= 113 count= 49032 - position= 114 count= 49032 - position= 115 count= 49032 - position= 116 count= 49032 - position= 117 count= 49032 - position= 118 count= 49032 - position= 119 count= 49032 - position= 120 count= 49032 - position= 121 count= 49032 - position= 122 count= 9375 - position= 123 count= 9375 - position= 124 count= 9375 - position= 125 count= 8631 - position= 126 count= 8631 - position= 127 count= 8631 - position= 128 count= 8631 - position= 129 count= 8631 - position= 130 count= 8631 - position= 131 count= 8631 - position= 132 count= 8631 - position= 133 count= 8631 - position= 134 count= 21777 - position= 135 count= 21777 - position= 136 count= 21777 - position= 137 count= 21777 - position= 138 count= 21777 - position= 139 count= 21777 - position= 140 count= 21777 - position= 141 count= 38666 - position= 142 count= 38666 - position= 143 count= 38666 - position= 144 count= 38666 - position= 145 count= 38666 - position= 146 count= 38666 - position= 147 count= 38666 - position= 148 count= 38666 - position= 149 count= 38666 - position= 150 count= 38565 - position= 151 count= 38565 - position= 152 count= 38565 - position= 153 count= 38565 - position= 154 count= 38565 - position= 155 count= 38565 - position= 156 count= 38565 - position= 157 count= 38565 - position= 158 count= 38565 - position= 159 count= 38565 - position= 160 count= 30414 - position= 161 count= 30414 - position= 162 count= 30414 - position= 163 count= 30414 - position= 164 count= 30414 - position= 165 count= 30414 - position= 166 count= 27984 - position= 167 count= 27984 - position= 168 count= 27984 - position= 169 count= 27984 - position= 170 count= 27984 +Appending count: 19793 length: 6 +Appending count: 36510 length: 7 +Appending count: 44836 length: 10 +Appending count: 12582 length: 7 +Appending count: 24030 length: 4 +Appending count: 36536 length: 9 +Appending count: 48424 length: 2 +Appending count: 12520 length: 6 +Appending count: 47909 length: 8 +Appending count: 3621 length: 8 +Appending count: 7420 length: 9 +Appending count: 27020 length: 1 +Appending count: 9875 length: 2 +Appending count: 10183 length: 6 +Appending count: 8806 length: 8 +Appending count: 13011 length: 3 +Appending count: 42407 length: 4 +Appending count: 1247 length: 10 +Appending count: 21680 length: 6 +Appending count: 13984 length: 1 +Appending count: 3684 length: 3 +Appending count: 21921 length: 9 +Appending count: 22771 length: 7 +Appending count: 3864 length: 1 +Appending count: 2428 length: 8 +Appending count: 31556 length: 2 +Appending count: 32733 length: 9 +Appending count: 754 length: 1 +Appending count: 965 length: 8 +Appending count: 33631 length: 9 + position= 0 count= 19793 + position= 1 count= 19793 + position= 2 count= 19793 + position= 3 count= 19793 + position= 4 count= 19793 + position= 5 count= 19793 + position= 6 count= 36510 + position= 7 count= 36510 + position= 8 count= 36510 + position= 9 count= 36510 + position= 10 count= 36510 + position= 11 count= 36510 + position= 12 count= 36510 + position= 13 count= 44836 + position= 14 count= 44836 + position= 15 count= 44836 + position= 16 count= 44836 + position= 17 count= 44836 + position= 18 count= 44836 + position= 19 count= 44836 + position= 20 count= 44836 + position= 21 count= 44836 + position= 22 count= 44836 + position= 23 count= 12582 + position= 24 count= 12582 + position= 25 count= 12582 + position= 26 count= 12582 + position= 27 count= 12582 + position= 28 count= 12582 + position= 29 count= 12582 + position= 30 count= 24030 + position= 31 count= 24030 + position= 32 count= 24030 + position= 33 count= 24030 + position= 34 count= 36536 + position= 35 count= 36536 + position= 36 count= 36536 + position= 37 count= 36536 + position= 38 count= 36536 + position= 39 count= 36536 + position= 40 count= 36536 + position= 41 count= 36536 + position= 42 count= 36536 + position= 43 count= 48424 + position= 44 count= 48424 + position= 45 count= 12520 + position= 46 count= 12520 + position= 47 count= 12520 + position= 48 count= 12520 + position= 49 count= 12520 + position= 50 count= 12520 + position= 51 count= 47909 + position= 52 count= 47909 + position= 53 count= 47909 + position= 54 count= 47909 + position= 55 count= 47909 + position= 56 count= 47909 + position= 57 count= 47909 + position= 58 count= 47909 + position= 59 count= 3621 + position= 60 count= 3621 + position= 61 count= 3621 + position= 62 count= 3621 + position= 63 count= 3621 + position= 64 count= 3621 + position= 65 count= 3621 + position= 66 count= 3621 + position= 67 count= 7420 + position= 68 count= 7420 + position= 69 count= 7420 + position= 70 count= 7420 + position= 71 count= 7420 + position= 72 count= 7420 + position= 73 count= 7420 + position= 74 count= 7420 + position= 75 count= 7420 + position= 76 count= 27020 + position= 77 count= 9875 + position= 78 count= 9875 + position= 79 count= 10183 + position= 80 count= 10183 + position= 81 count= 10183 + position= 82 count= 10183 + position= 83 count= 10183 + position= 84 count= 10183 + position= 85 count= 8806 + position= 86 count= 8806 + position= 87 count= 8806 + position= 88 count= 8806 + position= 89 count= 8806 + position= 90 count= 8806 + position= 91 count= 8806 + position= 92 count= 8806 + position= 93 count= 13011 + position= 94 count= 13011 + position= 95 count= 13011 + position= 96 count= 42407 + position= 97 count= 42407 + position= 98 count= 42407 + position= 99 count= 42407 + position= 100 count= 1247 + position= 101 count= 1247 + position= 102 count= 1247 + position= 103 count= 1247 + position= 104 count= 1247 + position= 105 count= 1247 + position= 106 count= 1247 + position= 107 count= 1247 + position= 108 count= 1247 + position= 109 count= 1247 + position= 110 count= 21680 + position= 111 count= 21680 + position= 112 count= 21680 + position= 113 count= 21680 + position= 114 count= 21680 + position= 115 count= 21680 + position= 116 count= 13984 + position= 117 count= 3684 + position= 118 count= 3684 + position= 119 count= 3684 + position= 120 count= 21921 + position= 121 count= 21921 + position= 122 count= 21921 + position= 123 count= 21921 + position= 124 count= 21921 + position= 125 count= 21921 + position= 126 count= 21921 + position= 127 count= 21921 + position= 128 count= 21921 + position= 129 count= 22771 + position= 130 count= 22771 + position= 131 count= 22771 + position= 132 count= 22771 + position= 133 count= 22771 + position= 134 count= 22771 + position= 135 count= 22771 + position= 136 count= 3864 + position= 137 count= 2428 + position= 138 count= 2428 + position= 139 count= 2428 + position= 140 count= 2428 + position= 141 count= 2428 + position= 142 count= 2428 + position= 143 count= 2428 + position= 144 count= 2428 + position= 145 count= 31556 + position= 146 count= 31556 + position= 147 count= 32733 + position= 148 count= 32733 + position= 149 count= 32733 + position= 150 count= 32733 + position= 151 count= 32733 + position= 152 count= 32733 + position= 153 count= 32733 + position= 154 count= 32733 + position= 155 count= 32733 + position= 156 count= 754 + position= 157 count= 965 + position= 158 count= 965 + position= 159 count= 965 + position= 160 count= 965 + position= 161 count= 965 + position= 162 count= 965 + position= 163 count= 965 + position= 164 count= 965 + position= 165 count= 33631 + position= 166 count= 33631 + position= 167 count= 33631 + position= 168 count= 33631 + position= 169 count= 33631 + position= 170 count= 33631 + position= 171 count= 33631 + position= 172 count= 33631 + position= 173 count= 33631 loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) @@ -5232,11 +5271,11 @@ 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 -07:01:39.310 WARN WiggleWindow - Not writing 101 7 -07:01:39.310 WARN WiggleWindow - Not writing 111 7 -07:01:39.310 WARN WiggleWindow - Not writing 131 8 -07:01:39.310 WARN WiggleWindow - Not writing 141 8 -07:01:39.310 WARN WiggleWindow - Not writing 151 8 +15:29:43.971 WARN WiggleWindow - Not writing 101 7 +15:29:43.971 WARN WiggleWindow - Not writing 111 7 +15:29:43.971 WARN WiggleWindow - Not writing 131 8 +15:29:43.971 WARN WiggleWindow - Not writing 141 8 +15:29:43.971 WARN WiggleWindow - Not writing 151 8 appending (count=0,length=1) appending (count=4,length=3) appending (count=1,length=3) @@ -5305,7 +5344,7 @@ appending (count=2,length=8) Hello appending (count=10,length=4) -07:01:39.366 WARN MessageChunksWriter - Using chunk-size=2 +15:29:43.991 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 0 Total bytes written: 31 Average bytes/logical entry: Infinity @@ -5314,7 +5353,7 @@ Number of queries: 2 Number of targets: 0 97 -07:01:39.373 WARN MessageChunksWriter - Using chunk-size=2 +15:29:43.998 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5322,7 +5361,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.381 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.006 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5330,7 +5369,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.384 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.010 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5338,7 +5377,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.388 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.014 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5346,10 +5385,10 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.394 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.401 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.412 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.416 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.020 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.025 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.037 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.039 WARN MessageChunksWriter - Using chunk-size=1000 0 23 Setting quality threshold to 0.02 @@ -5428,7 +5467,7 @@ read_index: 20 } -07:01:39.454 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.066 WARN MessageChunksWriter - Using chunk-size=1000 Total logical entries written: 20000 Total bytes written: 77210 Average bytes/logical entry: 3.8605 @@ -5436,15 +5475,15 @@ Max query index: 1999 Number of queries: 2000 Number of targets: 10 -07:01:39.543 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.545 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.546 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.556 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.557 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.558 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.569 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.570 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.573 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.137 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.138 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.140 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.148 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.149 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.150 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.158 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.159 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.161 WARN MessageChunksWriter - Using chunk-size=1000 entry.position(): 1 entry.position(): 2 entry.position(): 3 @@ -5457,24 +5496,24 @@ entry.position(): 10 entry.position(): 12 entry.position(): 99 -07:01:39.583 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.586 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.587 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.601 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.603 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.604 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.607 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. +15:29:44.169 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.171 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.172 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.182 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.184 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.185 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.187 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 -07:01:39.609 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. +15:29:44.189 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 -07:01:39.611 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. +15:29:44.190 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 -07:01:39.615 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.616 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.617 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.194 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.195 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.197 WARN MessageChunksWriter - Using chunk-size=1000 Processing queryIndex=8 with description '8 perfect start of ref' Processing queryIndex=9 with description '9 perfect start of ref reverse strand' Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' @@ -5501,7 +5540,7 @@ 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' -07:01:39.646 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.225 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5509,7 +5548,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.651 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.229 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5517,7 +5556,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.657 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.233 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5525,7 +5564,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.661 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.237 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5533,7 +5572,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.665 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.241 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5541,7 +5580,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.669 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.244 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5549,7 +5588,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.673 WARN MessageChunksWriter - Using chunk-size=2 +15:29:44.248 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5557,45 +5596,45 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -07:01:39.680 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.255 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.683 WARN MessageChunksWriter - Using chunk-size=1 -07:01:39.688 WARN MessageChunksWriter - Using chunk-size=1 -07:01:39.693 WARN MessageChunksWriter - Using chunk-size=1 -07:01:39.696 WARN MessageChunksWriter - Using chunk-size=1 -07:01:39.702 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.712 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.258 WARN MessageChunksWriter - Using chunk-size=1 +15:29:44.263 WARN MessageChunksWriter - Using chunk-size=1 +15:29:44.267 WARN MessageChunksWriter - Using chunk-size=1 +15:29:44.271 WARN MessageChunksWriter - Using chunk-size=1 +15:29:44.279 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.281 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 -07:01:39.718 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.728 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.288 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.289 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries -07:01:39.732 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.733 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.745 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.747 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.761 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.762 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.293 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.295 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.300 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.302 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.307 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.309 WARN MessageChunksWriter - Using chunk-size=1000 0 2 -07:01:39.776 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.778 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.314 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.316 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 -07:01:39.793 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.794 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.808 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.809 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.823 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.824 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.321 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.323 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.328 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.330 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.335 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.336 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 @@ -5624,25 +5663,25 @@ read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT -07:01:39.860 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.926 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.927 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:39.992 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.351 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.397 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.398 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.426 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:40.049 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.051 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.067 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. -07:01:40.110 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. -07:01:40.110 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. +15:29:44.453 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.454 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.462 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. +15:29:44.485 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. +15:29:44.485 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 -07:01:40.110 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. +15:29:44.485 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] +[main] INFO org.campagnelab.goby.alignments.Merge - 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: 5ms; used/avail/free/total/max mem: 895.63M/7.51G/178.11M/1.07G/8.40G -07:01:40.121 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 - Elapsed: 3ms; used/avail/free/total/max mem: 1.36G/7.04G/425.69M/1.79G/8.40G +15:29:44.492 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 @@ -5723,36 +5762,36 @@ multiplicity: 1 query_length: 35 -07:01:40.175 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. -07:01:40.186 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. -07:01:40.244 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. -07:01:40.244 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. -07:01:40.244 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. -07:01:40.244 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. +15:29:44.564 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. +15:29:44.568 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. +15:29:44.593 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. +15:29:44.594 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. +15:29:44.594 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. +15:29:44.594 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 -07:01:40.244 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. -07:01:40.244 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. +15:29:44.594 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. +15:29:44.594 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: 945.96M/7.46G/127.78M/1.07G/8.40G -07:01:40.247 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. -07:01:40.261 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. -07:01:40.312 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.354 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.356 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.387 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 411.40M/7.99G/1.38G/1.79G/8.40G +15:29:44.597 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. +15:29:44.608 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. +15:29:44.634 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.658 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.659 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.681 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:40.411 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.413 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.703 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.705 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: 1.04G/7.37G/37.60M/1.07G/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 503.67M/7.90G/1.28G/1.79G/8.40G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -5881,25 +5920,25 @@ multiplicity: 1 query_length: 35 -07:01:40.613 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.661 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.662 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.714 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.769 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.791 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.793 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.815 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:40.763 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.764 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.767 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. -07:01:40.818 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. -07:01:40.818 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. +15:29:44.838 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.839 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.842 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. +15:29:44.848 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. +15:29:44.848 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 -07:01:40.818 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. +15:29:44.849 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: 2ms [1 items, 1,000.00 items/s, 1.00 ms/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 436.14M/7.97G/645.99M/1.08G/8.40G -07:01:40.822 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 - Elapsed: 1ms; used/avail/free/total/max mem: 562.39M/7.84G/1.22G/1.79G/8.40G +15:29:44.851 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 @@ -5925,64 +5964,64 @@ multiplicity: 1 query_length: 35 -07:01:40.838 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.914 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.920 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:40.962 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.856 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.879 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.880 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.902 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:41.009 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.010 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.021 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. -07:01:41.022 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. -07:01:41.025 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. -07:01:41.025 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. -07:01:41.025 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. -07:01:41.026 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. +15:29:44.924 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.925 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.927 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. +15:29:44.929 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. +15:29:44.931 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. +15:29:44.932 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. +15:29:44.932 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. +15:29:44.932 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 -07:01:41.026 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. -07:01:41.026 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. +15:29:44.932 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. +15:29:44.932 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: 80.86M/8.32G/103.69M/184.55M/8.40G -07:01:41.036 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. -07:01:41.038 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. -07:01:41.041 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.088 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.089 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.136 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 589.65M/7.81G/1.20G/1.79G/8.40G +15:29:44.934 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. +15:29:44.935 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. +15:29:44.938 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.960 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.962 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:44.983 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:41.182 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.186 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.005 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.007 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) -07:01:41.188 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. +15:29:45.009 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) -07:01:41.189 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. +15:29:45.010 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. -07:01:41.201 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. -07:01:41.201 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. -07:01:41.201 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. -07:01:41.201 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. +15:29:45.013 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. +15:29:45.013 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. +15:29:45.013 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. +15:29:45.013 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 -07:01:41.201 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. -07:01:41.201 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. +15:29:45.013 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. +15:29:45.014 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 - 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: 2ms; used/avail/free/total/max mem: 108.12M/8.29G/76.43M/184.55M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 614.82M/7.79G/1.17G/1.79G/8.40G Second pass: writing the merged alignment. -07:01:41.207 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. -07:01:41.209 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. +15:29:45.016 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. +15:29:45.017 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 @@ -5992,25 +6031,25 @@ Number of queries: 10 Number of targets: 4 Percent aligned: 100.0 -07:01:41.216 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.265 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.266 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.313 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.021 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.043 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.044 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.066 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:41.363 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.365 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.367 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. -07:01:41.373 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. -07:01:41.373 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. +15:29:45.089 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.090 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.092 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. +15:29:45.094 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. +15:29:45.094 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 -07:01:41.373 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. +15:29:45.094 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: 1ms; used/avail/free/total/max mem: 133.28M/8.27G/51.26M/184.55M/8.40G -07:01:41.375 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 - Elapsed: 1ms; used/avail/free/total/max mem: 639.99M/7.76G/1.15G/1.79G/8.40G +15:29:45.096 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 @@ -6091,19 +6130,19 @@ multiplicity: 1 query_length: 35 -07:01:41.387 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.430 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.431 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.516 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.100 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.158 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.160 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.195 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:41.554 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.555 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.221 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.222 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] +[main] INFO org.campagnelab.goby.alignments.Merge - 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: 89.94M/8.31G/94.61M/184.55M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 698.71M/7.70G/1.09G/1.79G/8.40G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -6232,30 +6271,30 @@ multiplicity: 1 query_length: 35 -07:01:41.691 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.730 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.740 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.782 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.286 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.308 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.309 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.331 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -07:01:41.838 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.839 WARN MessageChunksWriter - Using chunk-size=1000 -07:01:41.851 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. -07:01:41.854 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. -07:01:41.899 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. -07:01:41.899 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. -07:01:41.899 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. -07:01:41.899 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. +15:29:45.352 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.354 WARN MessageChunksWriter - Using chunk-size=1000 +15:29:45.357 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. +15:29:45.360 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. +15:29:45.381 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. +15:29:45.381 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. +15:29:45.381 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. +15:29:45.381 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 -07:01:41.899 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. -07:01:41.899 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. +15:29:45.381 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. +15:29:45.381 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 - 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: 72.43M/8.33G/112.12M/184.55M/8.40G -07:01:41.902 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. -07:01:41.925 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 - Elapsed: 1ms; used/avail/free/total/max mem: 788.88M/7.61G/997.89M/1.79G/8.40G +15:29:45.384 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. +15:29:45.395 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 @@ -6442,8 +6481,8 @@ fragment_index: 0 ambiguity: 1 -07:01:42.041 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 -07:01:42.041 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds +15:29:45.481 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 +15:29:45.482 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 decoding: 4 @@ -6650,7 +6689,7 @@ Annotations loaded Annotations loaded Annotations loaded -[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 106.692 s - in TestSuite +[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 83.885 s - in TestSuite [INFO] [INFO] Results: [INFO] @@ -6659,14 +6698,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.115 s] -[INFO] Goby I/O ........................................... SUCCESS [ 15.391 s] -[INFO] Goby Full Distribution ............................. SUCCESS [02:29 min] +[INFO] Goby Framework ..................................... SUCCESS [ 0.084 s] +[INFO] Goby I/O ........................................... SUCCESS [ 7.859 s] +[INFO] Goby Full Distribution ............................. SUCCESS [02:00 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:45 min -[INFO] Finished at: 2025-04-27T07:03:16-12:00 +[INFO] Total time: 02:09 min +[INFO] Finished at: 2026-05-31T15:31:15+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -6737,14 +6776,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.337 s] -[INFO] Goby I/O ........................................... SUCCESS [ 0.055 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 0.037 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.332 s] +[INFO] Goby I/O ........................................... SUCCESS [ 0.056 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 0.040 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.597 s -[INFO] Finished at: 2025-04-27T07:03:18-12:00 +[INFO] Total time: 0.655 s +[INFO] Finished at: 2026-05-31T15:31:17+14:00 [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... @@ -6755,12 +6794,12 @@ > 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 27, 2025 7:03:24 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +May 31, 2026 3:31:24 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian > dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2 -Apr 27, 2025 7:03:29 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +May 31, 2026 3:31:29 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 @@ -6787,10 +6826,10 @@ 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: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} 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 @@ -6805,12 +6844,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3292973/tmp/hooks/B01_cleanup finished 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/271630 and its subdirectories -I: Current time: Sun Apr 27 07:03:40 -12 2025 -I: pbuilder-time-stamp: 1745780620 +I: removing directory /srv/workspace/pbuilder/3292973 and its subdirectories +I: Current time: Sun May 31 15:31:40 +14 2026 +I: pbuilder-time-stamp: 1780191100 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.diff: 92.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.diff.gz b2/build.log: 87.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.2% -- replaced with stdout Sun Apr 27 19:08:43 UTC 2025 I: diffoscope 294 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libgoby-java_unstable_arm64_1745780923 + touch /var/log/reproducible-builds/diffoscope_stamp_libgoby-java_unstable_arm64_1745780923 + RESULT=0 + systemd-run '--description=diffoscope on libgoby-java/3.3.1+dfsg2-11 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_10-69005 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp --run-session -c jenkins-reproducible-unstable-diffoscope-a46bdc84-ef93-47d7-b465-2966f7dcd39f -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/dbd-tmp-O0ftugZ ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/libgoby-java_3.3.1+dfsg2-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/libgoby-java_3.3.1+dfsg2-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/libgoby-java_3.3.1+dfsg2-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b1/libgoby-java_3.3.1+dfsg2-11_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b2/libgoby-java_3.3.1+dfsg2-11_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_10-69005.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/libgoby-java_3.3.1+dfsg2-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/libgoby-java_3.3.1+dfsg2-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/libgoby-java_3.3.1+dfsg2-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b1/libgoby-java_3.3.1+dfsg2-11_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.tP9jh8Dp/b2/libgoby-java_3.3.1+dfsg2-11_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.004s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 238ms CPU time consumed: 238ms _ _ _ _ _ | (_) |__ __ _ ___ | |__ _ _ (_) __ ___ ____ _ | | | '_ \ / _` |/ _ \| '_ \| | | |_____| |/ _` \ \ / / _` | | | | |_) | (_| | (_) | |_) | |_| |_____| | (_| |\ V / (_| | |_|_|_.__/ \__, |\___/|_.__/ \__, | _/ |\__,_| \_/ \__,_| |___/ |___/ |__/ Sun Apr 27 19:08:44 UTC 2025 I: diffoscope 294 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 27 19:08:44 UTC 2025 I: libgoby-java from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-04-27 19:08:45] INFO: Starting at 2025-04-27 19:08:45.052374 [2025-04-27 19:08:45] INFO: Generating the pages of 1 package(s) [2025-04-27 19:08:45] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/libgoby-java didn't produce a buildlog, even though it has been built. [2025-04-27 19:08:45] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:08:45] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:08:45] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:08:45] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:08:45] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/libgoby-java_3.3.1+dfsg2-9.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/libgoby-java_3.3.1+dfsg2-9.diff.gz is missing [2025-04-27 19:08:45] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/libgoby-java_3.3.1+dfsg2-9.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/libgoby-java_3.3.1+dfsg2-9.diff.gz is missing [2025-04-27 19:08:45] INFO: Finished at 2025-04-27 19:08:45.409820, took: 0:00:00.357450 Sun Apr 27 19:08:45 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/libgoby-java.html Sun Apr 27 19:08:45 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Apr 27 19:08:45 UTC 2025 I: Submitting 20K b1/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc https://buildinfo.debian.net/fb5c325e27dea308ba091e58d69b70961e520baa/libgoby-java_3.3.1+dfsg2-11_all Sun Apr 27 19:09:15 UTC 2025 I: Submitting 20K b2/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc https://buildinfo.debian.net/e9487100436a9cdc4156e00e66986d0fd0a33a95/libgoby-java_3.3.1+dfsg2-11_all Sun Apr 27 19:09:33 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 27 19:09:33 UTC 2025 I: Done submitting .buildinfo files. Sun Apr 27 19:09:33 UTC 2025 I: Removing signed libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc files: removed './b1/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc' removed './b2/libgoby-java_3.3.1+dfsg2-11_arm64.buildinfo.asc' 1745780973 arm64 unstable libgoby-java Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.rbuild.log: 86.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgoby-java_3.3.1+dfsg2-11.rbuild.log.gz [2025-04-27 19:09:33] INFO: Starting at 2025-04-27 19:09:33.555667 [2025-04-27 19:09:33] INFO: Generating the pages of 1 package(s) [2025-04-27 19:09:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:09:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:09:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:09:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/libgoby-java_3.3.1+dfsg2-11.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/libgoby-java_3.3.1+dfsg2-11.diff.gz is missing [2025-04-27 19:09:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/libgoby-java_3.3.1+dfsg2-9.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/libgoby-java_3.3.1+dfsg2-9.diff.gz is missing [2025-04-27 19:09:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/libgoby-java_3.3.1+dfsg2-9.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/libgoby-java_3.3.1+dfsg2-9.diff.gz is missing [2025-04-27 19:09:33] INFO: Finished at 2025-04-27 19:09:33.905447, took: 0:00:00.349784 All cleanup done. Sun Apr 27 19:09:34 UTC 2025 - total duration: 0h 13m 34s. Sun Apr 27 19:09:34 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-PuQIEshR, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 14min 23.457s CPU time consumed: 7.463s