Tue Apr 23 08:56:48 UTC 2024 I: starting to build libgoby-java/trixie/arm64 on jenkins on '2024-04-23 08:56' Tue Apr 23 08:56:48 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_2/31950/console.log Tue Apr 23 08:56:48 UTC 2024 I: Downloading source for trixie/libgoby-java=3.3.1+dfsg2-10 --2024-04-23 08:56:48-- http://deb.debian.org/debian/pool/main/libg/libgoby-java/libgoby-java_3.3.1%2bdfsg2-10.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3011 (2.9K) [text/prs.lines.tag] Saving to: ‘libgoby-java_3.3.1+dfsg2-10.dsc’ 0K .. 100% 401M=0s 2024-04-23 08:56:48 (401 MB/s) - ‘libgoby-java_3.3.1+dfsg2-10.dsc’ saved [3011/3011] Tue Apr 23 08:56:48 UTC 2024 I: libgoby-java_3.3.1+dfsg2-10.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+dfsg2-10 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet , Andreas Tille Homepage: https://campagnelab.org/software/goby/ Standards-Version: 4.6.2 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, pkg-config, 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 46a6a881da114175ba247880ac918fbd443d60ce 29336 libgoby-java_3.3.1+dfsg2-10.debian.tar.xz Checksums-Sha256: b76b19808f893790e238c91e65680441ff020794cc7708ad6695cf13f0767148 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz 89a405303356305fe1c53dafd4cab5ddf599f2d8e73ed203956b648fb1cef8cf 29336 libgoby-java_3.3.1+dfsg2-10.debian.tar.xz Files: 3a8dbf45ef2c54ec3073240850acbc75 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz c593b3185449e6d893941b7e40b7daf9 29336 libgoby-java_3.3.1+dfsg2-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmVsQ70ACgkQYAMWptwn dHZSGA/9GFdrIyK6c9r7P/KTdd0V7AOwl4p6awbMSE5MhS7N5hb/Vi333JaISTcg TV0t4ApvEnA4wwq9xBjMP52KIO0kWoTHcnRYD8OMaK7QWemEF45l4W2VClaFIyCh YeTPIYHs5JyM5e0RPDCErad84RaG46oHb66LqRk3l1+3IiLcUvhNQCBRFNN2jmsq 9mlL5Nn3TE8cs2IzgVzHN7dy3ak7tdI0oTWmRPfl21X8V4leZ/oQ1wQN9Q/I8CxZ lInN00ghgIUFb8f0sF6ZZfwtAKZ1WcyqvfkRIHEICqSFQ32dw7EulzB/tzN2Y2G5 ZPqbv1kLeFO6pdzknM9yu26s7uNo4KQjgT8J2vm5S6/Fn++jWIqHa8ekPgvggiLB ktunZ055EHMPrPTVpz3h+CnUGhh93FzXgD6BiQXUcH0/5wxNDa+33DLCHe/2JkQH hTXRpIdK7xyAR2a+prd9ygtGjZ+iBRpZIk5w7mM9JFHTWjfmrk9QZVbi/waQkmW/ r4Gdc6kBE/EpLc3cicdV5mWmEEbu3IklcgV/kyLupCwq34mETpNG5bjyZbWUCZvu VgLZ9vOBZXrw1agc8mDNQXcLrTuRxDMf7bv7THH53XlXJ5oeyPAdV5BdCC9mUT6p zFnVT2kMrjlczuNgLmdtdNKi4T6b8vyxzu6OiLCyEzMGLYIAEss= =oxEn -----END PGP SIGNATURE----- Tue Apr 23 08:56:48 UTC 2024 I: Checking whether the package is not for us Tue Apr 23 08:56:48 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Tue Apr 23 08:56:48 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Tue Apr 23 09:01:25 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 26 03:19:55 -12 2025 I: pbuilder-time-stamp: 1748272795 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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+dfsg2-10.dsc] I: copying [./libgoby-java_3.3.1+dfsg2.orig.tar.xz] I: copying [./libgoby-java_3.3.1+dfsg2-10.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Dec 3 09:00:45 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libgoby-java_3.3.1+dfsg2-10.dsc: no acceptable signature found 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+dfsg2-10.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/1102531/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='c7626c315e124c1a8e86c58b68353c1e' 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='1102531' 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.hG93ZCdI/pbuilderrc_ZwtR --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hG93ZCdI/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-10.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 codethink01-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 24 13:38 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1102531/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, pkg-config, 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 ... 19930 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 pkg-config; however: Package pkg-config 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} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbarclay-java{a} libbatik-java{a} libblas3{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcolt-free-java{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} libcups2{a} libcurl4{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdsiutils-java{a} libdynaloader-functions-perl{a} libeasymock-java{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastutil-java{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} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{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} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicb-utils-java{a} libice6{a} libicu4j-java{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libitext1-java{a} libjansi-java{a} libjavassist-java{a} libjaxb-api-java{a} libjaxen-java{a} libjaxp1.3-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} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libksba8{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm17{a} liblog4j1.2-java{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{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} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{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} libngs-java{a} libngs-jni{a} libnpth0{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{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} libpng16-16{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32{a} libprotobuf32{a} libprotoc32{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8{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} libssh2-1{a} libsub-override-perl{a} libsub-quote-perl{a} libsurefire-java{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxalan2-java{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{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} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxss1{a} libxstream-java{a} libxt6{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} ncbi-vdb-data{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra icc-profiles-free libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistlib-java-doc libdistro-info-perl libfile-mimeinfo-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian lynx mesa-vulkan-drivers pristine-tar psmisc publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended strace wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 432 newly installed, 0 to remove and 0 not upgraded. Need to get 371 MB of archives. After unpacking 942 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 binfmt-support arm64 2.2.2-7 [61.4 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.8-1 [811 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.8-1 [1848 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.6-1 [26.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-1 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-3 [69.1 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libreadline8 arm64 8.2-3+b1 [157 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1781 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.8-1 [597 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.6-1 [9224 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.6-1 [26.2 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.1.5-1 [1208 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3 [1127 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0 arm64 2.78.4-1 [1361 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 shared-mime-info arm64 2.4-1 [747 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-2+b2 [172 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libpng16-16 arm64 1.6.43-1 [271 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [106 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4 [263 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3+b1 [130 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 gtk-update-icon-cache arm64 3.24.41-1 [45.2 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 java-common all 0.75 [6640 B] Get: 50 http://deb.debian.org/debian trixie/main arm64 libavahi-common-data arm64 0.8-13+b1 [112 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libavahi-common3 arm64 0.8-13+b1 [42.4 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libdbus-1-3 arm64 1.14.10-4 [196 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libavahi-client3 arm64 0.8-13+b1 [45.8 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libcups2 arm64 2.4.7-1+b1 [230 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b1 [408 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.99-1 [1293 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libasound2-data all 1.2.10-3 [20.7 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libasound2 arm64 1.2.10-3 [333 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2 [2178 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libpcsclite1 arm64 2.0.1-1+b1 [50.3 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [42.7 MB] Get: 70 http://deb.debian.org/debian trixie/main arm64 default-jre-headless arm64 2:1.17-75 [3068 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 ant all 1.10.14-1 [2162 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 at-spi2-common all 2.50.0-1 [163 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 dctrl-tools arm64 2.24-3 [101 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 87 http://deb.debian.org/debian trixie/main arm64 libelf1 arm64 0.190-1+b1 [175 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1 [101 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libgtk2.0-common all 2.24.33-3 [2659 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libatk1.0-0 arm64 2.50.0-1+b1 [48.2 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1 [772 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-1+b1 [478 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.52.0+ds-1 [204 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.52.0+ds-1 [45.4 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.52.0+ds-1 [33.1 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libxcomposite1 arm64 1:0.4.5-1 [16.6 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libxfixes3 arm64 1:6.0.0-2 [22.9 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libxcursor1 arm64 1:1.2.1-1 [40.2 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libxdamage1 arm64 1:1.1.6-1 [15.2 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libxi6 arm64 2:1.8.1-1 [77.5 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libxinerama1 arm64 2:1.1.4-3 [17.8 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libxrandr2 arm64 2:1.5.4-1 [35.7 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libgtk2.0-0 arm64 2.24.33-3 [1661 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libglvnd0 arm64 1.7.0-1 [41.2 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 125 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libglapi-mesa arm64 23.3.5-1 [45.5 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [232 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get: 136 http://deb.debian.org/debian trixie/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libvulkan1 arm64 1.3.280.0-1 [119 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [18.7 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libdrm-radeon1 arm64 2.4.120-2 [21.1 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1 [88.9 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libllvm17 arm64 1:17.0.6-5 [21.3 MB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libsensors5 arm64 1:3.6.0-9 [33.9 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libgl1-mesa-dri arm64 23.3.5-1 [6928 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libglx-mesa0 arm64 23.3.5-1 [150 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libglx0 arm64 1.7.0-1 [30.7 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libgl1 arm64 1.7.0-1 [90.6 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libgif7 arm64 5.2.2-1 [43.7 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libxtst6 arm64 2:1.2.3-1.1 [27.8 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jre arm64 17.0.10+7-1 [173 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 default-jre arm64 2:1.17-75 [1056 B] Get: 155 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jdk-headless arm64 17.0.10+7-1 [70.6 MB] Get: 156 http://deb.debian.org/debian trixie/main arm64 default-jdk-headless arm64 2:1.17-75 [1108 B] Get: 157 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jdk arm64 17.0.10+7-1 [2370 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 default-jdk arm64 2:1.17-75 [1068 B] Get: 159 http://deb.debian.org/debian trixie/main arm64 libassuan0 arm64 2.5.6-1 [47.3 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 gpgconf arm64 2.2.40-1.1+b1 [558 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libksba8 arm64 1.6.6-1 [122 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libnpth0 arm64 1.6-3+b1 [17.9 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 dirmngr arm64 2.2.40-1.1+b1 [771 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 gnupg-utils arm64 2.2.40-1.1+b1 [881 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 gpg arm64 2.2.40-1.1+b1 [903 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 pinentry-curses arm64 1.2.1-3 [75.7 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 gpg-agent arm64 2.2.40-1.1+b1 [676 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 gpg-wks-client arm64 2.2.40-1.1+b1 [533 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 gpg-wks-server arm64 2.2.40-1.1+b1 [525 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 gpgsm arm64 2.2.40-1.1+b1 [650 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 gnupg all 2.2.40-1.1 [846 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 177 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 180 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1 [33.8 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b2 [35.2 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b2 [10.7 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.008-2+b1 [15.2 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b2 [22.3 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.28-1 [98.6 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.81-1+b1 [97.1 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.46-1+b1 [13.6 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 207 http://deb.debian.org/debian trixie/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get: 208 http://deb.debian.org/debian trixie/main arm64 libnet-ssleay-perl arm64 1.94-1 [327 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 215 http://deb.debian.org/debian trixie/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 wdiff arm64 1.2.2-6 [118 kB] Get: 217 http://deb.debian.org/debian trixie/main arm64 devscripts all 2.23.7 [1068 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 fastjar arm64 2:0.98-7 [75.5 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 jarwrapper all 0.79 [10.1 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28 [157 kB] Get: 221 http://deb.debian.org/debian trixie/main arm64 java-wrappers all 0.4 [8916 B] Get: 222 http://deb.debian.org/debian trixie/main arm64 javahelper all 0.79 [84.6 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 224 http://deb.debian.org/debian trixie/main arm64 junit4 all 4.13.2-4 [349 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 226 http://deb.debian.org/debian trixie/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 227 http://deb.debian.org/debian trixie/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 228 http://deb.debian.org/debian trixie/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 229 http://deb.debian.org/debian trixie/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 junit5 all 5.10.1-1 [2458 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 232 http://deb.debian.org/debian trixie/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 233 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 234 http://deb.debian.org/debian trixie/main arm64 libasm-java all 9.7-1 [394 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 236 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 237 http://deb.debian.org/debian trixie/main arm64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 240 http://deb.debian.org/debian trixie/main arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 243 http://deb.debian.org/debian trixie/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 244 http://deb.debian.org/debian trixie/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 246 http://deb.debian.org/debian trixie/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 247 http://deb.debian.org/debian trixie/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 248 http://deb.debian.org/debian trixie/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 249 http://deb.debian.org/debian trixie/main arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get: 250 http://deb.debian.org/debian trixie/main arm64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 251 http://deb.debian.org/debian trixie/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 libcommons-io-java all 2.16.0-1 [484 kB] Get: 253 http://deb.debian.org/debian trixie/main arm64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 254 http://deb.debian.org/debian trixie/main arm64 libbatik-java all 1.17+dfsg-1 [3923 kB] Get: 255 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 256 http://deb.debian.org/debian trixie/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 257 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 258 http://deb.debian.org/debian trixie/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 259 http://deb.debian.org/debian trixie/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 260 http://deb.debian.org/debian trixie/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 261 http://deb.debian.org/debian trixie/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 262 http://deb.debian.org/debian trixie/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 263 http://deb.debian.org/debian trixie/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 264 http://deb.debian.org/debian trixie/main arm64 libmaven-parent-java all 35-1 [6140 B] Get: 265 http://deb.debian.org/debian trixie/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 266 http://deb.debian.org/debian trixie/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 267 http://deb.debian.org/debian trixie/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 268 http://deb.debian.org/debian trixie/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 269 http://deb.debian.org/debian trixie/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 270 http://deb.debian.org/debian trixie/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 271 http://deb.debian.org/debian trixie/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 272 http://deb.debian.org/debian trixie/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 273 http://deb.debian.org/debian trixie/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 274 http://deb.debian.org/debian trixie/main arm64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 275 http://deb.debian.org/debian trixie/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 276 http://deb.debian.org/debian trixie/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 277 http://deb.debian.org/debian trixie/main arm64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 278 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 279 http://deb.debian.org/debian trixie/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 280 http://deb.debian.org/debian trixie/main arm64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 281 http://deb.debian.org/debian trixie/main arm64 libbyte-buddy-java all 1.14.13-1 [4709 kB] Get: 282 http://deb.debian.org/debian trixie/main arm64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB] Get: 283 http://deb.debian.org/debian trixie/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 284 http://deb.debian.org/debian trixie/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 285 http://deb.debian.org/debian trixie/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 286 http://deb.debian.org/debian trixie/main arm64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 287 http://deb.debian.org/debian trixie/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 288 http://deb.debian.org/debian trixie/main arm64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 289 http://deb.debian.org/debian trixie/main arm64 libcommons-digester-java all 1.8.1-6 [137 kB] Get: 290 http://deb.debian.org/debian trixie/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 291 http://deb.debian.org/debian trixie/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 292 http://deb.debian.org/debian trixie/main arm64 libcommons-math-java all 2.2-8 [926 kB] Get: 293 http://deb.debian.org/debian trixie/main arm64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 294 http://deb.debian.org/debian trixie/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 295 http://deb.debian.org/debian trixie/main arm64 libsnappy1v5 arm64 1.1.10-1+b1 [27.1 kB] Get: 296 http://deb.debian.org/debian trixie/main arm64 libsnappy-jni arm64 1.1.10.5-2 [6440 B] Get: 297 http://deb.debian.org/debian trixie/main arm64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 298 http://deb.debian.org/debian trixie/main arm64 libxz-java all 1.9-1 [143 kB] Get: 299 http://deb.debian.org/debian trixie/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 300 http://deb.debian.org/debian trixie/main arm64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 301 http://deb.debian.org/debian trixie/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 302 http://deb.debian.org/debian trixie/main arm64 libcommons-text-java all 1.11.0-1 [217 kB] Get: 303 http://deb.debian.org/debian trixie/main arm64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 304 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 305 http://deb.debian.org/debian trixie/main arm64 libpsl5 arm64 0.21.2-1+b1 [59.0 kB] Get: 306 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 307 http://deb.debian.org/debian trixie/main arm64 libssh2-1 arm64 1.11.0-4 [206 kB] Get: 308 http://deb.debian.org/debian trixie/main arm64 libcurl4 arm64 8.5.0-2 [400 kB] Get: 309 http://deb.debian.org/debian trixie/main arm64 libdistlib-java all 1.0-4 [72.1 kB] Get: 310 http://deb.debian.org/debian trixie/main arm64 libjaxen-java all 1.1.6-4 [214 kB] Get: 311 http://deb.debian.org/debian trixie/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 312 http://deb.debian.org/debian trixie/main arm64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 313 http://deb.debian.org/debian trixie/main arm64 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 314 http://deb.debian.org/debian trixie/main arm64 libqdox-java all 1.12.1-3 [172 kB] Get: 315 http://deb.debian.org/debian trixie/main arm64 libfop-java all 1:2.8-3 [10.1 MB] Get: 316 http://deb.debian.org/debian trixie/main arm64 libitext1-java all 1.4-7 [1257 kB] Get: 317 http://deb.debian.org/debian trixie/main arm64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 318 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 319 http://deb.debian.org/debian trixie/main arm64 libdoxia-java all 1.12.0-1 [459 kB] Get: 320 http://deb.debian.org/debian trixie/main arm64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 321 http://deb.debian.org/debian trixie/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 322 http://deb.debian.org/debian trixie/main arm64 velocity all 1.7-7 [431 kB] Get: 323 http://deb.debian.org/debian trixie/main arm64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 324 http://deb.debian.org/debian trixie/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 325 http://deb.debian.org/debian trixie/main arm64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 326 http://deb.debian.org/debian trixie/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 327 http://deb.debian.org/debian trixie/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 328 http://deb.debian.org/debian trixie/main arm64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 329 http://deb.debian.org/debian trixie/main arm64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 330 http://deb.debian.org/debian trixie/main arm64 libfastutil-java all 8.5.12+dfsg-1 [19.6 MB] Get: 331 http://deb.debian.org/debian trixie/main arm64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 332 http://deb.debian.org/debian trixie/main arm64 libxstream-java all 1.4.20-1 [565 kB] Get: 333 http://deb.debian.org/debian trixie/main arm64 libjsap-java all 2.1-5 [102 kB] Get: 334 http://deb.debian.org/debian trixie/main arm64 liblogback-java all 1:1.2.11-5 [701 kB] Get: 335 http://deb.debian.org/debian trixie/main arm64 libdsiutils-java all 2.7.3+dfsg-1 [524 kB] Get: 336 http://deb.debian.org/debian trixie/main arm64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 337 http://deb.debian.org/debian trixie/main arm64 libeasymock-java all 5.2.0-1 [131 kB] Get: 338 http://deb.debian.org/debian trixie/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 339 http://deb.debian.org/debian trixie/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 340 http://deb.debian.org/debian trixie/main arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 341 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240201-3 [360 kB] Get: 342 http://deb.debian.org/debian trixie/main arm64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 343 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto7 arm64 2.28.7-1 [266 kB] Get: 344 http://deb.debian.org/debian trixie/main arm64 libmbedx509-1 arm64 2.28.7-1 [130 kB] Get: 345 http://deb.debian.org/debian trixie/main arm64 libmbedtls14 arm64 2.28.7-1 [159 kB] Get: 346 http://deb.debian.org/debian trixie/main arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 347 http://deb.debian.org/debian trixie/main arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [977 kB] Get: 348 http://deb.debian.org/debian trixie/main arm64 libncbi-ngs3 arm64 3.0.3+dfsg-6 [141 kB] Get: 349 http://deb.debian.org/debian trixie/main arm64 libngs-jni arm64 3.0.3+dfsg-6 [23.4 kB] Get: 350 http://deb.debian.org/debian trixie/main arm64 libngs-java arm64 3.0.3+dfsg-6 [110 kB] Get: 351 http://deb.debian.org/debian trixie/main arm64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 352 http://deb.debian.org/debian trixie/main arm64 libhtsjdk-java all 4.1.0+dfsg-1 [1833 kB] Get: 353 http://deb.debian.org/debian trixie/main arm64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get: 354 http://deb.debian.org/debian trixie/main arm64 libicu4j-java all 73.2-1 [16.4 MB] Get: 355 http://deb.debian.org/debian trixie/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 356 http://deb.debian.org/debian trixie/main arm64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB] Get: 357 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 358 http://deb.debian.org/debian trixie/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 359 http://deb.debian.org/debian trixie/main arm64 libjavassist-java all 1:3.27.0-1 [731 kB] Get: 360 http://deb.debian.org/debian trixie/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 361 http://deb.debian.org/debian trixie/main arm64 libjboss-logging-java all 3.5.3-1 [56.2 kB] Get: 362 http://deb.debian.org/debian trixie/main arm64 libjboss-vfs-java all 3.2.15.Final-3 [130 kB] Get: 363 http://deb.debian.org/debian trixie/main arm64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get: 364 http://deb.debian.org/debian trixie/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 365 http://deb.debian.org/debian trixie/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 366 http://deb.debian.org/debian trixie/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 367 http://deb.debian.org/debian trixie/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 368 http://deb.debian.org/debian trixie/main arm64 libjetty9-java all 9.4.54-1 [2980 kB] Get: 369 http://deb.debian.org/debian trixie/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 370 http://deb.debian.org/debian trixie/main arm64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 371 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 372 http://deb.debian.org/debian trixie/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 373 http://deb.debian.org/debian trixie/main arm64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 374 http://deb.debian.org/debian trixie/main arm64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 375 http://deb.debian.org/debian trixie/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 376 http://deb.debian.org/debian trixie/main arm64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 377 http://deb.debian.org/debian trixie/main arm64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 378 http://deb.debian.org/debian trixie/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 379 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 380 http://deb.debian.org/debian trixie/main arm64 libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get: 381 http://deb.debian.org/debian trixie/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 382 http://deb.debian.org/debian trixie/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 383 http://deb.debian.org/debian trixie/main arm64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 384 http://deb.debian.org/debian trixie/main arm64 libmaven-dependency-analyzer-java all 1.13.0-1 [30.4 kB] Get: 385 http://deb.debian.org/debian trixie/main arm64 libmaven-dependency-tree-java all 3.2.1-1 [34.7 kB] Get: 386 http://deb.debian.org/debian trixie/main arm64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 387 http://deb.debian.org/debian trixie/main arm64 libmaven-dependency-plugin-java all 3.5.0-1 [173 kB] Get: 388 http://deb.debian.org/debian trixie/main arm64 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 389 http://deb.debian.org/debian trixie/main arm64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 390 http://deb.debian.org/debian trixie/main arm64 libmaven-javadoc-plugin-java all 3.4.1-3 [454 kB] Get: 391 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 392 http://deb.debian.org/debian trixie/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 393 http://deb.debian.org/debian trixie/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 394 http://deb.debian.org/debian trixie/main arm64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 395 http://deb.debian.org/debian trixie/main arm64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 396 http://deb.debian.org/debian trixie/main arm64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 397 http://deb.debian.org/debian trixie/main arm64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 398 http://deb.debian.org/debian trixie/main arm64 libmaven-source-plugin-java all 3.2.1-2 [27.6 kB] Get: 399 http://deb.debian.org/debian trixie/main arm64 libpaper1 arm64 1.1.29 [12.6 kB] Get: 400 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 1.1.29 [8776 B] Get: 401 http://deb.debian.org/debian trixie/main arm64 libpicard-java all 3.1.1+dfsg-1 [1743 kB] Get: 402 http://deb.debian.org/debian trixie/main arm64 libpj-java all 0.0~20150107+dfsg-5 [1389 kB] Get: 403 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 404 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3+b1 [916 kB] Get: 405 http://deb.debian.org/debian trixie/main arm64 libprotobuf32 arm64 3.21.12-8+b1 [851 kB] Get: 406 http://deb.debian.org/debian trixie/main arm64 libprotobuf-lite32 arm64 3.21.12-8+b1 [249 kB] Get: 407 http://deb.debian.org/debian trixie/main arm64 libprotobuf-dev arm64 3.21.12-8+b1 [1257 kB] Get: 408 http://deb.debian.org/debian trixie/main arm64 libprotobuf-java all 3.21.12-8 [1259 kB] Get: 409 http://deb.debian.org/debian trixie/main arm64 libprotoc32 arm64 3.21.12-8+b1 [748 kB] Get: 410 http://deb.debian.org/debian trixie/main arm64 libreflections-java all 0.10.2+dfsg-2 [125 kB] Get: 411 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 412 http://deb.debian.org/debian trixie/main arm64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 413 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1 [975 kB] Get: 414 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB] Get: 415 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 416 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.14-1 [732 kB] Get: 417 http://deb.debian.org/debian trixie/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 418 http://deb.debian.org/debian trixie/main arm64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 419 http://deb.debian.org/debian trixie/main arm64 libxml2-utils arm64 2.9.14+dfsg-1.3+b2 [97.5 kB] Get: 420 http://deb.debian.org/debian trixie/main arm64 libxt6 arm64 1:1.2.1-1.1 [172 kB] Get: 421 http://deb.debian.org/debian trixie/main arm64 maven all 3.8.7-2 [19.3 kB] Get: 422 http://deb.debian.org/debian trixie/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 423 http://deb.debian.org/debian trixie/main arm64 maven-debian-helper all 2.6.4 [108 kB] Get: 424 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 425 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 426 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 427 http://deb.debian.org/debian trixie/main arm64 protobuf-compiler arm64 3.21.12-8+b1 [84.5 kB] Get: 428 http://deb.debian.org/debian trixie/main arm64 zip arm64 3.0-13 [223 kB] Get: 429 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 430 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.3.2-1 [26.5 MB] Get: 431 http://deb.debian.org/debian trixie/main arm64 r-cran-rjava arm64 1.0-11-1 [701 kB] Get: 432 http://deb.debian.org/debian trixie/main arm64 testng all 6.9.12-4 [795 kB] Fetched 371 MB in 2s (149 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19930 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../binfmt-support_2.2.2-7_arm64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_arm64.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 20269 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_arm64.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../5-libreadline8_8.2-3+b1_arm64.deb ... Unpacking libreadline8:arm64 (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_arm64.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... 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 ... 21257 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_arm64.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-4_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-4_arm64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.1.5-1_arm64.deb ... Unpacking openssl (3.1.5-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../008-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-3_arm64.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... 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Current default time zone: 'Etc/UTC' Local time is now: Mon May 26 15:21:02 UTC 2025. Universal Time is now: Mon May 26 15:21:02 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.10-3) ... Setting up libjavassist-java (1:3.27.0-1) ... Setting up zip (3.0-13) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libblas3:arm64 (3.12.0-3) ... 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 (1.8.1-1+b2) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2+b2) ... Setting up libjaxen-java (1.1.6-4) ... 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Setting up libdrm-common (2.4.120-2) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:arm64 (0.190-1+b1) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up readline-common (8.2-3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liburi-perl (5.28-1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3) ... Setting up libprotoc32:arm64 (3.21.12-8+b1) ... Setting up libnet-ssleay-perl:arm64 (1.94-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libice6:arm64 (2:1.0.10-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxstream-java (1.4.20-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.12.0-3) ... 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 libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libjetty9-java (9.4.54-1) ... Setting up libxcb-xfixes0:arm64 (1.15-1) ... Setting up java-wrappers (0.4) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libmbedx509-1:arm64 (2.28.7-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up protobuf-compiler (3.21.12-8+b1) ... Setting up libmbedtls14:arm64 (2.28.7-1) ... Setting up libjboss-vfs-java (3.2.15.Final-3) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:arm64 (3.1-20230828-1) ... Setting up libreadline8:arm64 (8.2-3+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-13+b1) ... Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:arm64 (2:3.99-1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libdevel-callchecker-perl:arm64 (0.008-2+b1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:arm64 (3.21.12-8+b1) ... Setting up libxcb-present0:arm64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:arm64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b1) ... Setting up libxcb-sync1:arm64 (1.15-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up testng (6.9.12-4) ... Setting up shared-mime-info (2.4-1) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libxcb-dri2-0:arm64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up dwz (0.15-1) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up groff-base (1.23.0-3) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libhtml-parser-perl:arm64 (3.81-1+b1) ... Setting up gpgconf (2.2.40-1.1+b1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libcurl4:arm64 (8.5.0-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:arm64 (2:1.8.7-1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3+b1) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-configuration-java (1.10-6) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.9.14+dfsg-1.3+b2) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libllvm17:arm64 (1:17.0.6-5) ... Setting up libxcomposite1:arm64 (1:0.4.5-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libreflections-java (0.10.2+dfsg-2) ... Setting up libavahi-client3:arm64 (0.8-13+b1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-1.1+b1) ... Setting up gnupg-utils (2.2.40-1.1+b1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-6) ... Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up libpaper1:arm64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.41-1) ... Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-7) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libngs-jni:arm64 (3.0.3+dfsg-6) ... Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... Setting up libxdamage1:arm64 (1:1.1.6-1) ... Setting up gpg-agent (2.2.40-1.1+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.16.0-1) ... Setting up libdrm-radeon1:arm64 (2.4.120-2) ... Setting up libcommons-digester-java (1.8.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... Setting up libdistlib-java (1.0-4) ... Setting up libparams-classify-perl:arm64 (0.015-2+b2) ... Setting up gpgsm (2.2.40-1.1+b1) ... Setting up libpango-1.0-0:arm64 (1.52.0+ds-1) ... Setting up libgl1-mesa-dri:arm64 (23.3.5-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up libpaper-utils (1.1.29) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-1+b1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-1.1+b1) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (46.0-1) ... 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 (0.016-2) ... Setting up libxfixes3:arm64 (1:6.0.0-2) ... Setting up libxinerama1:arm64 (2:1.1.4-3) ... Setting up libxrandr2:arm64 (2:1.5.4-1) ... Setting up libxt6:arm64 (1:1.2.1-1.1) ... Setting up gpg-wks-server (2.2.40-1.1+b1) ... Setting up libcups2:arm64 (2.4.7-1+b1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-dependency-tree-java (3.2.1-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libngs-java:arm64 (3.0.3+dfsg-6) ... Setting up libpangoft2-1.0-0:arm64 (1.52.0+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libhtsjdk-java (4.1.0+dfsg-1) ... Setting up libpangocairo-1.0-0:arm64 (1.52.0+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libxft2:arm64 (2.3.6-1+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:arm64 (23.3.5-1) ... Setting up libxi6:arm64 (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.40-1.1+b1) ... Setting up libglx0:arm64 (1.7.0-1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:arm64 (2:1.2.3-1.1) ... Setting up libbatik-java (1.17+dfsg-1) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libtk8.6:arm64 (8.6.14-1) ... Setting up libxcursor1:arm64 (1:1.2.1-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up libgl1:arm64 (1.7.0-1) ... Setting up r-base-core (4.3.2-1) ... Creating config file /etc/R/Renviron with new version Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up libfop-java (1:2.8-3) ... Setting up libgkl-java (0.8.11+dfsg-2) ... Setting up libgtk2.0-0:arm64 (2.24.33-3) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up libpicard-java (3.1.1+dfsg-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.79) ... Setting up libprotobuf-java (3.21.12-8) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-interactivity-api-java (1.1-2) ... Setting up libplexus-velocity-java (1.2-3.1) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libmaven-shared-incremental-java (1.1-4) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libmaven-dependency-analyzer-java (1.13.0-1) ... Setting up libplexus-compiler-java (2.12.1-2) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libmaven-source-plugin-java (3.2.1-2) ... Setting up libbyte-buddy-java (1.14.13-1) ... Setting up libbuild-helper-maven-plugin-java (3.3.0-1) ... Setting up libeasymock-java (5.2.0-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-1) ... Setting up libcommons-text-java (1.11.0-1) ... Setting up libdoxia-core-java (1.12.0-1) ... Setting up libdoxia-java (1.12.0-1) ... Setting up libmaven-reporting-api-java (3.1.1-1) ... Setting up libmaven-reporting-exec-java (1.6.0-1) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.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-repo-helper (1.11) ... Setting up maven (3.8.7-2) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk-headless:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up default-jre-headless (2:1.17-75) ... Setting up ant-contrib (1.0~b3+svn177-12) ... Setting up openjdk-17-jre:arm64 (17.0.10+7-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up default-jdk-headless (2:1.17-75) ... Setting up libjsap-java (2.1-5) ... Setting up r-cran-rjava (1.0-11-1) ... Setting up libdsiutils-java (2.7.3+dfsg-1) ... Setting up junit5 (5.10.1-1) ... Setting up default-jdk (2:1.17-75) ... Setting up libicb-utils-java (2.0.1+git20161002.afee1d9-5) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-javadoc-plugin-java (3.4.1-3) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-dependency-plugin-java (3.5.0-1) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.4) ... Processing triggers for ca-certificates (20240203) ... 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+dfsg2-10_source.changes dpkg-buildpackage: info: source package libgoby-java dpkg-buildpackage: info: source version 3.3.1+dfsg2-10 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 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] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0 [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 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:2.4 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [INFO] [INFO] --- build-helper-maven-plugin: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] --- maven-antrun-plugin: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] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-io --- [INFO] Copying 2 resources [INFO] Copying 1 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 260 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [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/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal 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] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io --- [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] --- maven-resources-plugin:3.3.0: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] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin: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] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-io >>> [INFO] [INFO] --- build-helper-maven-plugin: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] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-io <<< [INFO] [INFO] [INFO] --- maven-source-plugin:3.2.1: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] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-io --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package samples... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby.util.pool... [WARNING] Loading source files for package org.campagnelab.goby.util.motifs... [WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... [WARNING] Loading source files for package org.campagnelab.goby.util.commits... [WARNING] Loading source files for package org.campagnelab.goby.util.barcode... [WARNING] Loading source files for package org.campagnelab.goby.util... [WARNING] Loading source files for package org.campagnelab.goby.stats... [WARNING] Loading source files for package org.campagnelab.goby.reads... [WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... [WARNING] Loading source files for package org.campagnelab.goby.readers.sam... [WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.predictions... [WARNING] Loading source files for package org.campagnelab.goby.parsers... [WARNING] Loading source files for package org.campagnelab.goby.modes... [WARNING] Loading source files for package org.campagnelab.goby.modes.formats... [WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... [WARNING] Loading source files for package org.campagnelab.goby.modes.core... [WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package org.campagnelab.goby.exception... [WARNING] Loading source files for package org.campagnelab.goby.counts.compound... [WARNING] Loading source files for package org.campagnelab.goby.counts... [WARNING] Loading source files for package org.campagnelab.goby.config... [WARNING] Loading source files for package org.campagnelab.goby.compression... [WARNING] Loading source files for package org.campagnelab.goby.cli... [WARNING] Loading source files for package org.campagnelab.goby.baseinfo... [WARNING] Loading source files for package org.campagnelab.goby.alignments... [WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... [WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... [WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... [WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.R... [WARNING] Loading source files for package org.campagnelab.dl.varanalysis.protobuf... [WARNING] Constructing Javadoc information... [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] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.10+7-Debian-1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeaderOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndexOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHitsOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMappingOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntryOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequencyOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutputOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/CodecHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePositionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.BaseOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SampleOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutputOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequencyOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfoOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/config/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/exception/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/help-doc.html... [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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-distribution --- [INFO] Copying 3 resources [INFO] Copying 72 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 525 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/classes [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/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal 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] --- maven-resources-plugin:3.3.0: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] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 120 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/test-classes [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] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin: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] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-distribution >>> [INFO] [INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-distribution <<< [INFO] [INFO] [INFO] --- maven-source-plugin:3.2.1: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] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-distribution --- [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package samples... [WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package org.campagnelab.goby.util.pool... [WARNING] Loading source files for package org.campagnelab.goby.util.motifs... [WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... [WARNING] Loading source files for package org.campagnelab.goby.util.commits... [WARNING] Loading source files for package org.campagnelab.goby.util.barcode... [WARNING] Loading source files for package org.campagnelab.goby.util... [WARNING] Loading source files for package org.campagnelab.goby.stats... [WARNING] Loading source files for package org.campagnelab.goby.reads... [WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... [WARNING] Loading source files for package org.campagnelab.goby.readers.sam... [WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.predictions... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DataProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DisplaySequenceVariationsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DumpTargetInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionClient.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ElementIndexComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/EmpiricalPMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EmpiricalPValueEstimator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/EntropicIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/EntryFlagHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/EquivalentIndelRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EquivalentIndelRegionCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EstimatedTestDistributions.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EvidenceCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ExportableAlignmentEntryData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ExportSplicingEvents.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ExtractSplicingEventsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FalseDiscoveryRateMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/FastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoder.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: Tag @see: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder(MG4J). [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J). [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderOrder1.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderPlus.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoder.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: Tag @see: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder(MG4J) [WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J) [WARNING] ^ [WARNING] Date: 1/15/12 [WARNING] Time: 11:02 AM [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderI.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: Tag @link: 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: Tag @link: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderOrder1.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: Tag @link: 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: Tag @link: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderPlus.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: Tag @link: 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: Tag @link: reference not found: #BITS [WARNING] * @return the current bit stream window in the lower {@link #BITS} bits. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FastaToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.html... 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[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: Tag @link: 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: Tag @link: 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: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IOUtil.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IsDone.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/LastParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/Merge.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/MethylStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/ModifyAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadSet.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SamplePair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SortMode.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/StatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/StreamSignal.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html... [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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Timer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TrimMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: Tag @link: 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: Tag @link: 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: Tag @link: 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: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int) [WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/help-doc.html... [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] --- maven-assembly-plugin:3.4.2:single (make-assembly) @ goby-distribution --- [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 [ 0.040 s] [INFO] Goby I/O ........................................... SUCCESS [ 22.851 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 22.760 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 45.763 s [INFO] Finished at: 2025-05-26T03:22:11-12:00 [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] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --------------------< org.campagnelab.goby:goby-io >-------------------- [INFO] Building Goby I/O 3.3.1 [2/3] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0 [WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3 [INFO] [INFO] --- build-helper-maven-plugin: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] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-io --- [INFO] Copying 2 resources [INFO] Copying 1 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 260 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes [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/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal 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] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io --- [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] --- maven-resources-plugin:3.3.0: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] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin: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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-distribution --- [INFO] Copying 3 resources [INFO] Copying 72 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 525 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/classes [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/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal 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] --- maven-resources-plugin:3.3.0: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] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 120 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/test-classes [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] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite 03:22:30.929 INFO RLoggerMainLoopCallback - 03:22:30.941 INFO RLoggerMainLoopCallback - R version 4.3.2 (2023-10-31) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 03:22:30.942 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. 03:22:30.942 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. 03:22:30.942 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] 03:22:31.581 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 AGC03:22:35.486 WARN MessageChunksWriter - Using chunk-size=10000 03:22:35.486 WARN MessageChunksWriter - Using chunk-size=9 03:22:35.491 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 03:22:35.494 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 03:22:35.499 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. 03:22:35.629 INFO BullardUpperQuartileNormalization - normalization denominator 46900.1 for sample B-7 03:22:35.629 INFO BullardUpperQuartileNormalization - normalization denominator 47604.9 for sample B-3 03:22:35.629 INFO BullardUpperQuartileNormalization - normalization denominator 93800.1 for sample A-3 03:22:35.629 INFO BullardUpperQuartileNormalization - normalization denominator 94248.6 for sample A-12 03:22:35.629 INFO BullardUpperQuartileNormalization - normalization denominator 48373.7 for sample B-15 03:22:35.630 INFO BullardUpperQuartileNormalization - normalization denominator 47989.3 for sample B-14 03:22:35.630 INFO BullardUpperQuartileNormalization - normalization denominator 48630.0 for sample B-11 03:22:35.630 INFO BullardUpperQuartileNormalization - normalization denominator 97067.8 for sample A-17 03:22:35.630 INFO BullardUpperQuartileNormalization - normalization denominator 47668.9 for sample B-2 03:22:35.631 INFO BullardUpperQuartileNormalization - normalization denominator 46323.4 for sample B-10 03:22:35.631 INFO BullardUpperQuartileNormalization - normalization denominator 99502.5 for sample A-16 03:22:35.631 INFO BullardUpperQuartileNormalization - normalization denominator 48181.5 for sample B-8 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 49398.8 for sample B-4 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 96106.7 for sample A-2 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 94761.2 for sample A-0 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 46964.1 for sample B-6 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 90532.5 for sample A-9 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 96234.8 for sample A-8 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 93159.4 for sample A-5 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 97708.5 for sample A-4 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 97644.4 for sample A-6 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 95978.6 for sample A-7 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 48309.6 for sample B-5 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 96234.8 for sample A-10 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 93351.6 for sample A-14 03:22:35.632 INFO BullardUpperQuartileNormalization - normalization denominator 48437.8 for sample B-9 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 97131.8 for sample A-1 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 47220.4 for sample B-0 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 47348.6 for sample B-12 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 48373.7 for sample B-13 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 93736.1 for sample A-19 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 97003.7 for sample A-18 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 98028.8 for sample A-15 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 48437.8 for sample B-1 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 94440.9 for sample A-13 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 96491.1 for sample A-11 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 48501.8 for sample B-16 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 48758.1 for sample B-17 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 45939.0 for sample B-19 03:22:35.633 INFO BullardUpperQuartileNormalization - normalization denominator 47092.3 for sample B-18 Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T]03:22:35.736 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 03:22:35.780 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 03:22:35.780 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 03:22:35.796 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 03:22:35.796 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value 03:22:35.938 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. 03:22:35.982 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. 03:22:35.982 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value 03:22:36.094 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. 03:22:36.115 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 [1.0059300153936155, 0.5027518854310272, 0.00852993739323232, -0.9920815079203505, 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 03:22:51.070 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 03:22:51.074 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 03:22:51.077 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 03:22:51.080 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 03:22:51.082 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 03:22:51.085 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 03:22:51.087 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 03:22:51.090 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 03:22:51.092 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 03:22:51.095 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 03:22:51.200 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 03:22:51.203 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 03:22:51.205 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 03:22:51.207 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 03:22:51.210 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 03:22:51.212 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 03:22:51.215 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 03:22:51.219 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 03:22:51.221 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 03:22:51.223 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 03:22:51.301 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 03:22:51.302 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 03:22:51.304 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 03:22:51.306 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 03:22:51.308 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 03:22:51.310 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 03:22:51.313 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 03:22:51.314 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 03:22:51.316 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 03:22:51.318 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 03:22:51.457 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 03:22:51.460 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 03:22:51.462 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 03:22:51.465 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 03:22:51.469 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 03:22:51.472 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 03:22:51.476 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 03:22:51.480 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 03:22:51.482 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 03:22:51.484 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 03:22:51.574 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 03:22:51.575 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 03:22:51.577 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 03:22:51.579 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 03:22:51.581 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 03:22:51.583 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 03:22:51.585 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 03:22:51.587 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 03:22:51.589 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 03:22:51.591 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 03:22:51.661 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 03:22:51.663 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 03:22:51.664 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 03:22:51.666 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 03:22:51.668 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 03:22:51.669 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 03:22:51.671 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 03:22:51.673 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 03:22:51.674 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 03:22:51.676 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 03:22:51.740 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 03:22:51.742 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 03:22:51.744 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 03:22:51.746 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 03:22:51.748 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 03:22:51.750 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 03:22:51.752 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 03:22:51.754 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 03:22:51.756 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 03:22:51.758 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 03:22:51.826 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 03:22:51.828 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 03:22:51.829 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 03:22:51.831 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 03:22:51.833 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 03:22:51.834 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 03:22:51.836 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 03:22:51.837 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 03:22:51.839 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 03:22:51.840 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 03:22:51.898 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 03:22:51.900 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 03:22:51.902 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 03:22:51.903 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 03:22:51.905 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 03:22:51.906 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 03:22:51.908 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 03:22:51.910 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 03:22:51.911 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 03:22:51.913 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 03:22:51.996 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 03:22:51.998 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 03:22:52.000 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 03:22:52.002 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 03:22:52.003 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 03:22:52.006 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 03:22:52.008 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 03:22:52.010 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 03:22:52.012 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 03:22:52.014 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 03:22:52.076 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 03:22:52.077 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 03:22:52.079 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 03:22:52.080 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 03:22:52.082 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 03:22:52.083 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 03:22:52.085 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 03:22:52.087 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 03:22:52.088 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 03:22:52.090 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 03:22:52.177 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 03:22:52.178 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 03:22:52.180 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 03:22:52.182 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 03:22:52.183 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 03:22:52.185 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 03:22:52.187 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 03:22:52.189 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 03:22:52.190 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 03:22:52.192 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: 41455 length: 2 Appending count: 31168 length: 8 Appending count: 9791 length: 2 Appending count: 4858 length: 1 Appending count: 47444 length: 8 Appending count: 44452 length: 4 Appending count: 38658 length: 6 Appending count: 34057 length: 6 Appending count: 9469 length: 6 Appending count: 5135 length: 10 Appending count: 12379 length: 8 Appending count: 2392 length: 4 Appending count: 32146 length: 2 Appending count: 27159 length: 7 Appending count: 7836 length: 10 Appending count: 21071 length: 10 Appending count: 48713 length: 1 Appending count: 29911 length: 10 Appending count: 44627 length: 8 Appending count: 45978 length: 1 Appending count: 42892 length: 1 Appending count: 14892 length: 8 Appending count: 43779 length: 3 Appending count: 4870 length: 3 Appending count: 2134 length: 6 Appending count: 8626 length: 5 Appending count: 30674 length: 1 Appending count: 16850 length: 5 Appending count: 43317 length: 4 Appending count: 11819 length: 9 position= 0 count= 41455 position= 1 count= 41455 position= 2 count= 31168 position= 3 count= 31168 position= 4 count= 31168 position= 5 count= 31168 position= 6 count= 31168 position= 7 count= 31168 position= 8 count= 31168 position= 9 count= 31168 position= 10 count= 9791 position= 11 count= 9791 position= 12 count= 4858 position= 13 count= 47444 position= 14 count= 47444 position= 15 count= 47444 position= 16 count= 47444 position= 17 count= 47444 position= 18 count= 47444 position= 19 count= 47444 position= 20 count= 47444 position= 21 count= 44452 position= 22 count= 44452 position= 23 count= 44452 position= 24 count= 44452 position= 25 count= 38658 position= 26 count= 38658 position= 27 count= 38658 position= 28 count= 38658 position= 29 count= 38658 position= 30 count= 38658 position= 31 count= 34057 position= 32 count= 34057 position= 33 count= 34057 position= 34 count= 34057 position= 35 count= 34057 position= 36 count= 34057 position= 37 count= 9469 position= 38 count= 9469 position= 39 count= 9469 position= 40 count= 9469 position= 41 count= 9469 position= 42 count= 9469 position= 43 count= 5135 position= 44 count= 5135 position= 45 count= 5135 position= 46 count= 5135 position= 47 count= 5135 position= 48 count= 5135 position= 49 count= 5135 position= 50 count= 5135 position= 51 count= 5135 position= 52 count= 5135 position= 53 count= 12379 position= 54 count= 12379 position= 55 count= 12379 position= 56 count= 12379 position= 57 count= 12379 position= 58 count= 12379 position= 59 count= 12379 position= 60 count= 12379 position= 61 count= 2392 position= 62 count= 2392 position= 63 count= 2392 position= 64 count= 2392 position= 65 count= 32146 position= 66 count= 32146 position= 67 count= 27159 position= 68 count= 27159 position= 69 count= 27159 position= 70 count= 27159 position= 71 count= 27159 position= 72 count= 27159 position= 73 count= 27159 position= 74 count= 7836 position= 75 count= 7836 position= 76 count= 7836 position= 77 count= 7836 position= 78 count= 7836 position= 79 count= 7836 position= 80 count= 7836 position= 81 count= 7836 position= 82 count= 7836 position= 83 count= 7836 position= 84 count= 21071 position= 85 count= 21071 position= 86 count= 21071 position= 87 count= 21071 position= 88 count= 21071 position= 89 count= 21071 position= 90 count= 21071 position= 91 count= 21071 position= 92 count= 21071 position= 93 count= 21071 position= 94 count= 48713 position= 95 count= 29911 position= 96 count= 29911 position= 97 count= 29911 position= 98 count= 29911 position= 99 count= 29911 position= 100 count= 29911 position= 101 count= 29911 position= 102 count= 29911 position= 103 count= 29911 position= 104 count= 29911 position= 105 count= 44627 position= 106 count= 44627 position= 107 count= 44627 position= 108 count= 44627 position= 109 count= 44627 position= 110 count= 44627 position= 111 count= 44627 position= 112 count= 44627 position= 113 count= 45978 position= 114 count= 42892 position= 115 count= 14892 position= 116 count= 14892 position= 117 count= 14892 position= 118 count= 14892 position= 119 count= 14892 position= 120 count= 14892 position= 121 count= 14892 position= 122 count= 14892 position= 123 count= 43779 position= 124 count= 43779 position= 125 count= 43779 position= 126 count= 4870 position= 127 count= 4870 position= 128 count= 4870 position= 129 count= 2134 position= 130 count= 2134 position= 131 count= 2134 position= 132 count= 2134 position= 133 count= 2134 position= 134 count= 2134 position= 135 count= 8626 position= 136 count= 8626 position= 137 count= 8626 position= 138 count= 8626 position= 139 count= 8626 position= 140 count= 30674 position= 141 count= 16850 position= 142 count= 16850 position= 143 count= 16850 position= 144 count= 16850 position= 145 count= 16850 position= 146 count= 43317 position= 147 count= 43317 position= 148 count= 43317 position= 149 count= 43317 position= 150 count= 11819 position= 151 count= 11819 position= 152 count= 11819 position= 153 count= 11819 position= 154 count= 11819 position= 155 count= 11819 position= 156 count= 11819 position= 157 count= 11819 position= 158 count= 11819 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 03:22:53.767 WARN WiggleWindow - Not writing 101 7 03:22:53.768 WARN WiggleWindow - Not writing 111 7 03:22:53.768 WARN WiggleWindow - Not writing 131 8 03:22:53.768 WARN WiggleWindow - Not writing 141 8 03:22:53.768 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) 03:22:53.793 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 03:22:53.804 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 03:22:53.814 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 03:22:53.819 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 03:22:53.825 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 03:22:53.833 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.840 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.851 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.854 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 } 03:22:53.879 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 03:22:53.958 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.959 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.961 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.969 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.970 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.971 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.978 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.979 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.981 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 03:22:53.989 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.991 WARN MessageChunksWriter - Using chunk-size=1000 03:22:53.992 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.003 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.007 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.008 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.010 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 03:22:54.011 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 03:22:54.013 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 03:22:54.016 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.017 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.018 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' 03:22:54.051 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 03:22:54.055 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 03:22:54.059 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 03:22:54.062 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 03:22:54.066 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 03:22:54.069 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 03:22:54.073 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 03:22:54.079 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.082 WARN MessageChunksWriter - Using chunk-size=1 03:22:54.086 WARN MessageChunksWriter - Using chunk-size=1 03:22:54.090 WARN MessageChunksWriter - Using chunk-size=1 03:22:54.093 WARN MessageChunksWriter - Using chunk-size=1 03:22:54.099 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.102 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 03:22:54.107 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.108 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries 03:22:54.112 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.113 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.118 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.119 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.124 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.125 WARN MessageChunksWriter - Using chunk-size=1000 0 2 03:22:54.130 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.131 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 03:22:54.136 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.138 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.143 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.144 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.148 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.149 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 03:22:54.162 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.205 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.206 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.231 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:54.256 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.257 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.264 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. 03:22:54.290 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. 03:22:54.290 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 03:22:54.290 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: 300.62M/15.48G/68.47M/369.10M/15.78G 03:22:54.298 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 03:22:54.331 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. 03:22:54.335 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. 03:22:54.365 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. 03:22:54.365 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. 03:22:54.365 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. 03:22:54.365 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 03:22:54.365 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. 03:22:54.365 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: 84.67M/15.69G/284.43M/369.10M/15.78G 03:22:54.368 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. 03:22:54.385 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. 03:22:54.424 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.451 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.453 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.476 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:54.498 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.499 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: 176.94M/15.60G/192.16M/369.10M/15.78G found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 03:22:54.559 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.581 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.582 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.607 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:54.628 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.629 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.631 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. 03:22:54.636 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. 03:22:54.636 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 03:22:54.636 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: 235.66M/15.54G/133.44M/369.10M/15.78G 03:22:54.638 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 03:22:54.642 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.664 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.665 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.686 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:54.707 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.709 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.711 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. 03:22:54.712 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. 03:22:54.715 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. 03:22:54.715 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. 03:22:54.715 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. 03:22:54.715 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 03:22:54.716 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. 03:22:54.716 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: 260.83M/15.52G/108.27M/369.10M/15.78G 03:22:54.717 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. 03:22:54.719 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. 03:22:54.722 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.746 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.747 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.768 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:54.789 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.790 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) 03:22:54.792 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. Found input file with 2 target(s) 03:22:54.793 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. 03:22:54.795 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. 03:22:54.795 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. 03:22:54.795 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. 03:22:54.796 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 03:22:54.797 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. 03:22:54.797 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: 74.90M/15.70G/294.20M/369.10M/15.78G Second pass: writing the merged alignment. 03:22:54.801 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. 03:22:54.804 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 03:22:54.811 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.851 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.853 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.880 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:54.903 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.904 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.905 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. 03:22:54.906 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. 03:22:54.907 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 03:22:54.907 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: 104.32M/15.67G/264.78M/369.10M/15.78G 03:22:54.908 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 03:22:54.912 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.933 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.934 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.954 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:54.975 WARN MessageChunksWriter - Using chunk-size=1000 03:22:54.976 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: 158.81M/15.62G/210.29M/369.10M/15.78G found entry: query_index: 2 target_index: 1999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 1999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 1999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 1999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 1999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 1999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 1999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 1999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 2 target_index: 3999 position: 19993 score: 20022.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 3 target_index: 3999 position: 19994 score: 20023.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 4 target_index: 3999 position: 19995 score: 20024.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 5 target_index: 3999 position: 19996 score: 20025.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 6 target_index: 3999 position: 19997 score: 20026.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 7 target_index: 3999 position: 19998 score: 20027.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 8 target_index: 3999 position: 19999 score: 20028.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 found entry: query_index: 9 target_index: 3999 position: 20000 score: 20029.0 matching_reverse_strand: false multiplicity: 1 query_length: 35 03:22:55.038 WARN MessageChunksWriter - Using chunk-size=1000 03:22:55.059 WARN MessageChunksWriter - Using chunk-size=1000 03:22:55.060 WARN MessageChunksWriter - Using chunk-size=1000 03:22:55.081 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 03:22:55.102 WARN MessageChunksWriter - Using chunk-size=1000 03:22:55.103 WARN MessageChunksWriter - Using chunk-size=1000 03:22:55.106 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. 03:22:55.110 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. 03:22:55.129 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. 03:22:55.129 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. 03:22:55.129 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. 03:22:55.129 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 03:22:55.130 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. 03:22:55.130 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: 251.06M/15.53G/118.04M/369.10M/15.78G 03:22:55.132 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. 03:22:55.146 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 03:22:55.196 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 03:22:55.196 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 [ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits [ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 {1} {0}decoding: 4 {0} {0}decoding: 4 {0} {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0}decoding: 4 decoding: 4 {0} {0} {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0} {0} {0}decoding: 3 decoding: 4 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0} {0}decoding: 2 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0} {0} {0}decoding: 3 {0} {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 {0} {0} {0}decoding: 2 {0} {0}decoding: 1 [ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits [ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 4 decoding: 1 decoding: 2 decoding: 3 decoding: 4 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 3 decoding: 1 decoding: 2 decoding: 1 decoding: 2 decoding: 1 count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} count keys [0, 3, 5, 11, 13] -1 0.0 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 0.0 overlapping count 15, 17 0.0 overlapping count 9, 18 2.0 overlapping count 3, 8 2.0 overlapping count 11, 12 0.0 overlapping count 9, 10 1.0 overlapping count 8, 9 0.0 overlapping count 8, 8 0.0 overlapping count 5, 6 0.0 overlapping count 3, 3 0.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 0.0 -1 0.0 0 0.0 1 0.0 2 0.0 3 2.0 4 2.0 5 3.0 6 3.0 7 3.0 8 3.0 9 3.0 10 3.0 11 2.0 12 2.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 overlapping count 3, 4 2.0 overlapping count 2, 3 2.0 overlapping count 3, 8 4.0 overlapping count 11, 12 2.0 overlapping count 9, 10 3.0 overlapping count 8, 9 4.0 overlapping count 8, 8 3.0 overlapping count 5, 6 3.0 overlapping count 3, 3 2.0 overlapping count 3, 12 5.0 overlapping count -1, 2 0.0 overlapping count 0, 45 6.0 overlapping count 13, 15 1.0 Total logical entries written: 4 Total bytes written: 0 Average bytes/logical entry: 0.0 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 Total logical entries written: 4 Total bytes written: 62 Average bytes/logical entry: 15.5 Min query index: 1 Max query index: 1 Number of queries: 1 Number of targets: 2 [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 Annotations loaded Annotations loaded Annotations loaded Annotations loaded Annotations loaded [WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 82.086 s - in TestSuite 03:23:51.989 INFO GobyRengine - Shutdown hook is terminating R [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 [ 0.043 s] [INFO] Goby I/O ........................................... SUCCESS [ 9.028 s] [INFO] Goby Full Distribution ............................. SUCCESS [01:37 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:46 min [INFO] Finished at: 2025-05-26T03:23:58-12:00 [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] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin: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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin: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] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin: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 [ 0.060 s] [INFO] Goby Full Distribution ............................. SUCCESS [ 0.042 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.581 s [INFO] Finished at: 2025-05-26T03:24:00-12:00 [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 May 26, 2025 3:24:07 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 May 26, 2025 3:24:12 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian ERROR: goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian goby-io/pom.xml: dependency is not packaged in the Maven repository for Debian: org.itadaki:bzip2:debian -------- Some problems were found in this project, exiting... mh_unpatchpoms -plibgoby-io-java dh_install jh_installjavadoc dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_exec jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-10_all.deb'. dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-10_all.deb'. dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-10_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/1102531 and its subdirectories I: Current time: Mon May 26 03:24:22 -12 2025 I: pbuilder-time-stamp: 1748273062 Tue Apr 23 09:01:26 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Tue Apr 23 09:01:26 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Tue Apr 23 09:06:50 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Tue Apr 23 09:06:51 UTC 2024 I: libgoby-java_3.3.1+dfsg2-10_arm64.changes: Format: 1.8 Date: Sun, 03 Dec 2023 08:03:09 +0100 Source: libgoby-java Binary: goby-java libgoby-io-java Architecture: all Version: 3.3.1+dfsg2-10 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 Closes: 1045612 Changes: libgoby-java (3.3.1+dfsg2-10) unstable; urgency=medium . * Fixing the clean target (Closes: #1045612) * Update standards version to 4.6.2, no changes needed. Checksums-Sha1: f626e4040f1ffbc8014c00f66541e31384972323 1580036 goby-java_3.3.1+dfsg2-10_all.deb b2f83e7b57e0e930edbdb93da902a6c3faff23fb 977040 libgoby-io-java_3.3.1+dfsg2-10_all.deb 644fe8e42641420e2390e55200d7ad439c32bde2 18858 libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo Checksums-Sha256: 8c841ad040d1b04a02f3c28dd3eee873d8baada2bca45de02117acefe39ef0dd 1580036 goby-java_3.3.1+dfsg2-10_all.deb 7012982af1d0b12756f0e9d38c8ed91314e8a55b54e0344c14c5b32ddebb666e 977040 libgoby-io-java_3.3.1+dfsg2-10_all.deb b27bf781f64ee345ebc9ab30b996b559e3fa503165f3f8db17dc41365e77306e 18858 libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo Files: 32259d996532b05cf3b23de7a9038cb6 1580036 science optional goby-java_3.3.1+dfsg2-10_all.deb c8f2aacb4ead9c3a4e8437af0843aae7 977040 science optional libgoby-io-java_3.3.1+dfsg2-10_all.deb f3ed4293c626b855e69a233ae32e1ccf 18858 science optional libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo Tue Apr 23 09:06:52 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_2-31950.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hG93ZCdI/libgoby-java_3.3.1+dfsg2-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hG93ZCdI/libgoby-java_3.3.1+dfsg2-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hG93ZCdI/libgoby-java_3.3.1+dfsg2-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hG93ZCdI/b1/libgoby-java_3.3.1+dfsg2-10_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.hG93ZCdI/b2/libgoby-java_3.3.1+dfsg2-10_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 abc.DotChangesFile ## main (total time: 0.349s) 0.349s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.042s) 0.042s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 651ms CPU time consumed: 651ms Tue Apr 23 09:06:53 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 23 09:06:53 UTC 2024 I: libgoby-java from trixie built successfully and reproducibly on arm64. Tue Apr 23 09:06:54 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 23 09:06:54 UTC 2024 I: Submitting 20K b1/libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo.asc Tue Apr 23 09:06:55 UTC 2024 I: Submitting 20K b2/libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo.asc Tue Apr 23 09:06:56 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 23 09:06:56 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 23 09:06:56 UTC 2024 I: Removing signed libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo.asc files: removed './b1/libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo.asc' removed './b2/libgoby-java_3.3.1+dfsg2-10_arm64.buildinfo.asc'