Running as unit: rb-build-amd64_24-49031.service ==================================================================================== Fri Feb 21 20:22:12 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_24) on jenkins, called using "ionos15-amd64 ionos11-amd64" as arguments. Fri Feb 21 20:22:12 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Vo1MC3ss" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Feb 21 20:22:12 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Feb 21 20:22:12 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-VqMBsH' Fri Feb 21 20:22:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Fri Feb 21 20:22:13 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-ZjxlbF' ok, let's check if snippy is building anywhere yet… ok, snippy is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of snippy in trixie on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Fri Feb 21 20:22:17 UTC 2025 I: starting to build snippy/trixie/amd64 on jenkins on '2025-02-21 20:22' Fri Feb 21 20:22:17 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_24/49031/console.log 1740169337 amd64 trixie snippy Fri Feb 21 20:22:17 UTC 2025 I: Downloading source for trixie/snippy=4.6.0+dfsg-5 --2025-02-21 20:22:17-- http://deb.debian.org/debian/pool/main/s/snippy/snippy_4.6.0%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2353 (2.3K) [text/prs.lines.tag] Saving to: ‘snippy_4.6.0+dfsg-5.dsc’ 0K .. 100% 427M=0s 2025-02-21 20:22:17 (427 MB/s) - ‘snippy_4.6.0+dfsg-5.dsc’ saved [2353/2353] --2025-02-21 20:22:17-- http://deb.debian.org/debian/pool/main/s/snippy/snippy_4.6.0%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2353 (2.3K) [text/prs.lines.tag] Saving to: ‘snippy_4.6.0+dfsg-5.dsc’ 0K .. 100% 427M=0s 2025-02-21 20:22:17 (427 MB/s) - ‘snippy_4.6.0+dfsg-5.dsc’ saved [2353/2353] Fri Feb 21 20:22:17 UTC 2025 I: snippy_4.6.0+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: snippy Binary: snippy, snippy-examples Architecture: all Version: 4.6.0+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/tseemann/snippy/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/snippy Vcs-Git: https://salsa.debian.org/med-team/snippy.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), any2fasta , bcftools , bedtools , bwa , freebayes , libbio-perl-perl , libvcflib-tools , minimap2 , parallel , samtools , samclip , seqtk , snp-sites , snpeff , vt Package-List: snippy deb science optional arch=all snippy-examples deb science optional arch=all Checksums-Sha1: 15848811ce5c2056e10ac5b3d34e173119c5f7d3 271400 snippy_4.6.0+dfsg.orig.tar.xz 23674b8c55b8be1479021ca0db27a69252f28af8 5340 snippy_4.6.0+dfsg-5.debian.tar.xz Checksums-Sha256: 96c9dea7aeab6f362100fb1774d3c4377f12c2209a1fdc63b2926de912997524 271400 snippy_4.6.0+dfsg.orig.tar.xz 273a6903a280928fed9a2fdd7aef35ed5581fa6565f958bf635fc1cf6b201b78 5340 snippy_4.6.0+dfsg-5.debian.tar.xz Files: a4eea48e48f44589cb998e609fdd27ea 271400 snippy_4.6.0+dfsg.orig.tar.xz df32178e8bc17e472dfb199ccd7563ff 5340 snippy_4.6.0+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdYYcMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGSkQ/9HOirKl+sfE5asJrJNkByUzvnmnO0QmhN 5efPSe36CaYnfMUA0jMLTBTPeOQwNaLvEOQTw9uUH6pE8L5mGBxCdh1W3/AriQi9 OcNz0YauRxvB113mGwX8r7ngIwlvgv/tTaXaR/t+h+TKxCKrnlVmOtD1Iir1qC8Z 7kamnCZF+cqwXlCpO6BmG3kG1iStzsTUBnzFy4S8AJ/lrSXFXiOCfc+7hK0TK6sM lsZAdLCc7vuQvfwUk0xeNEY9aN7fCprRbAwFND6gTJCAufrsRMi7XPFfEPU5YiNX cHkq1s0hiHoCNPtfajNMoOYG0HsZ1BsA9uID3bQC44PnmdtvJJJfhGe35wEZbnrX lyk8vw/3znpgiKvu9DLFlO95BlbRNcw2gtdrd22Y7ynt80oNVie3tIhkVGEKrTYL b5JIVC0n/97vaDn162V0nSls47h248ZwMyg7KrdzmWTcqIS+vRgLDkcsM9PKTCym HMbItp8Ojxv62dQMi5R5ieUD+LphInu82vuL0nM0AkSmIuuQZVRJBndjrTPCLiIe hIDR2kZOQM44BNfCG+iYVf8FwsMV8y+6neNehAhBKoQPEpEceR0x5C/7a4bOnJVS +n4BEkXbr5URMXG37tky4wEa1OC8wadOFnC2UYVvgiX2wv7Nr8LNJh0a59MrQidi gYuMLhIvrJU= =x0wx -----END PGP SIGNATURE----- Fri Feb 21 20:22:17 UTC 2025 I: Checking whether the package is not for us Fri Feb 21 20:22:17 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri Feb 21 20:22:17 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri Feb 21 20:22:17 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Feb 21 20:22:17 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-iskoDW' ==================================================================================== Fri Mar 27 02:45:18 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 snippy trixie /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe 4.6.0+dfsg-5" as arguments. Fri Mar 27 02:45:18 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-bLjC7Ptd" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Mar 27 02:45:18 UTC 2026 I: Downloading source for trixie/snippy=4.6.0+dfsg-5 Reading package lists... NOTICE: 'snippy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snippy.git Please use: git clone https://salsa.debian.org/med-team/snippy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 279 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (dsc) [2353 B] Get:2 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (tar) [271 kB] Get:3 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (diff) [5340 B] Fetched 279 kB in 0s (5038 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snippy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snippy.git Please use: git clone https://salsa.debian.org/med-team/snippy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 279 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (dsc) [2353 B] Get:2 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (tar) [271 kB] Get:3 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (diff) [5340 B] Fetched 279 kB in 0s (5038 kB/s) Download complete and in download only mode ============================================================================= Building snippy in trixie on amd64 on ionos15-amd64 now. Date: Fri Mar 27 02:45:19 UTC 2026 Date UTC: Fri Mar 27 02:45:19 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 26 14:45:19 -12 2026 I: pbuilder-time-stamp: 1774579519 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 [snippy_4.6.0+dfsg-5.dsc] I: copying [./snippy_4.6.0+dfsg.orig.tar.xz] I: copying [./snippy_4.6.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snippy_4.6.0+dfsg-5.dsc: unsupported subcommand dpkg-source: info: extracting snippy in snippy-4.6.0+dfsg dpkg-source: info: unpacking snippy_4.6.0+dfsg.orig.tar.xz dpkg-source: info: unpacking snippy_4.6.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian_packaged_libs.patch dpkg-source: info: applying snpeff.config.patch dpkg-source: info: applying snpeff_v5.1+.patch dpkg-source: info: applying make-4.4.1.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3521208/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='df57c7856d35463d9ff17e9ac7d2dcea' 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='3521208' 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.6PMZ3CYe/pbuilderrc_E8U9 --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.6PMZ3CYe/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3521208/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19809 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 any2fasta; however: Package any2fasta is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on freebayes; however: Package freebayes is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools; however: Package libvcflib-tools is not installed. pbuilder-satisfydepends-dummy depends on minimap2; however: Package minimap2 is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on samclip; however: Package samclip is not installed. pbuilder-satisfydepends-dummy depends on seqtk; however: Package seqtk is not installed. pbuilder-satisfydepends-dummy depends on snp-sites; however: Package snp-sites is not installed. pbuilder-satisfydepends-dummy depends on snpeff; however: Package snpeff is not installed. pbuilder-satisfydepends-dummy depends on vt; however: Package vt 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-optional{a} any2fasta{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bedtools{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} freebayes{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbio-perl-perl{a} libbiojava6-java{a} libblas3{a} libbrotli1{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libcharts4j-java{a} libciftools-java{a} libcloudproviders0{a} libcodemodel-java{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-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} libcups2t64{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-stag-perl{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdisorder0{a} libdistlib-java{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libedit2{a} libelf1t64{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastahack0{a} libfastinfoset-java{a} libfastutil-java{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfml0{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgbm1{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} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libice6{a} libicu72{a} libidn2-0{a} libinchi1.07{a} libio-string-perl{a} libistack-commons-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjson-java{a} libjson-simple-java{a} libjsoncpp26{a} libjsoup-java{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} liblog4j1.2-java{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-jar-plugin-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmmtf-java{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-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-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib2{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsmithwaterman0{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsnp-sites1{a} libsnpeff-java{a} libssh2-1t64{a} libssw0{a} libstax-ex-java{a} libstreambuffer-java{a} libsystemd-shared{a} libtabixpp0t64{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtrove3-java{a} libtxw2-java{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} libvcflib-tools{a} libvcflib2{a} libvecmath-java{a} libvulkan1{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwfa2-0{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxom-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxss1{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} littler{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} minimap2{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} parallel{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} samclip{a} samtools{a} sensible-utils{a} seqtk{a} shared-mime-info{a} snp-sites{a} snpeff{a} sysstat{a} systemd{a} systemd-sysv{a} tzdata{a} ucf{a} unzip{a} vt{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf at-spi2-core bioperl-run chrony curl fonts-dejavu-extra krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libatk-wrapper-java-jni libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libfile-mimeinfo-perl libgd-perl libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libgtk-3-bin libhtml-parser-perl libhtml-tableextract-perl libjansi-java libkmod2 libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libnet-dbus-perl libnss-systemd libpostscript-perl librsvg2-common libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd perl-tk psmisc publicsuffix python3-gffutils python3-matplotlib r-base-dev r-cran-abind r-cran-bench r-cran-bit64 r-cran-blob r-cran-brio r-cran-callr r-cran-covr r-cran-crayon r-cran-dbi r-cran-diagrammer r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-evaluate r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-here r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-multcomp r-cran-mvtnorm r-cran-nanotime r-cran-palmerpenguins r-cran-pkgbuild r-cran-pkgdown r-cran-pkgload r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-purrr r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-survival r-cran-svglite r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-units r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 418 newly installed, 0 to remove and 0 not upgraded. Need to get 326 MB of archives. After unpacking 961 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-4 [42.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.3-1 [3092 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.3-1 [293 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0049 [42.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.17.4+ds-4 [51.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 62 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.108-1 [1393 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 67 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 68 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 any2fasta all 0.4.2-2 [6232 B] Get: 71 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.55.2-1 [170 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 87 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-2 [365 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.21-1 [784 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 115 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-1 [26.5 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-1 [11.4 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-1 [5452 B] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 174 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.3.4-3 [38.5 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.3.4-3 [9492 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-1 [34.0 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.3.4-3 [43.7 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.3.4-3 [45.2 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.3.4-3 [143 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 209 http://deb.debian.org/debian trixie/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b3 [172 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get: 215 http://deb.debian.org/debian trixie/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libwfa2-0 amd64 2.3.3-4+b2 [60.9 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libvcflib2 amd64 1.0.12+dfsg-1 [233 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 freebayes amd64 1.3.9-1 [1523 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 223 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 224 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 231 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 232 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 236 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 261 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 268 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 271 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 281 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get: 312 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 315 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 322 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 349 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB] Get: 353 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 354 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 356 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libsnp-sites1 amd64 2.5.1-2+b2 [14.8 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 363 http://deb.debian.org/debian trixie/main amd64 libsnpeff-java all 5.2.f+dfsg-1 [2156 kB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 367 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 374 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 375 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-2 [16.0 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.5-1 [1712 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB] Get: 387 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 388 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.167-1 [2331 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-2-1 [4155 kB] Get: 390 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 400 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 402 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 409 http://deb.debian.org/debian trixie/main amd64 libvcflib-tools amd64 1.0.12+dfsg-1 [608 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 minimap2 amd64 2.27+dfsg-1+b2 [391 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 samclip all 0.4.0-4 [20.1 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.21-1 [667 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 snpeff all 5.2.f+dfsg-1 [7244 B] Get: 418 http://deb.debian.org/debian trixie/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] Fetched 326 MB in 29s (11.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19809 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-4_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-4) ... Setting up libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package systemd. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19822 files and directories currently installed.) Preparing to unpack .../systemd_257.3-1_amd64.deb ... Unpacking systemd (257.3-1) ... Setting up libapparmor1:amd64 (3.1.7-4) ... Setting up systemd (257.3-1) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20765 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_257.3-1_amd64.deb ... Unpacking systemd-sysv (257.3-1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../1-libdbus-1-3_1.16.0-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.16.0-1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../2-dbus-bin_1.16.0-1_amd64.deb ... Unpacking dbus-bin (1.16.0-1) ... 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Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 27 02:48:31 UTC 2026. Universal Time is now: Fri Mar 27 02:48:31 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.13-1) ... Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-14) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libasound2t64:amd64 (1.2.13-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:amd64 (0.8-16) ... Setting up libncurses6:amd64 (6.5+20250125-2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:amd64 (1.16.0-1) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.3.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up libvulkan1:amd64 (1.4.304.0-1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libapfloat-java (1.14.0-2) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up libtrove3-java (3.0.3-5) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b3) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.55.2-1) ... Setting up libcommons-math-java (2.2-9) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.0-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-7) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libjackson2-core-java (2.14.1-1) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libsnp-sites1:amd64 (2.5.1-2+b2) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libcommons-math3-java (3.6.1-4) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libwayland-egl1:amd64 (1.23.1-1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libpaper2:amd64 (2.2.5-0.3+b1) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up dbus-system-bus-common (1.16.0-1) ... useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Setting up librelaxng-datatype-java (1.0+ds1-4) ... Setting up openssl (3.4.1-1) ... Setting up libinchi1.07 (1.07.2+dfsg-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up libssw0:amd64 (1.1-15+b2) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up dbus-bin (1.16.0-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libxkbcommon0:amd64 (1.7.0-2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libwayland-client0:amd64 (1.23.1-1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:amd64 (1:19.1.7-1+b1) ... Setting up libwayland-server0:amd64 (1.23.1-1) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libnss3:amd64 (2:3.108-1) ... Setting up libciftools-java (6.0.0-1) ... Setting up dbus-daemon (1.16.0-1) ... Setting up libpaper-utils (2.2.5-0.3+b1) ... Setting up libxom-java (1.3.9-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjackson2-databind-java (2.14.0+ds-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:amd64 (2.83.3-2) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up dbus (1.16.0-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0049) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up librngom-java (2.3.0.1-11) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libjni-inchi-jni (0.8+dfsg-8) ... Setting up libjgraphx-java (2.1.0.7-5) ... Setting up snp-sites (2.5.1-2+b2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:amd64 (1.23.1-1) ... Setting up libpam-systemd:amd64 (257.3-1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libxsom-java (2.3.0.1-11) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.17.1-1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-collect.timer' -> '/usr/lib/systemd/system/sysstat-collect.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-rotate.timer' -> '/usr/lib/systemd/system/sysstat-rotate.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-summary.timer' -> '/usr/lib/systemd/system/sysstat-summary.timer'. Created symlink '/etc/systemd/system/multi-user.target.wants/sysstat.service' -> '/usr/lib/systemd/system/sysstat.service'. Setting up libavahi-client3:amd64 (0.8-16) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.17.4+ds-4) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up libatk1.0-0t64:amd64 (2.55.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.2-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libpango-1.0-0:amd64 (1.56.1-1) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up python3 (3.13.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up dbus-user-session (1.16.0-1) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (47.0-2) ... 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 librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:amd64 (2.55.2-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up parallel (20240222+ds-2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfastinfoset-java (1.2.12-4) ... Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ... Setting up mesa-libgallium:amd64 (24.3.4-3) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:amd64 (8.12.1-2) ... Setting up libgbm1:amd64 (24.3.4-3) ... Setting up libgl1-mesa-dri:amd64 (24.3.4-3) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-2) ... Setting up debhelper (13.24.1) ... Setting up dconf-service (0.40.0-5) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.167-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7+b2) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b3) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up r-cran-rlang (1.1.5-1) ... Setting up libglx-mesa0:amd64 (24.3.4-3) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up vt (0.57721+ds-3+b1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up bcftools (1.21-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up r-cran-mass (7.3-64-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up samtools (1.21-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-2-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up libgtk-3-common (3.24.48-4) ... Setting up r-cran-pillar (1.10.1+dfsg-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-3) ... Setting up libvcflib2:amd64 (1.0.12+dfsg-1) ... Setting up libgtk-3-0t64:amd64 (3.24.48-4) ... Setting up r-cran-scales (1.3.0-1) ... Setting up freebayes (1.3.9-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libvcflib-tools (1.0.12+dfsg-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libmaven3-core-java (3.9.9-1) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libjni-inchi-java (0.8+dfsg-8) ... Setting up libmaven-file-management-java (3.0.0-2) ... Setting up libjmol-java (16.2.33+dfsg-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.12.0-1) ... Setting up libmsgpack-java (0.9.6-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.2-1) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for systemd (257.3-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.6+7-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up ant-optional (1.10.15-1) ... Setting up junit5 (5.10.3-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ... Setting up libtxw2-java (2.3.0.1-11) ... Setting up libjaxb-java (2.3.0.1-11) ... Setting up libbiojava6-java (6.1.0+dfsg-5) ... Setting up libsnpeff-java (5.2.f+dfsg-1) ... Setting up snpeff (5.2.f+dfsg-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && 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 > ../snippy_4.6.0+dfsg-5_source.changes dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg' cd test && /usr/bin/make make[2]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg/test' mkdir -p S1 wgsim -S 1 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S1/R1.fq S1/R2.fq > S1/dwgsim.tab [wgsim] seed = 1 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq [14:49:06] This is snippy 4.6.0 [14:49:06] Written by Torsten Seemann [14:49:06] Obtained from https://github.com/tseemann/snippy [14:49:06] Detected operating system: linux [14:49:06] Enabling bundled linux tools. [14:49:06] Found bwa - /usr/bin/bwa [14:49:06] Found bcftools - /usr/bin/bcftools [14:49:06] Found samtools - /usr/bin/samtools [14:49:06] Found java - /usr/bin/java [14:49:06] Found snpEff - /usr/bin/snpEff [14:49:06] Found samclip - /usr/bin/samclip [14:49:06] Found seqtk - /usr/bin/seqtk [14:49:06] Found parallel - /usr/bin/parallel [14:49:06] Found freebayes - /usr/bin/freebayes [14:49:06] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:06] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:06] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:06] Found vcfuniq - /usr/bin/vcfuniq [14:49:06] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:06] Found gzip - /usr/bin/gzip [14:49:06] Found vt - /usr/bin/vt [14:49:06] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:06] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:06] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:07] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:07] Treating reference as 'fasta' format. [14:49:07] Will use 2 CPU cores. [14:49:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq [14:49:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq [14:49:07] Used --force, will overwrite existing S1 [14:49:07] Changing working directory: S1 [14:49:07] Creating reference folder: reference [14:49:07] Extracting FASTA and GFF from reference. [14:49:07] Wrote 3 sequences to ref.fa [14:49:07] Wrote 0 features to ref.gff [14:49:07] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:07] Using BAM RG (Read Group) ID: S1 [14:49:07] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:07] Running: bwa index reference/ref.fa 2>> snps.log [14:49:07] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:07] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:07] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:07] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:07] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11587, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 233) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 369) [M::mem_pestat] mean and std.dev: (199.53, 48.89) [M::mem_pestat] low and high boundaries for proper pairs: (1, 437) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.179 CPU sec, 1.185 real sec [main] Version: 0.7.18-r1243-dirty [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq [main] Real time: 1.355 sec; CPU: 2.228 sec [14:49:09] Running: samtools index snps.bam 2>> snps.log [14:49:09] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:09] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:11] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 10 no. right trimmed : 33 no. left and right trimmed : 4 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 47 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 47 total no. variants observed : 261 total no. reference observed : 0 Time elapsed: 0.01s [14:49:11] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:11] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:12] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:12] Marked 749 heterozygous sites with 'n' [14:49:12] Creating extra output files: BED GFF CSV TXT HTML [14:49:12] Identified 261 variants. [14:49:12] Result folder: S1 [14:49:12] Result files: [14:49:12] * S1/snps.aligned.fa [14:49:12] * S1/snps.bam [14:49:12] * S1/snps.bam.bai [14:49:12] * S1/snps.bed [14:49:12] * S1/snps.consensus.fa [14:49:12] * S1/snps.consensus.subs.fa [14:49:12] * S1/snps.csv [14:49:12] * S1/snps.filt.vcf [14:49:12] * S1/snps.gff [14:49:12] * S1/snps.html [14:49:12] * S1/snps.log [14:49:12] * S1/snps.raw.vcf [14:49:12] * S1/snps.subs.vcf [14:49:12] * S1/snps.tab [14:49:12] * S1/snps.txt [14:49:12] * S1/snps.vcf [14:49:12] * S1/snps.vcf.gz [14:49:12] * S1/snps.vcf.gz.csi [14:49:12] Walltime used: 6 seconds [14:49:12] May the SNPs be with you. [14:49:12] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S2/R1.fq S2/R2.fq > S2/dwgsim.tab [wgsim] seed = 2 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq [14:49:12] This is snippy 4.6.0 [14:49:12] Written by Torsten Seemann [14:49:12] Obtained from https://github.com/tseemann/snippy [14:49:12] Detected operating system: linux [14:49:12] Enabling bundled linux tools. [14:49:12] Found bwa - /usr/bin/bwa [14:49:12] Found bcftools - /usr/bin/bcftools [14:49:12] Found samtools - /usr/bin/samtools [14:49:12] Found java - /usr/bin/java [14:49:12] Found snpEff - /usr/bin/snpEff [14:49:12] Found samclip - /usr/bin/samclip [14:49:12] Found seqtk - /usr/bin/seqtk [14:49:12] Found parallel - /usr/bin/parallel [14:49:12] Found freebayes - /usr/bin/freebayes [14:49:12] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:12] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:12] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:12] Found vcfuniq - /usr/bin/vcfuniq [14:49:13] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:13] Found gzip - /usr/bin/gzip [14:49:13] Found vt - /usr/bin/vt [14:49:13] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:13] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:13] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:13] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:13] Treating reference as 'fasta' format. [14:49:13] Will use 2 CPU cores. [14:49:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq [14:49:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq [14:49:13] Used --force, will overwrite existing S2 [14:49:13] Changing working directory: S2 [14:49:13] Creating reference folder: reference [14:49:13] Extracting FASTA and GFF from reference. [14:49:13] Wrote 3 sequences to ref.fa [14:49:13] Wrote 0 features to ref.gff [14:49:13] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:13] Using BAM RG (Read Group) ID: S2 [14:49:13] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:13] Running: bwa index reference/ref.fa 2>> snps.log [14:49:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:13] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:13] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 366) [M::mem_pestat] mean and std.dev: (199.27, 48.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.076 CPU sec, 1.053 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq [main] Real time: 1.223 sec; CPU: 2.128 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. [14:49:15] Running: samtools index snps.bam 2>> snps.log [14:49:15] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:15] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:16] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 10 no. right trimmed : 28 no. left and right trimmed : 1 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 39 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 39 total no. variants observed : 246 total no. reference observed : 0 Time elapsed: 0.01s [14:49:16] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:16] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:17] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:17] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:17] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:17] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:17] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:18] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:18] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:18] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:18] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:19] Marked 841 heterozygous sites with 'n' [14:49:19] Creating extra output files: BED GFF CSV TXT HTML [14:49:19] Identified 246 variants. [14:49:19] Result folder: S2 [14:49:19] Result files: [14:49:19] * S2/snps.aligned.fa [14:49:19] * S2/snps.bam [14:49:19] * S2/snps.bam.bai [14:49:19] * S2/snps.bed [14:49:19] * S2/snps.consensus.fa [14:49:19] * S2/snps.consensus.subs.fa [14:49:19] * S2/snps.csv [14:49:19] * S2/snps.filt.vcf [14:49:19] * S2/snps.gff [14:49:19] * S2/snps.html [14:49:19] * S2/snps.log [14:49:19] * S2/snps.raw.vcf [14:49:19] * S2/snps.subs.vcf [14:49:19] * S2/snps.tab [14:49:19] * S2/snps.txt [14:49:19] * S2/snps.vcf [14:49:19] * S2/snps.vcf.gz [14:49:19] * S2/snps.vcf.gz.csi [14:49:19] Walltime used: 7 seconds [14:49:19] Wishing you a life free of homopolymer errors. [14:49:19] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S3/R1.fq S3/R2.fq > S3/dwgsim.tab [wgsim] seed = 3 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq [14:49:19] This is snippy 4.6.0 [14:49:19] Written by Torsten Seemann [14:49:19] Obtained from https://github.com/tseemann/snippy [14:49:19] Detected operating system: linux [14:49:19] Enabling bundled linux tools. [14:49:19] Found bwa - /usr/bin/bwa [14:49:19] Found bcftools - /usr/bin/bcftools [14:49:19] Found samtools - /usr/bin/samtools [14:49:19] Found java - /usr/bin/java [14:49:19] Found snpEff - /usr/bin/snpEff [14:49:19] Found samclip - /usr/bin/samclip [14:49:19] Found seqtk - /usr/bin/seqtk [14:49:19] Found parallel - /usr/bin/parallel [14:49:19] Found freebayes - /usr/bin/freebayes [14:49:19] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:19] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:19] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:19] Found vcfuniq - /usr/bin/vcfuniq [14:49:19] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:19] Found gzip - /usr/bin/gzip [14:49:19] Found vt - /usr/bin/vt [14:49:19] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:19] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:19] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:19] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:19] Treating reference as 'fasta' format. [14:49:19] Will use 2 CPU cores. [14:49:19] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq [14:49:19] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq [14:49:19] Used --force, will overwrite existing S3 [14:49:19] Changing working directory: S3 [14:49:19] Creating reference folder: reference [14:49:19] Extracting FASTA and GFF from reference. [14:49:19] Wrote 3 sequences to ref.fa [14:49:19] Wrote 0 features to ref.gff [14:49:19] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:19] Using BAM RG (Read Group) ID: S3 [14:49:19] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:19] Running: bwa index reference/ref.fa 2>> snps.log [14:49:19] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:19] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:19] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:19] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:19] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368) [M::mem_pestat] mean and std.dev: (198.46, 48.83) [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.062 CPU sec, 1.137 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq [main] Real time: 1.247 sec; CPU: 2.107 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. [14:49:21] Running: samtools index snps.bam 2>> snps.log [14:49:21] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:21] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:23] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 11 no. right trimmed : 30 no. left and right trimmed : 1 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 42 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 42 total no. variants observed : 254 total no. reference observed : 0 Time elapsed: 0.01s [14:49:23] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:23] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:23] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:23] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:23] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:23] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:23] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:23] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:23] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:23] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:23] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:23] Marked 846 heterozygous sites with 'n' [14:49:23] Creating extra output files: BED GFF CSV TXT HTML [14:49:23] Identified 254 variants. [14:49:23] Result folder: S3 [14:49:23] Result files: [14:49:23] * S3/snps.aligned.fa [14:49:23] * S3/snps.bam [14:49:23] * S3/snps.bam.bai [14:49:23] * S3/snps.bed [14:49:23] * S3/snps.consensus.fa [14:49:23] * S3/snps.consensus.subs.fa [14:49:23] * S3/snps.csv [14:49:23] * S3/snps.filt.vcf [14:49:23] * S3/snps.gff [14:49:23] * S3/snps.html [14:49:23] * S3/snps.log [14:49:23] * S3/snps.raw.vcf [14:49:23] * S3/snps.subs.vcf [14:49:23] * S3/snps.tab [14:49:23] * S3/snps.txt [14:49:23] * S3/snps.vcf [14:49:23] * S3/snps.vcf.gz [14:49:23] * S3/snps.vcf.gz.csi [14:49:23] Walltime used: 4 seconds [14:49:23] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues [14:49:23] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S4/R1.fq S4/R2.fq > S4/dwgsim.tab [wgsim] seed = 4 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq [14:49:23] This is snippy 4.6.0 [14:49:23] Written by Torsten Seemann [14:49:23] Obtained from https://github.com/tseemann/snippy [14:49:23] Detected operating system: linux [14:49:23] Enabling bundled linux tools. [14:49:23] Found bwa - /usr/bin/bwa [14:49:23] Found bcftools - /usr/bin/bcftools [14:49:23] Found samtools - /usr/bin/samtools [14:49:23] Found java - /usr/bin/java [14:49:23] Found snpEff - /usr/bin/snpEff [14:49:23] Found samclip - /usr/bin/samclip [14:49:23] Found seqtk - /usr/bin/seqtk [14:49:24] Found parallel - /usr/bin/parallel [14:49:24] Found freebayes - /usr/bin/freebayes [14:49:24] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:24] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:24] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:24] Found vcfuniq - /usr/bin/vcfuniq [14:49:24] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:24] Found gzip - /usr/bin/gzip [14:49:24] Found vt - /usr/bin/vt [14:49:24] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:24] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:24] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:24] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:24] Treating reference as 'fasta' format. [14:49:24] Will use 2 CPU cores. [14:49:24] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq [14:49:24] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq [14:49:24] Used --force, will overwrite existing S4 [14:49:24] Changing working directory: S4 [14:49:24] Creating reference folder: reference [14:49:24] Extracting FASTA and GFF from reference. [14:49:24] Wrote 3 sequences to ref.fa [14:49:24] Wrote 0 features to ref.gff [14:49:24] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:24] Using BAM RG (Read Group) ID: S4 [14:49:24] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:24] Running: bwa index reference/ref.fa 2>> snps.log [14:49:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:24] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:24] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11573, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 198, 230) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (35, 360) [M::mem_pestat] mean and std.dev: (198.20, 48.15) [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.376 CPU sec, 0.693 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. [main] Real time: 0.809 sec; CPU: 1.418 sec [14:49:25] Running: samtools index snps.bam 2>> snps.log [14:49:25] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:25] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:26] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 12 no. right trimmed : 35 no. left and right trimmed : 3 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 50 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 50 total no. variants observed : 257 total no. reference observed : 0 Time elapsed: 0.01s [14:49:26] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:26] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:26] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:26] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:26] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:26] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:26] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:27] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:27] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:27] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:27] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:27] Marked 799 heterozygous sites with 'n' [14:49:27] Creating extra output files: BED GFF CSV TXT HTML [14:49:27] Identified 257 variants. [14:49:27] Result folder: S4 [14:49:27] Result files: [14:49:27] * S4/snps.aligned.fa [14:49:27] * S4/snps.bam [14:49:27] * S4/snps.bam.bai [14:49:27] * S4/snps.bed [14:49:27] * S4/snps.consensus.fa [14:49:27] * S4/snps.consensus.subs.fa [14:49:27] * S4/snps.csv [14:49:27] * S4/snps.filt.vcf [14:49:27] * S4/snps.gff [14:49:27] * S4/snps.html [14:49:27] * S4/snps.log [14:49:27] * S4/snps.raw.vcf [14:49:27] * S4/snps.subs.vcf [14:49:27] * S4/snps.tab [14:49:27] * S4/snps.txt [14:49:27] * S4/snps.vcf [14:49:27] * S4/snps.vcf.gz [14:49:27] * S4/snps.vcf.gz.csi [14:49:27] Walltime used: 4 seconds [14:49:27] Did you know? Snippy is a combination of SNP, Skippy, and snappy. [14:49:27] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Will mask 0 regions totalling 0 bp ~ 0.00% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core.tab Opening: core.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core-mask.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Loading mask bed file: example.bed Will mask 8 regions totalling 3101 bp ~ 0.98% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core-mask.tab Opening: core-mask.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Masking alignment at 8 regions Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln This analysis is totally hard-core! Done. wc -l S?/snps.tab 262 S1/snps.tab 247 S2/snps.tab 255 S3/snps.tab 258 S4/snps.tab 1022 total make[2]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg' dh_install sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snippy' in '../snippy_4.6.0+dfsg-5_all.deb'. dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../snippy_4.6.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../snippy_4.6.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3521208 and its subdirectories I: Current time: Thu Mar 26 14:49:31 -12 2026 I: pbuilder-time-stamp: 1774579771 Fri Mar 27 02:49:31 UTC 2026 I: Signing ./b1/snippy_4.6.0+dfsg-5_amd64.buildinfo as snippy_4.6.0+dfsg-5_amd64.buildinfo.asc Fri Mar 27 02:49:31 UTC 2026 I: Signed ./b1/snippy_4.6.0+dfsg-5_amd64.buildinfo as ./b1/snippy_4.6.0+dfsg-5_amd64.buildinfo.asc Fri Mar 27 02:49:31 UTC 2026 - build #1 for snippy/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Fri Mar 27 02:49:31 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-bLjC7Ptd, removing. /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 20:26 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 20:22 b2 -rw------- 1 jenkins jenkins 3471 Feb 21 20:22 rbuildlog.dMpcRee -rw-r--r-- 1 jenkins jenkins 2353 Dec 10 15:50 snippy_4.6.0+dfsg-5.dsc /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b1: total 592 -rw-r--r-- 1 jenkins jenkins 203762 Feb 21 20:26 build.log -rw-r--r-- 1 jenkins jenkins 310484 Feb 21 20:26 snippy-examples_4.6.0+dfsg-5_all.deb -rw-r--r-- 1 jenkins jenkins 5340 Feb 21 20:26 snippy_4.6.0+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2353 Feb 21 20:26 snippy_4.6.0+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 26892 Feb 21 20:26 snippy_4.6.0+dfsg-5_all.deb -rw-r--r-- 1 jenkins jenkins 17307 Feb 21 20:26 snippy_4.6.0+dfsg-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 18189 Feb 21 20:26 snippy_4.6.0+dfsg-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1523 Feb 21 20:26 snippy_4.6.0+dfsg-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 1297 Feb 21 20:26 snippy_4.6.0+dfsg-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b2: total 0 Fri Feb 21 20:26:32 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 26 14:45:19 -12 2026 I: pbuilder-time-stamp: 1774579519 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 [snippy_4.6.0+dfsg-5.dsc] I: copying [./snippy_4.6.0+dfsg.orig.tar.xz] I: copying [./snippy_4.6.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snippy_4.6.0+dfsg-5.dsc: unsupported subcommand dpkg-source: info: extracting snippy in snippy-4.6.0+dfsg dpkg-source: info: unpacking snippy_4.6.0+dfsg.orig.tar.xz dpkg-source: info: unpacking snippy_4.6.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian_packaged_libs.patch dpkg-source: info: applying snpeff.config.patch dpkg-source: info: applying snpeff_v5.1+.patch dpkg-source: info: applying make-4.4.1.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3521208/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='df57c7856d35463d9ff17e9ac7d2dcea' 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='3521208' 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.6PMZ3CYe/pbuilderrc_E8U9 --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.6PMZ3CYe/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3521208/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19809 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 any2fasta; however: Package any2fasta is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on freebayes; however: Package freebayes is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools; however: Package libvcflib-tools is not installed. pbuilder-satisfydepends-dummy depends on minimap2; however: Package minimap2 is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on samclip; however: Package samclip is not installed. pbuilder-satisfydepends-dummy depends on seqtk; however: Package seqtk is not installed. pbuilder-satisfydepends-dummy depends on snp-sites; however: Package snp-sites is not installed. pbuilder-satisfydepends-dummy depends on snpeff; however: Package snpeff is not installed. pbuilder-satisfydepends-dummy depends on vt; however: Package vt 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-optional{a} any2fasta{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bedtools{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} freebayes{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbio-perl-perl{a} libbiojava6-java{a} libblas3{a} libbrotli1{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libcharts4j-java{a} libciftools-java{a} libcloudproviders0{a} libcodemodel-java{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-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} libcups2t64{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-stag-perl{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdisorder0{a} libdistlib-java{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libedit2{a} libelf1t64{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastahack0{a} libfastinfoset-java{a} libfastutil-java{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfml0{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgbm1{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} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libice6{a} libicu72{a} libidn2-0{a} libinchi1.07{a} libio-string-perl{a} libistack-commons-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjson-java{a} libjson-simple-java{a} libjsoncpp26{a} libjsoup-java{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} liblog4j1.2-java{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-jar-plugin-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmmtf-java{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-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-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib2{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsmithwaterman0{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsnp-sites1{a} libsnpeff-java{a} libssh2-1t64{a} libssw0{a} libstax-ex-java{a} libstreambuffer-java{a} libsystemd-shared{a} libtabixpp0t64{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtrove3-java{a} libtxw2-java{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} libvcflib-tools{a} libvcflib2{a} libvecmath-java{a} libvulkan1{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwfa2-0{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxom-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxss1{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} littler{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} minimap2{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} parallel{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} samclip{a} samtools{a} sensible-utils{a} seqtk{a} shared-mime-info{a} snp-sites{a} snpeff{a} sysstat{a} systemd{a} systemd-sysv{a} tzdata{a} ucf{a} unzip{a} vt{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf at-spi2-core bioperl-run chrony curl fonts-dejavu-extra krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libatk-wrapper-java-jni libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libfile-mimeinfo-perl libgd-perl libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libgtk-3-bin libhtml-parser-perl libhtml-tableextract-perl libjansi-java libkmod2 libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libnet-dbus-perl libnss-systemd libpostscript-perl librsvg2-common libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd perl-tk psmisc publicsuffix python3-gffutils python3-matplotlib r-base-dev r-cran-abind r-cran-bench r-cran-bit64 r-cran-blob r-cran-brio r-cran-callr r-cran-covr r-cran-crayon r-cran-dbi r-cran-diagrammer r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-evaluate r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-here r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-multcomp r-cran-mvtnorm r-cran-nanotime r-cran-palmerpenguins r-cran-pkgbuild r-cran-pkgdown r-cran-pkgload r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-purrr r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-survival r-cran-svglite r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-units r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 418 newly installed, 0 to remove and 0 not upgraded. Need to get 326 MB of archives. After unpacking 961 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-4 [42.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.3-1 [3092 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.3-1 [293 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0049 [42.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.17.4+ds-4 [51.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 62 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.108-1 [1393 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 67 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 68 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 any2fasta all 0.4.2-2 [6232 B] Get: 71 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.55.2-1 [170 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 87 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-2 [365 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.21-1 [784 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 115 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-1 [26.5 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-1 [11.4 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-1 [5452 B] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 174 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.3.4-3 [38.5 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.3.4-3 [9492 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-1 [34.0 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.3.4-3 [43.7 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.3.4-3 [45.2 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.3.4-3 [143 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 209 http://deb.debian.org/debian trixie/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b3 [172 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get: 215 http://deb.debian.org/debian trixie/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libwfa2-0 amd64 2.3.3-4+b2 [60.9 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libvcflib2 amd64 1.0.12+dfsg-1 [233 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 freebayes amd64 1.3.9-1 [1523 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 223 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 224 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 231 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 232 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 236 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 261 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 268 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 271 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 281 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get: 312 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 315 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 322 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 349 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB] Get: 353 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 354 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 356 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libsnp-sites1 amd64 2.5.1-2+b2 [14.8 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 363 http://deb.debian.org/debian trixie/main amd64 libsnpeff-java all 5.2.f+dfsg-1 [2156 kB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 367 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 374 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 375 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-2 [16.0 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.5-1 [1712 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB] Get: 387 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 388 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.167-1 [2331 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-2-1 [4155 kB] Get: 390 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 400 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 402 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 409 http://deb.debian.org/debian trixie/main amd64 libvcflib-tools amd64 1.0.12+dfsg-1 [608 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 minimap2 amd64 2.27+dfsg-1+b2 [391 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 samclip all 0.4.0-4 [20.1 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.21-1 [667 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 snpeff all 5.2.f+dfsg-1 [7244 B] Get: 418 http://deb.debian.org/debian trixie/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] Fetched 326 MB in 29s (11.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19809 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-4_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-4) ... 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Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up bwa (0.7.18-1) ... Setting up libglvnd0:amd64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up minimap2 (2.27+dfsg-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpicocli-java (4.6.2-2) ... Setting up libasm-java (9.7.1-1) ... Setting up x11-common (1:7.7+24) ... Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-10) ... Setting up libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12+b2) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up xkb-data (2.42-1) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up any2fasta (0.4.2-2) ... Setting up libantlr4-runtime-java (4.9.2-3) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libjson-simple-java (2.3.0-2) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libfml0:amd64 (0.1+git20221215.85f159e-1) ... Setting up libfastahack0:amd64 (1.0.0+dfsg-11+b2) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up samclip (0.4.0-4) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libsnappy1v5:amd64 (1.2.1-1+b1) ... Setting up libcharts4j-java (1.3-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 27 02:48:31 UTC 2026. Universal Time is now: Fri Mar 27 02:48:31 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.13-1) ... Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-14) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libasound2t64:amd64 (1.2.13-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:amd64 (0.8-16) ... Setting up libncurses6:amd64 (6.5+20250125-2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libdbus-1-3:amd64 (1.16.0-1) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.3.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up libvulkan1:amd64 (1.4.304.0-1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libapfloat-java (1.14.0-2) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up libtrove3-java (3.0.3-5) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b3) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.55.2-1) ... Setting up libcommons-math-java (2.2-9) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.0-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-7) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libjackson2-core-java (2.14.1-1) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libsnp-sites1:amd64 (2.5.1-2+b2) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libcommons-math3-java (3.6.1-4) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libwayland-egl1:amd64 (1.23.1-1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libpaper2:amd64 (2.2.5-0.3+b1) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up dbus-system-bus-common (1.16.0-1) ... useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Setting up librelaxng-datatype-java (1.0+ds1-4) ... Setting up openssl (3.4.1-1) ... Setting up libinchi1.07 (1.07.2+dfsg-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up libssw0:amd64 (1.1-15+b2) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up dbus-bin (1.16.0-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libxkbcommon0:amd64 (1.7.0-2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libwayland-client0:amd64 (1.23.1-1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:amd64 (1:19.1.7-1+b1) ... Setting up libwayland-server0:amd64 (1.23.1-1) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libnss3:amd64 (2:3.108-1) ... Setting up libciftools-java (6.0.0-1) ... Setting up dbus-daemon (1.16.0-1) ... Setting up libpaper-utils (2.2.5-0.3+b1) ... Setting up libxom-java (1.3.9-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjackson2-databind-java (2.14.0+ds-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:amd64 (2.83.3-2) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up dbus (1.16.0-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0049) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up librngom-java (2.3.0.1-11) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libjni-inchi-jni (0.8+dfsg-8) ... Setting up libjgraphx-java (2.1.0.7-5) ... Setting up snp-sites (2.5.1-2+b2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:amd64 (1.23.1-1) ... Setting up libpam-systemd:amd64 (257.3-1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libxsom-java (2.3.0.1-11) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.17.1-1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-collect.timer' -> '/usr/lib/systemd/system/sysstat-collect.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-rotate.timer' -> '/usr/lib/systemd/system/sysstat-rotate.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-summary.timer' -> '/usr/lib/systemd/system/sysstat-summary.timer'. Created symlink '/etc/systemd/system/multi-user.target.wants/sysstat.service' -> '/usr/lib/systemd/system/sysstat.service'. Setting up libavahi-client3:amd64 (0.8-16) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.17.4+ds-4) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up libatk1.0-0t64:amd64 (2.55.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.2-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libpango-1.0-0:amd64 (1.56.1-1) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up python3 (3.13.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up dbus-user-session (1.16.0-1) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (47.0-2) ... 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 librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:amd64 (2.55.2-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up parallel (20240222+ds-2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfastinfoset-java (1.2.12-4) ... Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ... Setting up mesa-libgallium:amd64 (24.3.4-3) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:amd64 (8.12.1-2) ... Setting up libgbm1:amd64 (24.3.4-3) ... Setting up libgl1-mesa-dri:amd64 (24.3.4-3) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-2) ... Setting up debhelper (13.24.1) ... Setting up dconf-service (0.40.0-5) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.167-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7+b2) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b3) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up r-cran-rlang (1.1.5-1) ... Setting up libglx-mesa0:amd64 (24.3.4-3) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up vt (0.57721+ds-3+b1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up bcftools (1.21-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up r-cran-mass (7.3-64-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up samtools (1.21-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-2-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up libgtk-3-common (3.24.48-4) ... Setting up r-cran-pillar (1.10.1+dfsg-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-3) ... Setting up libvcflib2:amd64 (1.0.12+dfsg-1) ... Setting up libgtk-3-0t64:amd64 (3.24.48-4) ... Setting up r-cran-scales (1.3.0-1) ... Setting up freebayes (1.3.9-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libvcflib-tools (1.0.12+dfsg-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libmaven3-core-java (3.9.9-1) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libjni-inchi-java (0.8+dfsg-8) ... Setting up libmaven-file-management-java (3.0.0-2) ... Setting up libjmol-java (16.2.33+dfsg-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.12.0-1) ... Setting up libmsgpack-java (0.9.6-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.2-1) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for systemd (257.3-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.6+7-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up ant-optional (1.10.15-1) ... Setting up junit5 (5.10.3-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ... Setting up libtxw2-java (2.3.0.1-11) ... Setting up libjaxb-java (2.3.0.1-11) ... Setting up libbiojava6-java (6.1.0+dfsg-5) ... Setting up libsnpeff-java (5.2.f+dfsg-1) ... Setting up snpeff (5.2.f+dfsg-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && 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 > ../snippy_4.6.0+dfsg-5_source.changes dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg' cd test && /usr/bin/make make[2]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg/test' mkdir -p S1 wgsim -S 1 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S1/R1.fq S1/R2.fq > S1/dwgsim.tab [wgsim] seed = 1 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq [14:49:06] This is snippy 4.6.0 [14:49:06] Written by Torsten Seemann [14:49:06] Obtained from https://github.com/tseemann/snippy [14:49:06] Detected operating system: linux [14:49:06] Enabling bundled linux tools. [14:49:06] Found bwa - /usr/bin/bwa [14:49:06] Found bcftools - /usr/bin/bcftools [14:49:06] Found samtools - /usr/bin/samtools [14:49:06] Found java - /usr/bin/java [14:49:06] Found snpEff - /usr/bin/snpEff [14:49:06] Found samclip - /usr/bin/samclip [14:49:06] Found seqtk - /usr/bin/seqtk [14:49:06] Found parallel - /usr/bin/parallel [14:49:06] Found freebayes - /usr/bin/freebayes [14:49:06] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:06] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:06] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:06] Found vcfuniq - /usr/bin/vcfuniq [14:49:06] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:06] Found gzip - /usr/bin/gzip [14:49:06] Found vt - /usr/bin/vt [14:49:06] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:06] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:06] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:07] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:07] Treating reference as 'fasta' format. [14:49:07] Will use 2 CPU cores. [14:49:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq [14:49:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq [14:49:07] Used --force, will overwrite existing S1 [14:49:07] Changing working directory: S1 [14:49:07] Creating reference folder: reference [14:49:07] Extracting FASTA and GFF from reference. [14:49:07] Wrote 3 sequences to ref.fa [14:49:07] Wrote 0 features to ref.gff [14:49:07] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:07] Using BAM RG (Read Group) ID: S1 [14:49:07] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:07] Running: bwa index reference/ref.fa 2>> snps.log [14:49:07] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:07] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:07] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:07] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:07] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11587, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 233) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 369) [M::mem_pestat] mean and std.dev: (199.53, 48.89) [M::mem_pestat] low and high boundaries for proper pairs: (1, 437) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.179 CPU sec, 1.185 real sec [main] Version: 0.7.18-r1243-dirty [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq [main] Real time: 1.355 sec; CPU: 2.228 sec [14:49:09] Running: samtools index snps.bam 2>> snps.log [14:49:09] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:09] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:11] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 10 no. right trimmed : 33 no. left and right trimmed : 4 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 47 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 47 total no. variants observed : 261 total no. reference observed : 0 Time elapsed: 0.01s [14:49:11] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:11] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:12] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:12] Marked 749 heterozygous sites with 'n' [14:49:12] Creating extra output files: BED GFF CSV TXT HTML [14:49:12] Identified 261 variants. [14:49:12] Result folder: S1 [14:49:12] Result files: [14:49:12] * S1/snps.aligned.fa [14:49:12] * S1/snps.bam [14:49:12] * S1/snps.bam.bai [14:49:12] * S1/snps.bed [14:49:12] * S1/snps.consensus.fa [14:49:12] * S1/snps.consensus.subs.fa [14:49:12] * S1/snps.csv [14:49:12] * S1/snps.filt.vcf [14:49:12] * S1/snps.gff [14:49:12] * S1/snps.html [14:49:12] * S1/snps.log [14:49:12] * S1/snps.raw.vcf [14:49:12] * S1/snps.subs.vcf [14:49:12] * S1/snps.tab [14:49:12] * S1/snps.txt [14:49:12] * S1/snps.vcf [14:49:12] * S1/snps.vcf.gz [14:49:12] * S1/snps.vcf.gz.csi [14:49:12] Walltime used: 6 seconds [14:49:12] May the SNPs be with you. [14:49:12] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S2/R1.fq S2/R2.fq > S2/dwgsim.tab [wgsim] seed = 2 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq [14:49:12] This is snippy 4.6.0 [14:49:12] Written by Torsten Seemann [14:49:12] Obtained from https://github.com/tseemann/snippy [14:49:12] Detected operating system: linux [14:49:12] Enabling bundled linux tools. [14:49:12] Found bwa - /usr/bin/bwa [14:49:12] Found bcftools - /usr/bin/bcftools [14:49:12] Found samtools - /usr/bin/samtools [14:49:12] Found java - /usr/bin/java [14:49:12] Found snpEff - /usr/bin/snpEff [14:49:12] Found samclip - /usr/bin/samclip [14:49:12] Found seqtk - /usr/bin/seqtk [14:49:12] Found parallel - /usr/bin/parallel [14:49:12] Found freebayes - /usr/bin/freebayes [14:49:12] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:12] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:12] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:12] Found vcfuniq - /usr/bin/vcfuniq [14:49:13] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:13] Found gzip - /usr/bin/gzip [14:49:13] Found vt - /usr/bin/vt [14:49:13] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:13] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:13] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:13] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:13] Treating reference as 'fasta' format. [14:49:13] Will use 2 CPU cores. [14:49:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq [14:49:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq [14:49:13] Used --force, will overwrite existing S2 [14:49:13] Changing working directory: S2 [14:49:13] Creating reference folder: reference [14:49:13] Extracting FASTA and GFF from reference. [14:49:13] Wrote 3 sequences to ref.fa [14:49:13] Wrote 0 features to ref.gff [14:49:13] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:13] Using BAM RG (Read Group) ID: S2 [14:49:13] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:13] Running: bwa index reference/ref.fa 2>> snps.log [14:49:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:13] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:13] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 366) [M::mem_pestat] mean and std.dev: (199.27, 48.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.076 CPU sec, 1.053 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq [main] Real time: 1.223 sec; CPU: 2.128 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. [14:49:15] Running: samtools index snps.bam 2>> snps.log [14:49:15] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:15] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:16] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 10 no. right trimmed : 28 no. left and right trimmed : 1 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 39 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 39 total no. variants observed : 246 total no. reference observed : 0 Time elapsed: 0.01s [14:49:16] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:16] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:17] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:17] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:17] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:17] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:17] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:18] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:18] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:18] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:18] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:19] Marked 841 heterozygous sites with 'n' [14:49:19] Creating extra output files: BED GFF CSV TXT HTML [14:49:19] Identified 246 variants. [14:49:19] Result folder: S2 [14:49:19] Result files: [14:49:19] * S2/snps.aligned.fa [14:49:19] * S2/snps.bam [14:49:19] * S2/snps.bam.bai [14:49:19] * S2/snps.bed [14:49:19] * S2/snps.consensus.fa [14:49:19] * S2/snps.consensus.subs.fa [14:49:19] * S2/snps.csv [14:49:19] * S2/snps.filt.vcf [14:49:19] * S2/snps.gff [14:49:19] * S2/snps.html [14:49:19] * S2/snps.log [14:49:19] * S2/snps.raw.vcf [14:49:19] * S2/snps.subs.vcf [14:49:19] * S2/snps.tab [14:49:19] * S2/snps.txt [14:49:19] * S2/snps.vcf [14:49:19] * S2/snps.vcf.gz [14:49:19] * S2/snps.vcf.gz.csi [14:49:19] Walltime used: 7 seconds [14:49:19] Wishing you a life free of homopolymer errors. [14:49:19] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S3/R1.fq S3/R2.fq > S3/dwgsim.tab [wgsim] seed = 3 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq [14:49:19] This is snippy 4.6.0 [14:49:19] Written by Torsten Seemann [14:49:19] Obtained from https://github.com/tseemann/snippy [14:49:19] Detected operating system: linux [14:49:19] Enabling bundled linux tools. [14:49:19] Found bwa - /usr/bin/bwa [14:49:19] Found bcftools - /usr/bin/bcftools [14:49:19] Found samtools - /usr/bin/samtools [14:49:19] Found java - /usr/bin/java [14:49:19] Found snpEff - /usr/bin/snpEff [14:49:19] Found samclip - /usr/bin/samclip [14:49:19] Found seqtk - /usr/bin/seqtk [14:49:19] Found parallel - /usr/bin/parallel [14:49:19] Found freebayes - /usr/bin/freebayes [14:49:19] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:19] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:19] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:19] Found vcfuniq - /usr/bin/vcfuniq [14:49:19] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:19] Found gzip - /usr/bin/gzip [14:49:19] Found vt - /usr/bin/vt [14:49:19] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:19] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:19] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:19] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:19] Treating reference as 'fasta' format. [14:49:19] Will use 2 CPU cores. [14:49:19] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq [14:49:19] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq [14:49:19] Used --force, will overwrite existing S3 [14:49:19] Changing working directory: S3 [14:49:19] Creating reference folder: reference [14:49:19] Extracting FASTA and GFF from reference. [14:49:19] Wrote 3 sequences to ref.fa [14:49:19] Wrote 0 features to ref.gff [14:49:19] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:19] Using BAM RG (Read Group) ID: S3 [14:49:19] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:19] Running: bwa index reference/ref.fa 2>> snps.log [14:49:19] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:19] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:19] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:19] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:19] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368) [M::mem_pestat] mean and std.dev: (198.46, 48.83) [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.062 CPU sec, 1.137 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq [main] Real time: 1.247 sec; CPU: 2.107 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. [14:49:21] Running: samtools index snps.bam 2>> snps.log [14:49:21] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:21] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:23] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 11 no. right trimmed : 30 no. left and right trimmed : 1 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 42 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 42 total no. variants observed : 254 total no. reference observed : 0 Time elapsed: 0.01s [14:49:23] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:23] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:23] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:23] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:23] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:23] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:23] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:23] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:23] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:23] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:23] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:23] Marked 846 heterozygous sites with 'n' [14:49:23] Creating extra output files: BED GFF CSV TXT HTML [14:49:23] Identified 254 variants. [14:49:23] Result folder: S3 [14:49:23] Result files: [14:49:23] * S3/snps.aligned.fa [14:49:23] * S3/snps.bam [14:49:23] * S3/snps.bam.bai [14:49:23] * S3/snps.bed [14:49:23] * S3/snps.consensus.fa [14:49:23] * S3/snps.consensus.subs.fa [14:49:23] * S3/snps.csv [14:49:23] * S3/snps.filt.vcf [14:49:23] * S3/snps.gff [14:49:23] * S3/snps.html [14:49:23] * S3/snps.log [14:49:23] * S3/snps.raw.vcf [14:49:23] * S3/snps.subs.vcf [14:49:23] * S3/snps.tab [14:49:23] * S3/snps.txt [14:49:23] * S3/snps.vcf [14:49:23] * S3/snps.vcf.gz [14:49:23] * S3/snps.vcf.gz.csi [14:49:23] Walltime used: 4 seconds [14:49:23] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues [14:49:23] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S4/R1.fq S4/R2.fq > S4/dwgsim.tab [wgsim] seed = 4 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq [14:49:23] This is snippy 4.6.0 [14:49:23] Written by Torsten Seemann [14:49:23] Obtained from https://github.com/tseemann/snippy [14:49:23] Detected operating system: linux [14:49:23] Enabling bundled linux tools. [14:49:23] Found bwa - /usr/bin/bwa [14:49:23] Found bcftools - /usr/bin/bcftools [14:49:23] Found samtools - /usr/bin/samtools [14:49:23] Found java - /usr/bin/java [14:49:23] Found snpEff - /usr/bin/snpEff [14:49:23] Found samclip - /usr/bin/samclip [14:49:23] Found seqtk - /usr/bin/seqtk [14:49:24] Found parallel - /usr/bin/parallel [14:49:24] Found freebayes - /usr/bin/freebayes [14:49:24] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:49:24] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:49:24] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:49:24] Found vcfuniq - /usr/bin/vcfuniq [14:49:24] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:49:24] Found gzip - /usr/bin/gzip [14:49:24] Found vt - /usr/bin/vt [14:49:24] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:49:24] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:49:24] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [14:49:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [14:49:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [14:49:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:49:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:49:24] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [14:49:24] Treating reference as 'fasta' format. [14:49:24] Will use 2 CPU cores. [14:49:24] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq [14:49:24] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq [14:49:24] Used --force, will overwrite existing S4 [14:49:24] Changing working directory: S4 [14:49:24] Creating reference folder: reference [14:49:24] Extracting FASTA and GFF from reference. [14:49:24] Wrote 3 sequences to ref.fa [14:49:24] Wrote 0 features to ref.gff [14:49:24] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:49:24] Using BAM RG (Read Group) ID: S4 [14:49:24] Running: samtools faidx reference/ref.fa 2>> snps.log [14:49:24] Running: bwa index reference/ref.fa 2>> snps.log [14:49:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:49:24] Running: ln -sf reference/ref.fa . 2>> snps.log [14:49:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:49:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:49:24] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11573, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 198, 230) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (35, 360) [M::mem_pestat] mean and std.dev: (198.20, 48.15) [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.376 CPU sec, 0.693 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. [main] Real time: 0.809 sec; CPU: 1.418 sec [14:49:25] Running: samtools index snps.bam 2>> snps.log [14:49:25] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:49:25] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:49:26] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 12 no. right trimmed : 35 no. left and right trimmed : 3 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 50 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 50 total no. variants observed : 257 total no. reference observed : 0 Time elapsed: 0.01s [14:49:26] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:49:26] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:49:26] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:49:26] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:49:26] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:49:26] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:49:26] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:49:27] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:49:27] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:49:27] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:49:27] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:49:27] Marked 799 heterozygous sites with 'n' [14:49:27] Creating extra output files: BED GFF CSV TXT HTML [14:49:27] Identified 257 variants. [14:49:27] Result folder: S4 [14:49:27] Result files: [14:49:27] * S4/snps.aligned.fa [14:49:27] * S4/snps.bam [14:49:27] * S4/snps.bam.bai [14:49:27] * S4/snps.bed [14:49:27] * S4/snps.consensus.fa [14:49:27] * S4/snps.consensus.subs.fa [14:49:27] * S4/snps.csv [14:49:27] * S4/snps.filt.vcf [14:49:27] * S4/snps.gff [14:49:27] * S4/snps.html [14:49:27] * S4/snps.log [14:49:27] * S4/snps.raw.vcf [14:49:27] * S4/snps.subs.vcf [14:49:27] * S4/snps.tab [14:49:27] * S4/snps.txt [14:49:27] * S4/snps.vcf [14:49:27] * S4/snps.vcf.gz [14:49:27] * S4/snps.vcf.gz.csi [14:49:27] Walltime used: 4 seconds [14:49:27] Did you know? Snippy is a combination of SNP, Skippy, and snappy. [14:49:27] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Will mask 0 regions totalling 0 bp ~ 0.00% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core.tab Opening: core.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core-mask.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Loading mask bed file: example.bed Will mask 8 regions totalling 3101 bp ~ 0.98% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core-mask.tab Opening: core-mask.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Masking alignment at 8 regions Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln This analysis is totally hard-core! Done. wc -l S?/snps.tab 262 S1/snps.tab 247 S2/snps.tab 255 S3/snps.tab 258 S4/snps.tab 1022 total make[2]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg' dh_install sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snippy' in '../snippy_4.6.0+dfsg-5_all.deb'. dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../snippy_4.6.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../snippy_4.6.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3521208 and its subdirectories I: Current time: Thu Mar 26 14:49:31 -12 2026 I: pbuilder-time-stamp: 1774579771 Fri Feb 21 20:26:32 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Fri Feb 21 20:26:32 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Fri Feb 21 20:26:33 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Fri Feb 21 20:26:33 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-6j08ZW' ==================================================================================== Fri Feb 21 20:26:34 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 snippy trixie /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe 4.6.0+dfsg-5" as arguments. Fri Feb 21 20:26:34 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-uSQJmy2Q" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Feb 21 20:26:34 UTC 2025 I: Downloading source for trixie/snippy=4.6.0+dfsg-5 Reading package lists... NOTICE: 'snippy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snippy.git Please use: git clone https://salsa.debian.org/med-team/snippy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 279 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (dsc) [2353 B] Get:2 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (tar) [271 kB] Get:3 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (diff) [5340 B] Fetched 279 kB in 0s (5955 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snippy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snippy.git Please use: git clone https://salsa.debian.org/med-team/snippy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 279 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (dsc) [2353 B] Get:2 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (tar) [271 kB] Get:3 http://deb.debian.org/debian trixie/main snippy 4.6.0+dfsg-5 (diff) [5340 B] Fetched 279 kB in 0s (5955 kB/s) Download complete and in download only mode ============================================================================= Re-Building snippy in trixie on amd64 on ionos11-amd64 now. Date: Fri Feb 21 20:26:34 UTC 2025 Date UTC: Fri Feb 21 20:26:34 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/pbuilderrc_magc + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' snippy = debian-installer -o snippy = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' snippy = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/pbuilderrc_magc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 22 10:26:35 +14 2025 I: pbuilder-time-stamp: 1740169595 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 [snippy_4.6.0+dfsg-5.dsc] I: copying [./snippy_4.6.0+dfsg.orig.tar.xz] I: copying [./snippy_4.6.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./snippy_4.6.0+dfsg-5.dsc: unsupported subcommand dpkg-source: info: extracting snippy in snippy-4.6.0+dfsg dpkg-source: info: unpacking snippy_4.6.0+dfsg.orig.tar.xz dpkg-source: info: unpacking snippy_4.6.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian_packaged_libs.patch dpkg-source: info: applying snpeff.config.patch dpkg-source: info: applying snpeff_v5.1+.patch dpkg-source: info: applying make-4.4.1.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 21 20:26 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=7c696e04a3684c36967e81004fbf72f5 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1827059 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/pbuilderrc_magc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19809 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 any2fasta; however: Package any2fasta is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on freebayes; however: Package freebayes is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools; however: Package libvcflib-tools is not installed. pbuilder-satisfydepends-dummy depends on minimap2; however: Package minimap2 is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on samclip; however: Package samclip is not installed. pbuilder-satisfydepends-dummy depends on seqtk; however: Package seqtk is not installed. pbuilder-satisfydepends-dummy depends on snp-sites; however: Package snp-sites is not installed. pbuilder-satisfydepends-dummy depends on snpeff; however: Package snpeff is not installed. pbuilder-satisfydepends-dummy depends on vt; however: Package vt 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-optional{a} any2fasta{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bedtools{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} freebayes{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbio-perl-perl{a} libbiojava6-java{a} libblas3{a} libbrotli1{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libcharts4j-java{a} libciftools-java{a} libcloudproviders0{a} libcodemodel-java{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-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} libcups2t64{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-stag-perl{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdisorder0{a} libdistlib-java{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libedit2{a} libelf1t64{a} libepoxy0{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libezmorph-java{a} libfastahack0{a} libfastinfoset-java{a} libfastutil-java{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfml0{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgbm1{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} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libice6{a} libicu72{a} libidn2-0{a} libinchi1.07{a} libio-string-perl{a} libistack-commons-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjson-java{a} libjson-simple-java{a} libjsoncpp26{a} libjsoup-java{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} liblog4j1.2-java{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-jar-plugin-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmmtf-java{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-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-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib2{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsmithwaterman0{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsnp-sites1{a} libsnpeff-java{a} libssh2-1t64{a} libssw0{a} libstax-ex-java{a} libstreambuffer-java{a} libsystemd-shared{a} libtabixpp0t64{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtrove3-java{a} libtxw2-java{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} libvcflib-tools{a} libvcflib2{a} libvecmath-java{a} libvulkan1{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwfa2-0{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxom-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxss1{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} littler{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} minimap2{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} parallel{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} samclip{a} samtools{a} sensible-utils{a} seqtk{a} shared-mime-info{a} snp-sites{a} snpeff{a} sysstat{a} systemd{a} systemd-sysv{a} tzdata{a} ucf{a} unzip{a} vt{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf at-spi2-core bioperl-run chrony curl fonts-dejavu-extra krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libatk-wrapper-java-jni libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libfile-mimeinfo-perl libgd-perl libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libgtk-3-bin libhtml-parser-perl libhtml-tableextract-perl libjansi-java libkmod2 libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libnet-dbus-perl libnss-systemd libpostscript-perl librsvg2-common libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd perl-tk psmisc publicsuffix python3-gffutils python3-matplotlib r-base-dev r-cran-abind r-cran-bench r-cran-bit64 r-cran-blob r-cran-brio r-cran-callr r-cran-covr r-cran-crayon r-cran-dbi r-cran-diagrammer r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-evaluate r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-here r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-multcomp r-cran-mvtnorm r-cran-nanotime r-cran-palmerpenguins r-cran-pkgbuild r-cran-pkgdown r-cran-pkgload r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-purrr r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-survival r-cran-svglite r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-units r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 418 newly installed, 0 to remove and 0 not upgraded. Need to get 326 MB of archives. After unpacking 961 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-4 [42.0 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.3-1 [3092 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.3-1 [293 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0049 [42.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.17.4+ds-4 [51.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 62 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.108-1 [1393 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 67 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 68 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 any2fasta all 0.4.2-2 [6232 B] Get: 71 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.55.2-1 [170 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 87 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-2 [365 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.21-1 [784 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 115 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-1 [26.5 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-1 [11.4 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-1 [5452 B] Get: 162 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 174 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.3.4-3 [38.5 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.3.4-3 [9492 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-1 [34.0 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.3.4-3 [43.7 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.3.4-3 [45.2 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.3.4-3 [143 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 209 http://deb.debian.org/debian trixie/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b3 [172 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get: 215 http://deb.debian.org/debian trixie/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libwfa2-0 amd64 2.3.3-4+b2 [60.9 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libvcflib2 amd64 1.0.12+dfsg-1 [233 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 freebayes amd64 1.3.9-1 [1523 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 223 http://deb.debian.org/debian trixie/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 224 http://deb.debian.org/debian trixie/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 231 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 232 http://deb.debian.org/debian trixie/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 236 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 261 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 268 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 271 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 281 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libjheaps-java all 0.14-2 [144 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get: 312 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 315 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 322 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 324 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 326 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 336 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 341 http://deb.debian.org/debian trixie/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 345 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 346 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 347 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 348 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 349 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 350 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB] Get: 351 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB] Get: 352 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB] Get: 353 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 354 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 355 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 356 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 357 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 358 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB] Get: 359 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB] Get: 360 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 361 http://deb.debian.org/debian trixie/main amd64 libsnp-sites1 amd64 2.5.1-2+b2 [14.8 kB] Get: 362 http://deb.debian.org/debian trixie/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 363 http://deb.debian.org/debian trixie/main amd64 libsnpeff-java all 5.2.f+dfsg-1 [2156 kB] Get: 364 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 365 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 366 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 367 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 368 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 369 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 370 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 371 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 372 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 373 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 374 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 375 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get: 376 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-2 [16.0 kB] Get: 377 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get: 379 http://deb.debian.org/debian trixie/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 380 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 381 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get: 382 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.5-1 [1712 kB] Get: 383 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 384 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 385 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 386 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB] Get: 387 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 388 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.167-1 [2331 kB] Get: 389 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-2-1 [4155 kB] Get: 390 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 391 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 392 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 393 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 394 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 395 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 396 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 397 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 398 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 399 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 400 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 401 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 402 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 403 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get: 404 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 405 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 408 http://deb.debian.org/debian trixie/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 409 http://deb.debian.org/debian trixie/main amd64 libvcflib-tools amd64 1.0.12+dfsg-1 [608 kB] Get: 410 http://deb.debian.org/debian trixie/main amd64 minimap2 amd64 2.27+dfsg-1+b2 [391 kB] Get: 411 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 412 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 samclip all 0.4.0-4 [20.1 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.21-1 [667 kB] Get: 415 http://deb.debian.org/debian trixie/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get: 416 http://deb.debian.org/debian trixie/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 snpeff all 5.2.f+dfsg-1 [7244 B] Get: 418 http://deb.debian.org/debian trixie/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] Fetched 326 MB in 21s (15.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19809 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-4_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-4) ... Setting up libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package systemd. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19822 files and directories currently installed.) Preparing to unpack .../systemd_257.3-1_amd64.deb ... Unpacking systemd (257.3-1) ... Setting up libapparmor1:amd64 (3.1.7-4) ... Setting up systemd (257.3-1) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20765 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_257.3-1_amd64.deb ... Unpacking systemd-sysv (257.3-1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../1-libdbus-1-3_1.16.0-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.16.0-1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../2-dbus-bin_1.16.0-1_amd64.deb ... Unpacking dbus-bin (1.16.0-1) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../3-dbus-session-bus-common_1.16.0-1_all.deb ... Unpacking dbus-session-bus-common (1.16.0-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../4-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../5-dbus-daemon_1.16.0-1_amd64.deb ... Unpacking dbus-daemon (1.16.0-1) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../6-dbus-system-bus-common_1.16.0-1_all.deb ... Unpacking dbus-system-bus-common (1.16.0-1) ... Selecting previously unselected package dbus. Preparing to unpack .../7-dbus_1.16.0-1_amd64.deb ... Unpacking dbus (1.16.0-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../8-libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../9-python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 21191 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... 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_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 22201 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_amd64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-7_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-7_amd64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.4.1-1_amd64.deb ... Unpacking openssl (3.4.1-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package libpam-systemd:amd64. Preparing to unpack .../012-libpam-systemd_257.3-1_amd64.deb ... Unpacking libpam-systemd:amd64 (257.3-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.4-3_amd64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../014-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libtext-charwidth-perl:amd64. Preparing to unpack .../016-libtext-charwidth-perl_0.04-11+b4_amd64.deb ... Unpacking libtext-charwidth-perl:amd64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../017-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../018-ucf_3.0049_all.deb ... Moving old data out of the way Unpacking ucf (3.0049) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../019-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../020-libglib2.0-0t64_2.83.3-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.83.3-2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../021-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../022-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../023-shared-mime-info_2.4-5+b2_amd64.deb ... Unpacking shared-mime-info (2.4-5+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../024-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../025-libpng16-16t64_1.6.46-4_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.46-4) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../026-libdeflate0_1.23-1+b1_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-1+b1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../027-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../028-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../029-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../030-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../031-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../032-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../033-gtk-update-icon-cache_4.17.4+ds-4_amd64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.17.4+ds-4) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../034-hicolor-icon-theme_0.18-2_all.deb ... Unpacking hicolor-icon-theme (0.18-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../035-adwaita-icon-theme_47.0-2_all.deb ... Unpacking adwaita-icon-theme (47.0-2) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../036-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../037-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../038-liblcms2-2_2.16-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../039-libnspr4_2%3a4.36-1_amd64.deb ... 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Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up dbus (1.16.0-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0049) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up librngom-java (2.3.0.1-11) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libjni-inchi-jni (0.8+dfsg-8) ... Setting up libjgraphx-java (2.1.0.7-5) ... Setting up snp-sites (2.5.1-2+b2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:amd64 (1.23.1-1) ... Setting up libpam-systemd:amd64 (257.3-1) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libxsom-java (2.3.0.1-11) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.17.1-1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-collect.timer' -> '/usr/lib/systemd/system/sysstat-collect.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-rotate.timer' -> '/usr/lib/systemd/system/sysstat-rotate.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-summary.timer' -> '/usr/lib/systemd/system/sysstat-summary.timer'. Created symlink '/etc/systemd/system/multi-user.target.wants/sysstat.service' -> '/usr/lib/systemd/system/sysstat.service'. Setting up libavahi-client3:amd64 (0.8-16) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.17.4+ds-4) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up libatk1.0-0t64:amd64 (2.55.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.2-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libpango-1.0-0:amd64 (1.56.1-1) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up python3 (3.13.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up dbus-user-session (1.16.0-1) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (47.0-2) ... 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 librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:amd64 (2.55.2-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up parallel (20240222+ds-2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfastinfoset-java (1.2.12-4) ... Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ... Setting up mesa-libgallium:amd64 (24.3.4-3) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:amd64 (8.12.1-2) ... Setting up libgbm1:amd64 (24.3.4-3) ... Setting up libgl1-mesa-dri:amd64 (24.3.4-3) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-2) ... Setting up debhelper (13.24.1) ... Setting up dconf-service (0.40.0-5) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.167-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7+b2) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b3) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up r-cran-rlang (1.1.5-1) ... Setting up libglx-mesa0:amd64 (24.3.4-3) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up vt (0.57721+ds-3+b1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up bcftools (1.21-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up r-cran-mass (7.3-64-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up samtools (1.21-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-2-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up libgtk-3-common (3.24.48-4) ... Setting up r-cran-pillar (1.10.1+dfsg-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-3) ... Setting up libvcflib2:amd64 (1.0.12+dfsg-1) ... Setting up libgtk-3-0t64:amd64 (3.24.48-4) ... Setting up r-cran-scales (1.3.0-1) ... Setting up freebayes (1.3.9-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libvcflib-tools (1.0.12+dfsg-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libmaven3-core-java (3.9.9-1) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libjni-inchi-java (0.8+dfsg-8) ... Setting up libmaven-file-management-java (3.0.0-2) ... Setting up libjmol-java (16.2.33+dfsg-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.12.0-1) ... Setting up libmsgpack-java (0.9.6-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.2-1) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for systemd (257.3-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.6+7-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up ant-optional (1.10.15-1) ... Setting up junit5 (5.10.3-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ... Setting up libtxw2-java (2.3.0.1-11) ... Setting up libjaxb-java (2.3.0.1-11) ... Setting up libbiojava6-java (6.1.0+dfsg-5) ... Setting up libsnpeff-java (5.2.f+dfsg-1) ... Setting up snpeff (5.2.f+dfsg-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snippy_4.6.0+dfsg-5_source.changes dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg' cd test && /usr/bin/make make[2]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg/test' mkdir -p S1 wgsim -S 1 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S1/R1.fq S1/R2.fq > S1/dwgsim.tab [wgsim] seed = 1 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq [10:34:50] This is snippy 4.6.0 [10:34:50] Written by Torsten Seemann [10:34:50] Obtained from https://github.com/tseemann/snippy [10:34:50] Detected operating system: linux [10:34:50] Enabling bundled linux tools. [10:34:50] Found bwa - /usr/bin/bwa [10:34:50] Found bcftools - /usr/bin/bcftools [10:34:51] Found samtools - /usr/bin/samtools [10:34:51] Found java - /usr/bin/java [10:34:51] Found snpEff - /usr/bin/snpEff [10:34:51] Found samclip - /usr/bin/samclip [10:34:51] Found seqtk - /usr/bin/seqtk [10:34:51] Found parallel - /usr/bin/parallel [10:34:51] Found freebayes - /usr/bin/freebayes [10:34:51] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [10:34:51] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [10:34:51] Found vcfstreamsort - /usr/bin/vcfstreamsort [10:34:51] Found vcfuniq - /usr/bin/vcfuniq [10:34:51] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [10:34:51] Found gzip - /usr/bin/gzip [10:34:51] Found vt - /usr/bin/vt [10:34:51] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [10:34:51] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [10:34:51] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [10:34:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [10:34:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [10:34:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [10:34:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [10:34:54] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [10:34:54] Treating reference as 'fasta' format. [10:34:54] Will use 2 CPU cores. [10:34:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq [10:34:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq [10:34:54] Used --force, will overwrite existing S1 [10:34:54] Changing working directory: S1 [10:34:54] Creating reference folder: reference [10:34:54] Extracting FASTA and GFF from reference. [10:34:54] Wrote 3 sequences to ref.fa [10:34:54] Wrote 0 features to ref.gff [10:34:54] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [10:34:54] Using BAM RG (Read Group) ID: S1 [10:34:54] Running: samtools faidx reference/ref.fa 2>> snps.log [10:34:54] Running: bwa index reference/ref.fa 2>> snps.log [10:34:55] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:34:55] Running: ln -sf reference/ref.fa . 2>> snps.log [10:34:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:34:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:34:55] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11587, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 233) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 369) [M::mem_pestat] mean and std.dev: (199.53, 48.89) [M::mem_pestat] low and high boundaries for proper pairs: (1, 437) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.851 CPU sec, 6.001 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq [main] Real time: 7.286 sec; CPU: 2.940 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. [10:35:07] Running: samtools index snps.bam 2>> snps.log [10:35:07] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [10:35:07] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [10:35:19] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 10 no. right trimmed : 33 no. left and right trimmed : 4 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 47 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 47 total no. variants observed : 261 total no. reference observed : 0 Time elapsed: 0.01s [10:35:19] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [10:35:19] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [10:35:19] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [10:35:20] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [10:35:20] Running: bcftools index -f snps.vcf.gz 2>> snps.log [10:35:20] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [10:35:20] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [10:35:21] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [10:35:21] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [10:35:21] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [10:35:21] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [10:35:24] Marked 749 heterozygous sites with 'n' [10:35:24] Creating extra output files: BED GFF CSV TXT HTML [10:35:24] Identified 261 variants. [10:35:24] Result folder: S1 [10:35:24] Result files: [10:35:24] * S1/snps.aligned.fa [10:35:24] * S1/snps.bam [10:35:24] * S1/snps.bam.bai [10:35:24] * S1/snps.bed [10:35:24] * S1/snps.consensus.fa [10:35:24] * S1/snps.consensus.subs.fa [10:35:24] * S1/snps.csv [10:35:24] * S1/snps.filt.vcf [10:35:24] * S1/snps.gff [10:35:24] * S1/snps.html [10:35:24] * S1/snps.log [10:35:24] * S1/snps.raw.vcf [10:35:24] * S1/snps.subs.vcf [10:35:24] * S1/snps.tab [10:35:24] * S1/snps.txt [10:35:24] * S1/snps.vcf [10:35:24] * S1/snps.vcf.gz [10:35:24] * S1/snps.vcf.gz.csi [10:35:24] Walltime used: 34 seconds [10:35:24] Found a bug? Post it at https://github.com/tseemann/snippy/issues [10:35:24] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S2/R1.fq S2/R2.fq > S2/dwgsim.tab [wgsim] seed = 2 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq [10:35:27] This is snippy 4.6.0 [10:35:27] Written by Torsten Seemann [10:35:27] Obtained from https://github.com/tseemann/snippy [10:35:27] Detected operating system: linux [10:35:27] Enabling bundled linux tools. [10:35:27] Found bwa - /usr/bin/bwa [10:35:27] Found bcftools - /usr/bin/bcftools [10:35:27] Found samtools - /usr/bin/samtools [10:35:27] Found java - /usr/bin/java [10:35:27] Found snpEff - /usr/bin/snpEff [10:35:28] Found samclip - /usr/bin/samclip [10:35:28] Found seqtk - /usr/bin/seqtk [10:35:28] Found parallel - /usr/bin/parallel [10:35:28] Found freebayes - /usr/bin/freebayes [10:35:28] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [10:35:28] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [10:35:28] Found vcfstreamsort - /usr/bin/vcfstreamsort [10:35:28] Found vcfuniq - /usr/bin/vcfuniq [10:35:28] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [10:35:28] Found gzip - /usr/bin/gzip [10:35:28] Found vt - /usr/bin/vt [10:35:28] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [10:35:28] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [10:35:28] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [10:35:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [10:35:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [10:35:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [10:35:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [10:35:30] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [10:35:30] Treating reference as 'fasta' format. [10:35:30] Will use 2 CPU cores. [10:35:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq [10:35:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq [10:35:30] Used --force, will overwrite existing S2 [10:35:30] Changing working directory: S2 [10:35:30] Creating reference folder: reference [10:35:30] Extracting FASTA and GFF from reference. [10:35:30] Wrote 3 sequences to ref.fa [10:35:30] Wrote 0 features to ref.gff [10:35:30] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [10:35:30] Using BAM RG (Read Group) ID: S2 [10:35:30] Running: samtools faidx reference/ref.fa 2>> snps.log [10:35:30] Running: bwa index reference/ref.fa 2>> snps.log [10:35:31] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:35:31] Running: ln -sf reference/ref.fa . 2>> snps.log [10:35:31] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:35:31] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:35:31] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 366) [M::mem_pestat] mean and std.dev: (199.27, 48.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.928 CPU sec, 6.646 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq [main] Real time: 7.799 sec; CPU: 3.019 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. [10:35:42] Running: samtools index snps.bam 2>> snps.log [10:35:42] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [10:35:42] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [10:35:52] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 10 no. right trimmed : 28 no. left and right trimmed : 1 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 39 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 39 total no. variants observed : 246 total no. reference observed : 0 Time elapsed: 0.01s [10:35:52] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [10:35:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [10:35:53] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [10:35:53] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [10:35:53] Running: bcftools index -f snps.vcf.gz 2>> snps.log [10:35:54] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [10:35:54] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [10:35:54] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [10:35:54] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [10:35:54] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [10:35:54] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [10:35:58] Marked 841 heterozygous sites with 'n' [10:35:58] Creating extra output files: BED GFF CSV TXT HTML [10:35:58] Identified 246 variants. [10:35:58] Result folder: S2 [10:35:58] Result files: [10:35:58] * S2/snps.aligned.fa [10:35:58] * S2/snps.bam [10:35:58] * S2/snps.bam.bai [10:35:58] * S2/snps.bed [10:35:58] * S2/snps.consensus.fa [10:35:58] * S2/snps.consensus.subs.fa [10:35:58] * S2/snps.csv [10:35:58] * S2/snps.filt.vcf [10:35:58] * S2/snps.gff [10:35:58] * S2/snps.html [10:35:58] * S2/snps.log [10:35:58] * S2/snps.raw.vcf [10:35:58] * S2/snps.subs.vcf [10:35:58] * S2/snps.tab [10:35:58] * S2/snps.txt [10:35:58] * S2/snps.vcf [10:35:58] * S2/snps.vcf.gz [10:35:58] * S2/snps.vcf.gz.csi [10:35:58] Walltime used: 31 seconds [10:35:58] Questionable SNP? Try the --report option to see the alignments. [10:35:58] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S3/R1.fq S3/R2.fq > S3/dwgsim.tab [wgsim] seed = 3 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq [10:36:01] This is snippy 4.6.0 [10:36:01] Written by Torsten Seemann [10:36:01] Obtained from https://github.com/tseemann/snippy [10:36:01] Detected operating system: linux [10:36:01] Enabling bundled linux tools. [10:36:01] Found bwa - /usr/bin/bwa [10:36:01] Found bcftools - /usr/bin/bcftools [10:36:01] Found samtools - /usr/bin/samtools [10:36:01] Found java - /usr/bin/java [10:36:01] Found snpEff - /usr/bin/snpEff [10:36:01] Found samclip - /usr/bin/samclip [10:36:01] Found seqtk - /usr/bin/seqtk [10:36:01] Found parallel - /usr/bin/parallel [10:36:01] Found freebayes - /usr/bin/freebayes [10:36:01] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [10:36:01] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [10:36:01] Found vcfstreamsort - /usr/bin/vcfstreamsort [10:36:02] Found vcfuniq - /usr/bin/vcfuniq [10:36:02] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [10:36:02] Found gzip - /usr/bin/gzip [10:36:02] Found vt - /usr/bin/vt [10:36:02] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [10:36:02] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [10:36:02] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [10:36:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [10:36:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [10:36:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [10:36:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [10:36:04] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [10:36:04] Treating reference as 'fasta' format. [10:36:04] Will use 2 CPU cores. [10:36:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq [10:36:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq [10:36:04] Used --force, will overwrite existing S3 [10:36:04] Changing working directory: S3 [10:36:04] Creating reference folder: reference [10:36:04] Extracting FASTA and GFF from reference. [10:36:04] Wrote 3 sequences to ref.fa [10:36:04] Wrote 0 features to ref.gff [10:36:04] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [10:36:04] Using BAM RG (Read Group) ID: S3 [10:36:04] Running: samtools faidx reference/ref.fa 2>> snps.log [10:36:04] Running: bwa index reference/ref.fa 2>> snps.log [10:36:05] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:36:05] Running: ln -sf reference/ref.fa . 2>> snps.log [10:36:05] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:36:05] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:36:05] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 24000 sequences (2400000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368) [M::mem_pestat] mean and std.dev: (198.46, 48.83) [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 3.132 CPU sec, 6.778 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq [main] Real time: 8.682 sec; CPU: 3.228 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. [10:36:19] Running: samtools index snps.bam 2>> snps.log [10:36:19] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [10:36:19] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [10:36:39] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 11 no. right trimmed : 30 no. left and right trimmed : 1 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 42 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 42 total no. variants observed : 254 total no. reference observed : 0 Time elapsed: 0.01s [10:36:39] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [10:36:39] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [10:36:41] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [10:36:41] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [10:36:41] Running: bcftools index -f snps.vcf.gz 2>> snps.log [10:36:41] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [10:36:42] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [10:36:42] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [10:36:42] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [10:36:42] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [10:36:42] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [10:36:45] Marked 846 heterozygous sites with 'n' [10:36:45] Creating extra output files: BED GFF CSV TXT HTML [10:36:45] Identified 254 variants. [10:36:45] Result folder: S3 [10:36:45] Result files: [10:36:45] * S3/snps.aligned.fa [10:36:45] * S3/snps.bam [10:36:45] * S3/snps.bam.bai [10:36:45] * S3/snps.bed [10:36:45] * S3/snps.consensus.fa [10:36:45] * S3/snps.consensus.subs.fa [10:36:45] * S3/snps.csv [10:36:45] * S3/snps.filt.vcf [10:36:45] * S3/snps.gff [10:36:45] * S3/snps.html [10:36:45] * S3/snps.log [10:36:45] * S3/snps.raw.vcf [10:36:45] * S3/snps.subs.vcf [10:36:45] * S3/snps.tab [10:36:45] * S3/snps.txt [10:36:45] * S3/snps.vcf [10:36:45] * S3/snps.vcf.gz [10:36:45] * S3/snps.vcf.gz.csi [10:36:45] Walltime used: 44 seconds [10:36:45] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md [10:36:45] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S4/R1.fq S4/R2.fq > S4/dwgsim.tab [wgsim] seed = 4 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq [10:36:48] This is snippy 4.6.0 [10:36:48] Written by Torsten Seemann [10:36:48] Obtained from https://github.com/tseemann/snippy [10:36:48] Detected operating system: linux [10:36:48] Enabling bundled linux tools. [10:36:48] Found bwa - /usr/bin/bwa [10:36:48] Found bcftools - /usr/bin/bcftools [10:36:48] Found samtools - /usr/bin/samtools [10:36:48] Found java - /usr/bin/java [10:36:49] Found snpEff - /usr/bin/snpEff [10:36:49] Found samclip - /usr/bin/samclip [10:36:49] Found seqtk - /usr/bin/seqtk [10:36:49] Found parallel - /usr/bin/parallel [10:36:49] Found freebayes - /usr/bin/freebayes [10:36:49] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [10:36:49] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [10:36:49] Found vcfstreamsort - /usr/bin/vcfstreamsort [10:36:49] Found vcfuniq - /usr/bin/vcfuniq [10:36:49] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [10:36:49] Found gzip - /usr/bin/gzip [10:36:49] Found vt - /usr/bin/vt [10:36:49] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [10:36:49] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [10:36:50] Checking version: samtools --version is >= 1.7 - ok, have 1.21 [10:36:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [10:36:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 [10:36:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [10:36:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [10:36:53] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [10:36:53] Treating reference as 'fasta' format. [10:36:53] Will use 2 CPU cores. [10:36:53] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq [10:36:53] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq [10:36:53] Used --force, will overwrite existing S4 [10:36:53] Changing working directory: S4 [10:36:53] Creating reference folder: reference [10:36:53] Extracting FASTA and GFF from reference. [10:36:53] Wrote 3 sequences to ref.fa [10:36:53] Wrote 0 features to ref.gff [10:36:53] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [10:36:53] Using BAM RG (Read Group) ID: S4 [10:36:53] Running: samtools faidx reference/ref.fa 2>> snps.log [10:36:53] Running: bwa index reference/ref.fa 2>> snps.log [10:36:54] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:36:54] Running: ln -sf reference/ref.fa . 2>> snps.log [10:36:54] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:36:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:36:55] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11573, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 198, 230) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (35, 360) [M::mem_pestat] mean and std.dev: (198.20, 48.15) [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 2.955 CPU sec, 9.167 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq [main] Real time: 10.951 sec; CPU: 3.046 sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. [10:37:11] Running: samtools index snps.bam 2>> snps.log [10:37:11] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [10:37:12] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [10:37:29] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa stats: biallelic no. left trimmed : 12 no. right trimmed : 35 no. left and right trimmed : 3 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 50 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 50 total no. variants observed : 257 total no. reference observed : 0 Time elapsed: 0.01s [10:37:29] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [10:37:29] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [10:37:31] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [10:37:31] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [10:37:31] Running: bcftools index -f snps.vcf.gz 2>> snps.log [10:37:31] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [10:37:31] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [10:37:32] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [10:37:32] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [10:37:32] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [10:37:32] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [10:37:40] Marked 799 heterozygous sites with 'n' [10:37:40] Creating extra output files: BED GFF CSV TXT HTML [10:37:40] Identified 257 variants. [10:37:40] Result folder: S4 [10:37:40] Result files: [10:37:40] * S4/snps.aligned.fa [10:37:40] * S4/snps.bam [10:37:40] * S4/snps.bam.bai [10:37:40] * S4/snps.bed [10:37:40] * S4/snps.consensus.fa [10:37:40] * S4/snps.consensus.subs.fa [10:37:40] * S4/snps.csv [10:37:40] * S4/snps.filt.vcf [10:37:40] * S4/snps.gff [10:37:40] * S4/snps.html [10:37:40] * S4/snps.log [10:37:40] * S4/snps.raw.vcf [10:37:40] * S4/snps.subs.vcf [10:37:40] * S4/snps.tab [10:37:40] * S4/snps.txt [10:37:40] * S4/snps.vcf [10:37:40] * S4/snps.vcf.gz [10:37:40] * S4/snps.vcf.gz.csi [10:37:40] Walltime used: 52 seconds [10:37:40] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues [10:37:40] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Will mask 0 regions totalling 0 bp ~ 0.00% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core.tab Opening: core.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln You can mask columns using '--mask BEDFILE --mask-char X' Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core-mask.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Loading mask bed file: example.bed Will mask 8 regions totalling 3101 bp ~ 0.98% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core-mask.tab Opening: core-mask.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Masking alignment at 8 regions Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln Found a bug? Post it at http://github.com/tseemann/snippy/issues Done. wc -l S?/snps.tab 262 S1/snps.tab 247 S2/snps.tab 255 S3/snps.tab 258 S4/snps.tab 1022 total make[2]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg' dh_install sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snippy' in '../snippy_4.6.0+dfsg-5_all.deb'. dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../snippy_4.6.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../snippy_4.6.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1827059 and its subdirectories I: Current time: Sat Feb 22 10:38:19 +14 2025 I: pbuilder-time-stamp: 1740170299 + false + set +x Fri Feb 21 20:38:19 UTC 2025 I: Signing ./b2/snippy_4.6.0+dfsg-5_amd64.buildinfo as snippy_4.6.0+dfsg-5_amd64.buildinfo.asc Fri Feb 21 20:38:19 UTC 2025 I: Signed ./b2/snippy_4.6.0+dfsg-5_amd64.buildinfo as ./b2/snippy_4.6.0+dfsg-5_amd64.buildinfo.asc Fri Feb 21 20:38:19 UTC 2025 - build #2 for snippy/trixie/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Fri Feb 21 20:38:19 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-uSQJmy2Q, removing. /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe: total 220 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 20:26 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 21 20:38 b2 -rw------- 1 jenkins jenkins 207522 Feb 21 20:26 rbuildlog.dMpcRee -rw-r--r-- 1 jenkins jenkins 2353 Dec 10 15:50 snippy_4.6.0+dfsg-5.dsc /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b1: total 600 -rw-r--r-- 1 jenkins jenkins 203762 Feb 21 20:26 build.log -rw-r--r-- 1 jenkins jenkins 310484 Feb 21 20:26 snippy-examples_4.6.0+dfsg-5_all.deb -rw-r--r-- 1 jenkins jenkins 5340 Feb 21 20:26 snippy_4.6.0+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2353 Feb 21 20:26 snippy_4.6.0+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 26892 Feb 21 20:26 snippy_4.6.0+dfsg-5_all.deb -rw-r--r-- 1 jenkins jenkins 17307 Feb 21 20:26 snippy_4.6.0+dfsg-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 18189 Feb 21 20:26 snippy_4.6.0+dfsg-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1523 Feb 21 20:26 snippy_4.6.0+dfsg-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 1297 Feb 21 20:26 snippy_4.6.0+dfsg-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b2: total 596 -rw-r--r-- 1 jenkins jenkins 205775 Feb 21 20:38 build.log -rw-r--r-- 1 jenkins jenkins 310484 Feb 21 20:38 snippy-examples_4.6.0+dfsg-5_all.deb -rw-r--r-- 1 jenkins jenkins 5340 Feb 21 20:38 snippy_4.6.0+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2353 Feb 21 20:38 snippy_4.6.0+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 26892 Feb 21 20:38 snippy_4.6.0+dfsg-5_all.deb -rw-r--r-- 1 jenkins jenkins 17298 Feb 21 20:38 snippy_4.6.0+dfsg-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 18180 Feb 21 20:38 snippy_4.6.0+dfsg-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1523 Feb 21 20:38 snippy_4.6.0+dfsg-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 1297 Feb 21 20:38 snippy_4.6.0+dfsg-5_source.changes Fri Feb 21 20:38:20 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Fri Feb 21 20:38:21 UTC 2025 I: snippy_4.6.0+dfsg-5_amd64.changes: Format: 1.8 Date: Tue, 10 Dec 2024 16:40:07 +0100 Source: snippy Binary: snippy snippy-examples Architecture: all Version: 4.6.0+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: snippy - rapid haploid variant calling and core genome alignment snippy-examples - rapid haploid variant calling and core genome alignment (examples Closes: 1089272 Changes: snippy (4.6.0+dfsg-5) unstable; urgency=medium . * Build with make 4.4.1 Closes: #1089272 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: a4d8284f46d0797e34650d021189df2a4e687350 310484 snippy-examples_4.6.0+dfsg-5_all.deb 6ad10c1afc5fdf8dd4712d3b1d30edbd982f2c0f 26892 snippy_4.6.0+dfsg-5_all.deb a988e550318663cd513872514b45688dfbaa00db 17307 snippy_4.6.0+dfsg-5_amd64.buildinfo Checksums-Sha256: c8134543767177b42148058c3935ebc162f1ee35fc7b41e9e52f5a66d49e51d5 310484 snippy-examples_4.6.0+dfsg-5_all.deb d7321afb39cd81a6e334006053c013645b8b0b24afc77fe2a20312dd4c4a20ab 26892 snippy_4.6.0+dfsg-5_all.deb f0084355a331495c82ed178fbfba7d0d58861fb6eb80969190c4156641ab2c28 17307 snippy_4.6.0+dfsg-5_amd64.buildinfo Files: 0ff66e00274eabc3924a37a0ac7eefe3 310484 science optional snippy-examples_4.6.0+dfsg-5_all.deb 55c312573e3588a17b80aa56628e8d09 26892 science optional snippy_4.6.0+dfsg-5_all.deb a2ac29cb4523bff29874171263e6ad81 17307 science optional snippy_4.6.0+dfsg-5_amd64.buildinfo Diff of the two buildlogs: -- --- b1/build.log 2025-02-21 20:26:32.474232616 +0000 +++ b2/build.log 2025-02-21 20:38:20.594061378 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Mar 26 14:45:19 -12 2026 -I: pbuilder-time-stamp: 1774579519 +I: Current time: Sat Feb 22 10:26:35 +14 2025 +I: pbuilder-time-stamp: 1740169595 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying make-4.4.1.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3521208/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 21 20:26 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='df57c7856d35463d9ff17e9ac7d2dcea' - 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='3521208' - PS1='# ' - PS2='> ' + INVOCATION_ID=7c696e04a3684c36967e81004fbf72f5 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1827059 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.6PMZ3CYe/pbuilderrc_E8U9 --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.6PMZ3CYe/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/pbuilderrc_magc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3521208/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -556,7 +588,7 @@ Get: 416 http://deb.debian.org/debian trixie/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB] Get: 417 http://deb.debian.org/debian trixie/main amd64 snpeff all 5.2.f+dfsg-1 [7244 B] Get: 418 http://deb.debian.org/debian trixie/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] -Fetched 326 MB in 29s (11.2 MB/s) +Fetched 326 MB in 21s (15.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19809 files and directories currently installed.) @@ -1931,8 +1963,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Mar 27 02:48:31 UTC 2026. -Universal Time is now: Fri Mar 27 02:48:31 UTC 2026. +Local time is now: Fri Feb 21 20:32:27 UTC 2025. +Universal Time is now: Fri Feb 21 20:32:27 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2460,7 +2492,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && 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 > ../snippy_4.6.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snippy_4.6.0+dfsg-5_source.changes dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -2486,54 +2522,54 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq -[14:49:06] This is snippy 4.6.0 -[14:49:06] Written by Torsten Seemann -[14:49:06] Obtained from https://github.com/tseemann/snippy -[14:49:06] Detected operating system: linux -[14:49:06] Enabling bundled linux tools. -[14:49:06] Found bwa - /usr/bin/bwa -[14:49:06] Found bcftools - /usr/bin/bcftools -[14:49:06] Found samtools - /usr/bin/samtools -[14:49:06] Found java - /usr/bin/java -[14:49:06] Found snpEff - /usr/bin/snpEff -[14:49:06] Found samclip - /usr/bin/samclip -[14:49:06] Found seqtk - /usr/bin/seqtk -[14:49:06] Found parallel - /usr/bin/parallel -[14:49:06] Found freebayes - /usr/bin/freebayes -[14:49:06] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[14:49:06] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[14:49:06] Found vcfstreamsort - /usr/bin/vcfstreamsort -[14:49:06] Found vcfuniq - /usr/bin/vcfuniq -[14:49:06] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[14:49:06] Found gzip - /usr/bin/gzip -[14:49:06] Found vt - /usr/bin/vt -[14:49:06] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[14:49:06] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[14:49:06] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[14:49:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[14:49:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[14:49:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[14:49:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[14:49:07] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[14:49:07] Treating reference as 'fasta' format. -[14:49:07] Will use 2 CPU cores. -[14:49:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq -[14:49:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[14:49:07] Used --force, will overwrite existing S1 -[14:49:07] Changing working directory: S1 -[14:49:07] Creating reference folder: reference -[14:49:07] Extracting FASTA and GFF from reference. -[14:49:07] Wrote 3 sequences to ref.fa -[14:49:07] Wrote 0 features to ref.gff -[14:49:07] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[14:49:07] Using BAM RG (Read Group) ID: S1 -[14:49:07] Running: samtools faidx reference/ref.fa 2>> snps.log -[14:49:07] Running: bwa index reference/ref.fa 2>> snps.log -[14:49:07] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[14:49:07] Running: ln -sf reference/ref.fa . 2>> snps.log -[14:49:07] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[14:49:07] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[14:49:07] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[10:34:50] This is snippy 4.6.0 +[10:34:50] Written by Torsten Seemann +[10:34:50] Obtained from https://github.com/tseemann/snippy +[10:34:50] Detected operating system: linux +[10:34:50] Enabling bundled linux tools. +[10:34:50] Found bwa - /usr/bin/bwa +[10:34:50] Found bcftools - /usr/bin/bcftools +[10:34:51] Found samtools - /usr/bin/samtools +[10:34:51] Found java - /usr/bin/java +[10:34:51] Found snpEff - /usr/bin/snpEff +[10:34:51] Found samclip - /usr/bin/samclip +[10:34:51] Found seqtk - /usr/bin/seqtk +[10:34:51] Found parallel - /usr/bin/parallel +[10:34:51] Found freebayes - /usr/bin/freebayes +[10:34:51] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[10:34:51] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[10:34:51] Found vcfstreamsort - /usr/bin/vcfstreamsort +[10:34:51] Found vcfuniq - /usr/bin/vcfuniq +[10:34:51] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[10:34:51] Found gzip - /usr/bin/gzip +[10:34:51] Found vt - /usr/bin/vt +[10:34:51] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[10:34:51] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[10:34:51] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[10:34:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[10:34:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[10:34:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[10:34:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[10:34:54] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[10:34:54] Treating reference as 'fasta' format. +[10:34:54] Will use 2 CPU cores. +[10:34:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq +[10:34:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[10:34:54] Used --force, will overwrite existing S1 +[10:34:54] Changing working directory: S1 +[10:34:54] Creating reference folder: reference +[10:34:54] Extracting FASTA and GFF from reference. +[10:34:54] Wrote 3 sequences to ref.fa +[10:34:54] Wrote 0 features to ref.gff +[10:34:54] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[10:34:54] Using BAM RG (Read Group) ID: S1 +[10:34:54] Running: samtools faidx reference/ref.fa 2>> snps.log +[10:34:54] Running: bwa index reference/ref.fa 2>> snps.log +[10:34:55] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[10:34:55] Running: ln -sf reference/ref.fa . 2>> snps.log +[10:34:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[10:34:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[10:34:55] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -2548,17 +2584,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 437) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 2.179 CPU sec, 1.185 real sec +[M::mem_process_seqs] Processed 24000 reads in 2.851 CPU sec, 6.001 real sec [main] Version: 0.7.18-r1243-dirty +[main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[main] Real time: 7.286 sec; CPU: 2.940 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. -[main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[main] Real time: 1.355 sec; CPU: 2.228 sec -[14:49:09] Running: samtools index snps.bam 2>> snps.log -[14:49:09] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[14:49:09] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[14:49:11] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[10:35:07] Running: samtools index snps.bam 2>> snps.log +[10:35:07] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[10:35:07] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[10:35:19] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2595,43 +2631,43 @@ Time elapsed: 0.01s -[14:49:11] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[14:49:11] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[14:49:12] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[14:49:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[14:49:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[14:49:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[14:49:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[14:49:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[14:49:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[14:49:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[14:49:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[14:49:12] Marked 749 heterozygous sites with 'n' -[14:49:12] Creating extra output files: BED GFF CSV TXT HTML -[14:49:12] Identified 261 variants. -[14:49:12] Result folder: S1 -[14:49:12] Result files: -[14:49:12] * S1/snps.aligned.fa -[14:49:12] * S1/snps.bam -[14:49:12] * S1/snps.bam.bai -[14:49:12] * S1/snps.bed -[14:49:12] * S1/snps.consensus.fa -[14:49:12] * S1/snps.consensus.subs.fa -[14:49:12] * S1/snps.csv -[14:49:12] * S1/snps.filt.vcf -[14:49:12] * S1/snps.gff -[14:49:12] * S1/snps.html -[14:49:12] * S1/snps.log -[14:49:12] * S1/snps.raw.vcf -[14:49:12] * S1/snps.subs.vcf -[14:49:12] * S1/snps.tab -[14:49:12] * S1/snps.txt -[14:49:12] * S1/snps.vcf -[14:49:12] * S1/snps.vcf.gz -[14:49:12] * S1/snps.vcf.gz.csi -[14:49:12] Walltime used: 6 seconds -[14:49:12] May the SNPs be with you. -[14:49:12] Done. +[10:35:19] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[10:35:19] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[10:35:19] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[10:35:20] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[10:35:20] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[10:35:20] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[10:35:20] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[10:35:21] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[10:35:21] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[10:35:21] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[10:35:21] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[10:35:24] Marked 749 heterozygous sites with 'n' +[10:35:24] Creating extra output files: BED GFF CSV TXT HTML +[10:35:24] Identified 261 variants. +[10:35:24] Result folder: S1 +[10:35:24] Result files: +[10:35:24] * S1/snps.aligned.fa +[10:35:24] * S1/snps.bam +[10:35:24] * S1/snps.bam.bai +[10:35:24] * S1/snps.bed +[10:35:24] * S1/snps.consensus.fa +[10:35:24] * S1/snps.consensus.subs.fa +[10:35:24] * S1/snps.csv +[10:35:24] * S1/snps.filt.vcf +[10:35:24] * S1/snps.gff +[10:35:24] * S1/snps.html +[10:35:24] * S1/snps.log +[10:35:24] * S1/snps.raw.vcf +[10:35:24] * S1/snps.subs.vcf +[10:35:24] * S1/snps.tab +[10:35:24] * S1/snps.txt +[10:35:24] * S1/snps.vcf +[10:35:24] * S1/snps.vcf.gz +[10:35:24] * S1/snps.vcf.gz.csi +[10:35:24] Walltime used: 34 seconds +[10:35:24] Found a bug? Post it at https://github.com/tseemann/snippy/issues +[10:35:24] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2640,54 +2676,54 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq -[14:49:12] This is snippy 4.6.0 -[14:49:12] Written by Torsten Seemann -[14:49:12] Obtained from https://github.com/tseemann/snippy -[14:49:12] Detected operating system: linux -[14:49:12] Enabling bundled linux tools. -[14:49:12] Found bwa - /usr/bin/bwa -[14:49:12] Found bcftools - /usr/bin/bcftools -[14:49:12] Found samtools - /usr/bin/samtools -[14:49:12] Found java - /usr/bin/java -[14:49:12] Found snpEff - /usr/bin/snpEff -[14:49:12] Found samclip - /usr/bin/samclip -[14:49:12] Found seqtk - /usr/bin/seqtk -[14:49:12] Found parallel - /usr/bin/parallel -[14:49:12] Found freebayes - /usr/bin/freebayes -[14:49:12] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[14:49:12] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[14:49:12] Found vcfstreamsort - /usr/bin/vcfstreamsort -[14:49:12] Found vcfuniq - /usr/bin/vcfuniq -[14:49:13] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[14:49:13] Found gzip - /usr/bin/gzip -[14:49:13] Found vt - /usr/bin/vt -[14:49:13] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[14:49:13] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[14:49:13] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[14:49:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[14:49:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[14:49:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[14:49:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[14:49:13] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[14:49:13] Treating reference as 'fasta' format. -[14:49:13] Will use 2 CPU cores. -[14:49:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq -[14:49:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[14:49:13] Used --force, will overwrite existing S2 -[14:49:13] Changing working directory: S2 -[14:49:13] Creating reference folder: reference -[14:49:13] Extracting FASTA and GFF from reference. -[14:49:13] Wrote 3 sequences to ref.fa -[14:49:13] Wrote 0 features to ref.gff -[14:49:13] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[14:49:13] Using BAM RG (Read Group) ID: S2 -[14:49:13] Running: samtools faidx reference/ref.fa 2>> snps.log -[14:49:13] Running: bwa index reference/ref.fa 2>> snps.log -[14:49:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[14:49:13] Running: ln -sf reference/ref.fa . 2>> snps.log -[14:49:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[14:49:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[14:49:13] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[10:35:27] This is snippy 4.6.0 +[10:35:27] Written by Torsten Seemann +[10:35:27] Obtained from https://github.com/tseemann/snippy +[10:35:27] Detected operating system: linux +[10:35:27] Enabling bundled linux tools. +[10:35:27] Found bwa - /usr/bin/bwa +[10:35:27] Found bcftools - /usr/bin/bcftools +[10:35:27] Found samtools - /usr/bin/samtools +[10:35:27] Found java - /usr/bin/java +[10:35:27] Found snpEff - /usr/bin/snpEff +[10:35:28] Found samclip - /usr/bin/samclip +[10:35:28] Found seqtk - /usr/bin/seqtk +[10:35:28] Found parallel - /usr/bin/parallel +[10:35:28] Found freebayes - /usr/bin/freebayes +[10:35:28] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[10:35:28] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[10:35:28] Found vcfstreamsort - /usr/bin/vcfstreamsort +[10:35:28] Found vcfuniq - /usr/bin/vcfuniq +[10:35:28] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[10:35:28] Found gzip - /usr/bin/gzip +[10:35:28] Found vt - /usr/bin/vt +[10:35:28] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[10:35:28] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[10:35:28] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[10:35:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[10:35:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[10:35:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[10:35:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[10:35:30] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[10:35:30] Treating reference as 'fasta' format. +[10:35:30] Will use 2 CPU cores. +[10:35:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq +[10:35:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq +[10:35:30] Used --force, will overwrite existing S2 +[10:35:30] Changing working directory: S2 +[10:35:30] Creating reference folder: reference +[10:35:30] Extracting FASTA and GFF from reference. +[10:35:30] Wrote 3 sequences to ref.fa +[10:35:30] Wrote 0 features to ref.gff +[10:35:30] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[10:35:30] Using BAM RG (Read Group) ID: S2 +[10:35:30] Running: samtools faidx reference/ref.fa 2>> snps.log +[10:35:30] Running: bwa index reference/ref.fa 2>> snps.log +[10:35:31] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[10:35:31] Running: ln -sf reference/ref.fa . 2>> snps.log +[10:35:31] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[10:35:31] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[10:35:31] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -2702,17 +2738,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 2.076 CPU sec, 1.053 real sec +[M::mem_process_seqs] Processed 24000 reads in 2.928 CPU sec, 6.646 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[main] Real time: 1.223 sec; CPU: 2.128 sec +[main] Real time: 7.799 sec; CPU: 3.019 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. -[14:49:15] Running: samtools index snps.bam 2>> snps.log -[14:49:15] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[14:49:15] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[14:49:16] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[10:35:42] Running: samtools index snps.bam 2>> snps.log +[10:35:42] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[10:35:42] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[10:35:52] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2749,43 +2785,43 @@ Time elapsed: 0.01s -[14:49:16] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[14:49:16] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[14:49:17] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[14:49:17] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[14:49:17] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[14:49:17] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[14:49:17] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[14:49:18] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[14:49:18] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[14:49:18] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[14:49:18] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[14:49:19] Marked 841 heterozygous sites with 'n' -[14:49:19] Creating extra output files: BED GFF CSV TXT HTML -[14:49:19] Identified 246 variants. -[14:49:19] Result folder: S2 -[14:49:19] Result files: -[14:49:19] * S2/snps.aligned.fa -[14:49:19] * S2/snps.bam -[14:49:19] * S2/snps.bam.bai -[14:49:19] * S2/snps.bed -[14:49:19] * S2/snps.consensus.fa -[14:49:19] * S2/snps.consensus.subs.fa -[14:49:19] * S2/snps.csv -[14:49:19] * S2/snps.filt.vcf -[14:49:19] * S2/snps.gff -[14:49:19] * S2/snps.html -[14:49:19] * S2/snps.log -[14:49:19] * S2/snps.raw.vcf -[14:49:19] * S2/snps.subs.vcf -[14:49:19] * S2/snps.tab -[14:49:19] * S2/snps.txt -[14:49:19] * S2/snps.vcf -[14:49:19] * S2/snps.vcf.gz -[14:49:19] * S2/snps.vcf.gz.csi -[14:49:19] Walltime used: 7 seconds -[14:49:19] Wishing you a life free of homopolymer errors. -[14:49:19] Done. +[10:35:52] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[10:35:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[10:35:53] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[10:35:53] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[10:35:53] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[10:35:54] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[10:35:54] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[10:35:54] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[10:35:54] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[10:35:54] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[10:35:54] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[10:35:58] Marked 841 heterozygous sites with 'n' +[10:35:58] Creating extra output files: BED GFF CSV TXT HTML +[10:35:58] Identified 246 variants. +[10:35:58] Result folder: S2 +[10:35:58] Result files: +[10:35:58] * S2/snps.aligned.fa +[10:35:58] * S2/snps.bam +[10:35:58] * S2/snps.bam.bai +[10:35:58] * S2/snps.bed +[10:35:58] * S2/snps.consensus.fa +[10:35:58] * S2/snps.consensus.subs.fa +[10:35:58] * S2/snps.csv +[10:35:58] * S2/snps.filt.vcf +[10:35:58] * S2/snps.gff +[10:35:58] * S2/snps.html +[10:35:58] * S2/snps.log +[10:35:58] * S2/snps.raw.vcf +[10:35:58] * S2/snps.subs.vcf +[10:35:58] * S2/snps.tab +[10:35:58] * S2/snps.txt +[10:35:58] * S2/snps.vcf +[10:35:58] * S2/snps.vcf.gz +[10:35:58] * S2/snps.vcf.gz.csi +[10:35:58] Walltime used: 31 seconds +[10:35:58] Questionable SNP? Try the --report option to see the alignments. +[10:35:58] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2794,59 +2830,59 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq -[14:49:19] This is snippy 4.6.0 -[14:49:19] Written by Torsten Seemann -[14:49:19] Obtained from https://github.com/tseemann/snippy -[14:49:19] Detected operating system: linux -[14:49:19] Enabling bundled linux tools. -[14:49:19] Found bwa - /usr/bin/bwa -[14:49:19] Found bcftools - /usr/bin/bcftools -[14:49:19] Found samtools - /usr/bin/samtools -[14:49:19] Found java - /usr/bin/java -[14:49:19] Found snpEff - /usr/bin/snpEff -[14:49:19] Found samclip - /usr/bin/samclip -[14:49:19] Found seqtk - /usr/bin/seqtk -[14:49:19] Found parallel - /usr/bin/parallel -[14:49:19] Found freebayes - /usr/bin/freebayes -[14:49:19] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[14:49:19] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[14:49:19] Found vcfstreamsort - /usr/bin/vcfstreamsort -[14:49:19] Found vcfuniq - /usr/bin/vcfuniq -[14:49:19] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[14:49:19] Found gzip - /usr/bin/gzip -[14:49:19] Found vt - /usr/bin/vt -[14:49:19] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[14:49:19] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[14:49:19] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[14:49:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[14:49:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[14:49:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[14:49:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[14:49:19] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[14:49:19] Treating reference as 'fasta' format. -[14:49:19] Will use 2 CPU cores. -[14:49:19] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq -[14:49:19] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[14:49:19] Used --force, will overwrite existing S3 -[14:49:19] Changing working directory: S3 -[14:49:19] Creating reference folder: reference -[14:49:19] Extracting FASTA and GFF from reference. -[14:49:19] Wrote 3 sequences to ref.fa -[14:49:19] Wrote 0 features to ref.gff -[14:49:19] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[14:49:19] Using BAM RG (Read Group) ID: S3 -[14:49:19] Running: samtools faidx reference/ref.fa 2>> snps.log -[14:49:19] Running: bwa index reference/ref.fa 2>> snps.log -[14:49:19] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[14:49:19] Running: ln -sf reference/ref.fa . 2>> snps.log -[14:49:19] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[14:49:19] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[14:49:19] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[10:36:01] This is snippy 4.6.0 +[10:36:01] Written by Torsten Seemann +[10:36:01] Obtained from https://github.com/tseemann/snippy +[10:36:01] Detected operating system: linux +[10:36:01] Enabling bundled linux tools. +[10:36:01] Found bwa - /usr/bin/bwa +[10:36:01] Found bcftools - /usr/bin/bcftools +[10:36:01] Found samtools - /usr/bin/samtools +[10:36:01] Found java - /usr/bin/java +[10:36:01] Found snpEff - /usr/bin/snpEff +[10:36:01] Found samclip - /usr/bin/samclip +[10:36:01] Found seqtk - /usr/bin/seqtk +[10:36:01] Found parallel - /usr/bin/parallel +[10:36:01] Found freebayes - /usr/bin/freebayes +[10:36:01] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[10:36:01] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[10:36:01] Found vcfstreamsort - /usr/bin/vcfstreamsort +[10:36:02] Found vcfuniq - /usr/bin/vcfuniq +[10:36:02] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[10:36:02] Found gzip - /usr/bin/gzip +[10:36:02] Found vt - /usr/bin/vt +[10:36:02] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[10:36:02] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[10:36:02] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[10:36:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[10:36:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[10:36:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[10:36:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[10:36:04] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[10:36:04] Treating reference as 'fasta' format. +[10:36:04] Will use 2 CPU cores. +[10:36:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq +[10:36:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[10:36:04] Used --force, will overwrite existing S3 +[10:36:04] Changing working directory: S3 +[10:36:04] Creating reference folder: reference +[10:36:04] Extracting FASTA and GFF from reference. +[10:36:04] Wrote 3 sequences to ref.fa +[10:36:04] Wrote 0 features to ref.gff +[10:36:04] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[10:36:04] Using BAM RG (Read Group) ID: S3 +[10:36:04] Running: samtools faidx reference/ref.fa 2>> snps.log +[10:36:04] Running: bwa index reference/ref.fa 2>> snps.log +[10:36:05] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[10:36:05] Running: ln -sf reference/ref.fa . 2>> snps.log +[10:36:05] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[10:36:05] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[10:36:05] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs -[M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai +[M::process] read 24000 sequences (2400000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... @@ -2856,17 +2892,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 2.062 CPU sec, 1.137 real sec +[M::mem_process_seqs] Processed 24000 reads in 3.132 CPU sec, 6.778 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[main] Real time: 1.247 sec; CPU: 2.107 sec +[main] Real time: 8.682 sec; CPU: 3.228 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. -[14:49:21] Running: samtools index snps.bam 2>> snps.log -[14:49:21] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[14:49:21] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[14:49:23] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[10:36:19] Running: samtools index snps.bam 2>> snps.log +[10:36:19] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[10:36:19] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[10:36:39] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2903,43 +2939,43 @@ Time elapsed: 0.01s -[14:49:23] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[14:49:23] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[14:49:23] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[14:49:23] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[14:49:23] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[14:49:23] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[14:49:23] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[14:49:23] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[14:49:23] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[14:49:23] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[14:49:23] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[14:49:23] Marked 846 heterozygous sites with 'n' -[14:49:23] Creating extra output files: BED GFF CSV TXT HTML -[14:49:23] Identified 254 variants. -[14:49:23] Result folder: S3 -[14:49:23] Result files: -[14:49:23] * S3/snps.aligned.fa -[14:49:23] * S3/snps.bam -[14:49:23] * S3/snps.bam.bai -[14:49:23] * S3/snps.bed -[14:49:23] * S3/snps.consensus.fa -[14:49:23] * S3/snps.consensus.subs.fa -[14:49:23] * S3/snps.csv -[14:49:23] * S3/snps.filt.vcf -[14:49:23] * S3/snps.gff -[14:49:23] * S3/snps.html -[14:49:23] * S3/snps.log -[14:49:23] * S3/snps.raw.vcf -[14:49:23] * S3/snps.subs.vcf -[14:49:23] * S3/snps.tab -[14:49:23] * S3/snps.txt -[14:49:23] * S3/snps.vcf -[14:49:23] * S3/snps.vcf.gz -[14:49:23] * S3/snps.vcf.gz.csi -[14:49:23] Walltime used: 4 seconds -[14:49:23] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues -[14:49:23] Done. +[10:36:39] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[10:36:39] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[10:36:41] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[10:36:41] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[10:36:41] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[10:36:41] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[10:36:42] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[10:36:42] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[10:36:42] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[10:36:42] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[10:36:42] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[10:36:45] Marked 846 heterozygous sites with 'n' +[10:36:45] Creating extra output files: BED GFF CSV TXT HTML +[10:36:45] Identified 254 variants. +[10:36:45] Result folder: S3 +[10:36:45] Result files: +[10:36:45] * S3/snps.aligned.fa +[10:36:45] * S3/snps.bam +[10:36:45] * S3/snps.bam.bai +[10:36:45] * S3/snps.bed +[10:36:45] * S3/snps.consensus.fa +[10:36:45] * S3/snps.consensus.subs.fa +[10:36:45] * S3/snps.csv +[10:36:45] * S3/snps.filt.vcf +[10:36:45] * S3/snps.gff +[10:36:45] * S3/snps.html +[10:36:45] * S3/snps.log +[10:36:45] * S3/snps.raw.vcf +[10:36:45] * S3/snps.subs.vcf +[10:36:45] * S3/snps.tab +[10:36:45] * S3/snps.txt +[10:36:45] * S3/snps.vcf +[10:36:45] * S3/snps.vcf.gz +[10:36:45] * S3/snps.vcf.gz.csi +[10:36:45] Walltime used: 44 seconds +[10:36:45] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md +[10:36:45] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2948,54 +2984,54 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq -[14:49:23] This is snippy 4.6.0 -[14:49:23] Written by Torsten Seemann -[14:49:23] Obtained from https://github.com/tseemann/snippy -[14:49:23] Detected operating system: linux -[14:49:23] Enabling bundled linux tools. -[14:49:23] Found bwa - /usr/bin/bwa -[14:49:23] Found bcftools - /usr/bin/bcftools -[14:49:23] Found samtools - /usr/bin/samtools -[14:49:23] Found java - /usr/bin/java -[14:49:23] Found snpEff - /usr/bin/snpEff -[14:49:23] Found samclip - /usr/bin/samclip -[14:49:23] Found seqtk - /usr/bin/seqtk -[14:49:24] Found parallel - /usr/bin/parallel -[14:49:24] Found freebayes - /usr/bin/freebayes -[14:49:24] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[14:49:24] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[14:49:24] Found vcfstreamsort - /usr/bin/vcfstreamsort -[14:49:24] Found vcfuniq - /usr/bin/vcfuniq -[14:49:24] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[14:49:24] Found gzip - /usr/bin/gzip -[14:49:24] Found vt - /usr/bin/vt -[14:49:24] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[14:49:24] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[14:49:24] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[14:49:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[14:49:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[14:49:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[14:49:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[14:49:24] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[14:49:24] Treating reference as 'fasta' format. -[14:49:24] Will use 2 CPU cores. -[14:49:24] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq -[14:49:24] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[14:49:24] Used --force, will overwrite existing S4 -[14:49:24] Changing working directory: S4 -[14:49:24] Creating reference folder: reference -[14:49:24] Extracting FASTA and GFF from reference. -[14:49:24] Wrote 3 sequences to ref.fa -[14:49:24] Wrote 0 features to ref.gff -[14:49:24] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[14:49:24] Using BAM RG (Read Group) ID: S4 -[14:49:24] Running: samtools faidx reference/ref.fa 2>> snps.log -[14:49:24] Running: bwa index reference/ref.fa 2>> snps.log -[14:49:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[14:49:24] Running: ln -sf reference/ref.fa . 2>> snps.log -[14:49:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[14:49:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[14:49:24] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[10:36:48] This is snippy 4.6.0 +[10:36:48] Written by Torsten Seemann +[10:36:48] Obtained from https://github.com/tseemann/snippy +[10:36:48] Detected operating system: linux +[10:36:48] Enabling bundled linux tools. +[10:36:48] Found bwa - /usr/bin/bwa +[10:36:48] Found bcftools - /usr/bin/bcftools +[10:36:48] Found samtools - /usr/bin/samtools +[10:36:48] Found java - /usr/bin/java +[10:36:49] Found snpEff - /usr/bin/snpEff +[10:36:49] Found samclip - /usr/bin/samclip +[10:36:49] Found seqtk - /usr/bin/seqtk +[10:36:49] Found parallel - /usr/bin/parallel +[10:36:49] Found freebayes - /usr/bin/freebayes +[10:36:49] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[10:36:49] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[10:36:49] Found vcfstreamsort - /usr/bin/vcfstreamsort +[10:36:49] Found vcfuniq - /usr/bin/vcfuniq +[10:36:49] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[10:36:49] Found gzip - /usr/bin/gzip +[10:36:49] Found vt - /usr/bin/vt +[10:36:49] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[10:36:49] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[10:36:50] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[10:36:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[10:36:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[10:36:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[10:36:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[10:36:53] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[10:36:53] Treating reference as 'fasta' format. +[10:36:53] Will use 2 CPU cores. +[10:36:53] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq +[10:36:53] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[10:36:53] Used --force, will overwrite existing S4 +[10:36:53] Changing working directory: S4 +[10:36:53] Creating reference folder: reference +[10:36:53] Extracting FASTA and GFF from reference. +[10:36:53] Wrote 3 sequences to ref.fa +[10:36:53] Wrote 0 features to ref.gff +[10:36:53] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[10:36:53] Using BAM RG (Read Group) ID: S4 +[10:36:53] Running: samtools faidx reference/ref.fa 2>> snps.log +[10:36:53] Running: bwa index reference/ref.fa 2>> snps.log +[10:36:54] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[10:36:54] Running: ln -sf reference/ref.fa . 2>> snps.log +[10:36:54] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[10:36:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[10:36:55] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -3010,17 +3046,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 1.376 CPU sec, 0.693 real sec +[M::mem_process_seqs] Processed 24000 reads in 2.955 CPU sec, 9.167 real sec [main] Version: 0.7.18-r1243-dirty -[main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 +[main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[main] Real time: 10.951 sec; CPU: 3.046 sec +[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. - -[main] Real time: 0.809 sec; CPU: 1.418 sec -[14:49:25] Running: samtools index snps.bam 2>> snps.log -[14:49:25] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[14:49:25] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[14:49:26] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[10:37:11] Running: samtools index snps.bam 2>> snps.log +[10:37:11] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[10:37:12] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[10:37:29] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -3057,43 +3093,43 @@ Time elapsed: 0.01s -[14:49:26] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[14:49:26] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[14:49:26] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[14:49:26] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[14:49:26] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[14:49:26] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[14:49:26] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[14:49:27] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[14:49:27] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[14:49:27] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[14:49:27] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[14:49:27] Marked 799 heterozygous sites with 'n' -[14:49:27] Creating extra output files: BED GFF CSV TXT HTML -[14:49:27] Identified 257 variants. -[14:49:27] Result folder: S4 -[14:49:27] Result files: -[14:49:27] * S4/snps.aligned.fa -[14:49:27] * S4/snps.bam -[14:49:27] * S4/snps.bam.bai -[14:49:27] * S4/snps.bed -[14:49:27] * S4/snps.consensus.fa -[14:49:27] * S4/snps.consensus.subs.fa -[14:49:27] * S4/snps.csv -[14:49:27] * S4/snps.filt.vcf -[14:49:27] * S4/snps.gff -[14:49:27] * S4/snps.html -[14:49:27] * S4/snps.log -[14:49:27] * S4/snps.raw.vcf -[14:49:27] * S4/snps.subs.vcf -[14:49:27] * S4/snps.tab -[14:49:27] * S4/snps.txt -[14:49:27] * S4/snps.vcf -[14:49:27] * S4/snps.vcf.gz -[14:49:27] * S4/snps.vcf.gz.csi -[14:49:27] Walltime used: 4 seconds -[14:49:27] Did you know? Snippy is a combination of SNP, Skippy, and snappy. -[14:49:27] Done. +[10:37:29] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[10:37:29] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[10:37:31] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[10:37:31] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[10:37:31] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[10:37:31] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[10:37:31] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[10:37:32] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[10:37:32] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[10:37:32] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[10:37:32] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[10:37:40] Marked 799 heterozygous sites with 'n' +[10:37:40] Creating extra output files: BED GFF CSV TXT HTML +[10:37:40] Identified 257 variants. +[10:37:40] Result folder: S4 +[10:37:40] Result files: +[10:37:40] * S4/snps.aligned.fa +[10:37:40] * S4/snps.bam +[10:37:40] * S4/snps.bam.bai +[10:37:40] * S4/snps.bed +[10:37:40] * S4/snps.consensus.fa +[10:37:40] * S4/snps.consensus.subs.fa +[10:37:40] * S4/snps.csv +[10:37:40] * S4/snps.filt.vcf +[10:37:40] * S4/snps.gff +[10:37:40] * S4/snps.html +[10:37:40] * S4/snps.log +[10:37:40] * S4/snps.raw.vcf +[10:37:40] * S4/snps.subs.vcf +[10:37:40] * S4/snps.tab +[10:37:40] * S4/snps.txt +[10:37:40] * S4/snps.vcf +[10:37:40] * S4/snps.vcf.gz +[10:37:40] * S4/snps.vcf.gz.csi +[10:37:40] Walltime used: 52 seconds +[10:37:40] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues +[10:37:40] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 @@ -3126,7 +3162,7 @@ Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln -Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues +You can mask columns using '--mask BEDFILE --mask-char X' Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy @@ -3160,7 +3196,7 @@ Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln -This analysis is totally hard-core! +Found a bug? Post it at http://github.com/tseemann/snippy/issues Done. wc -l S?/snps.tab 262 S1/snps.tab @@ -3198,12 +3234,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1827059/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3521208 and its subdirectories -I: Current time: Thu Mar 26 14:49:31 -12 2026 -I: pbuilder-time-stamp: 1774579771 +I: removing directory /srv/workspace/pbuilder/1827059 and its subdirectories +I: Current time: Sat Feb 22 10:38:19 +14 2025 +I: pbuilder-time-stamp: 1740170299 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snippy_4.6.0+dfsg-5.diff: 85.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snippy_4.6.0+dfsg-5.diff.gz b2/build.log: 82.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.5% -- replaced with stdout Fri Feb 21 20:38:22 UTC 2025 I: diffoscope 288 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_snippy_trixie_amd64_1740170302 + touch /var/log/reproducible-builds/diffoscope_stamp_snippy_trixie_amd64_1740170302 + RESULT=0 + systemd-run '--description=diffoscope on snippy/4.6.0+dfsg-5 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_24-49031 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe --run-session -c jenkins-reproducible-trixie-diffoscope-ce53db9e-1f09-4dea-9478-592bd3021ea8 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/dbd-tmp-ytEn2OU ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/snippy_4.6.0+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/snippy_4.6.0+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/snippy_4.6.0+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b1/snippy_4.6.0+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b2/snippy_4.6.0+dfsg-5_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_24-49031.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/snippy_4.6.0+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/snippy_4.6.0+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/snippy_4.6.0+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b1/snippy_4.6.0+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.6PMZ3CYe/b2/snippy_4.6.0+dfsg-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 228ms CPU time consumed: 228ms _ ___ _ __ (_)_ __ _ __ _ _ / __| '_ \| | '_ \| '_ \| | | | \__ \ | | | | |_) | |_) | |_| | |___/_| |_|_| .__/| .__/ \__, | |_| |_| |___/ Fri Feb 21 20:38:22 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 21 20:38:22 UTC 2025 I: snippy from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-02-21 20:38:23] INFO: Starting at 2025-02-21 20:38:23.479959 [2025-02-21 20:38:23] INFO: Generating the pages of 1 package(s) [2025-02-21 20:38:23] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/snippy_4.6.0+dfsg-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/snippy_4.6.0+dfsg-5.diff.gz is missing [2025-02-21 20:38:23] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/snippy_4.6.0+dfsg-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/snippy_4.6.0+dfsg-5.diff.gz is missing [2025-02-21 20:38:23] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/snippy didn't produce a buildlog, even though it has been built. [2025-02-21 20:38:23] INFO: Finished at 2025-02-21 20:38:23.721174, took: 0:00:00.241222 Fri Feb 21 20:38:23 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/snippy.html Fri Feb 21 20:38:23 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 21 20:38:23 UTC 2025 I: Submitting 20K b1/snippy_4.6.0+dfsg-5_amd64.buildinfo.asc https://buildinfo.debian.net/a988e550318663cd513872514b45688dfbaa00db/snippy_4.6.0+dfsg-5_all Fri Feb 21 20:38:24 UTC 2025 I: Submitting 20K b2/snippy_4.6.0+dfsg-5_amd64.buildinfo.asc https://buildinfo.debian.net/99f2e7c3f018073048747e1987514d1fafbf7ac8/snippy_4.6.0+dfsg-5_all Fri Feb 21 20:38:26 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 21 20:38:26 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 21 20:38:26 UTC 2025 I: Removing signed snippy_4.6.0+dfsg-5_amd64.buildinfo.asc files: removed './b1/snippy_4.6.0+dfsg-5_amd64.buildinfo.asc' removed './b2/snippy_4.6.0+dfsg-5_amd64.buildinfo.asc' 1740170306 amd64 trixie snippy Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snippy_4.6.0+dfsg-5.rbuild.log: 81.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snippy_4.6.0+dfsg-5.rbuild.log.gz [2025-02-21 20:38:26] INFO: Starting at 2025-02-21 20:38:26.866160 [2025-02-21 20:38:26] INFO: Generating the pages of 1 package(s) [2025-02-21 20:38:27] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/snippy_4.6.0+dfsg-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/snippy_4.6.0+dfsg-5.diff.gz is missing [2025-02-21 20:38:27] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/snippy_4.6.0+dfsg-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/snippy_4.6.0+dfsg-5.diff.gz is missing [2025-02-21 20:38:27] INFO: Finished at 2025-02-21 20:38:27.092469, took: 0:00:00.226314 All cleanup done. Fri Feb 21 20:38:27 UTC 2025 - total duration: 0h 16m 10s. Fri Feb 21 20:38:27 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Vo1MC3ss, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 16min 14.546s CPU time consumed: 7.348s