I: pbuilder: network access will be disabled during build I: Current time: Tue Feb 3 17:29:49 +14 2026 I: pbuilder-time-stamp: 1770089389 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [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/17200/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 3 03:29 /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/17200/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/17200/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=f5b1df5233af4240ba0813305db23e67 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=17200 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.q7ZAMuxm/pbuilderrc_66Dz --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.q7ZAMuxm/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/17200/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19975 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-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} libldap-2.5-0{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} libnsl2{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} 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} libpython3.12-minimal{a} libpython3.12-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} 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-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} 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} python3.12{a} python3.12-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-bit64 r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics 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-mockr r-cran-multcomp r-cran-mvtnorm r-cran-pkgdown r-cran-png r-cran-processx r-cran-profvis r-cran-ps 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-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer 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, 416 newly installed, 0 to remove and 0 not upgraded. Need to get 314 MB of archives. After unpacking 965 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libapparmor1 arm64 3.1.7-1+b3 [41.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libsystemd-shared arm64 257.1-5 [1909 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 systemd arm64 257.1-5 [3368 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 systemd-sysv arm64 257.1-5 [60.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.0-1 [168 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 dbus-bin arm64 1.16.0-1 [77.7 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 dbus-daemon arm64 1.16.0-1 [150 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 dbus arm64 1.16.0-1 [69.4 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.8-3 [810 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.8-3 [1941 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-4 [256 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.8-3 [1906 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.8-3 [677 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B] Get: 33 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.8-1 [27.9 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-3 [198 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libpam-systemd arm64 257.1-5 [271 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-13 [91.4 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0046 [41.1 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.4-1 [1411 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b1 [755 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1+b1 [131 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 gtk-update-icon-cache arm64 4.16.7+ds-1 [49.8 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B] Get: 69 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.106-1 [1292 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.1-1 [55.3 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.6~6ea-1 [40.6 MB] Get: 74 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 75 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 ant-optional all 1.10.15-1 [456 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 any2fasta all 0.4.2-2 [6232 B] Get: 78 http://deb.debian.org/debian unstable/main arm64 at-spi2-common all 2.54.0-1 [170 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-3 [723 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.19+dfsg-1 [175 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.1-1 [332 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 bcftools arm64 1.20-2+b1 [694 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 bedtools arm64 2.31.1+dfsg-2+b1 [601 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 bwa arm64 0.7.18-1 [198 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 dbus-user-session arm64 1.16.0-1 [51.0 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libdconf1 arm64 0.40.0-4+b3 [40.4 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 dconf-service arm64 0.40.0-4+b3 [31.1 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 dconf-gsettings-backend arm64 0.40.0-4+b3 [27.4 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 116 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-3 [1532 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.23 [919 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libatk1.0-0t64 arm64 2.54.0-1 [49.7 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libatspi2.0-0t64 arm64 2.54.0-1 [72.9 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libatk-bridge2.0-0t64 arm64 2.54.0-1 [64.4 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libcloudproviders0 arm64 0.3.6-1+b1 [27.7 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libcolord2 arm64 1.4.7-1+b2 [130 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-15 [112 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-15 [43.3 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-15 [46.8 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.1.0-2 [443 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.55.0+ds-3 [212 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.55.0+ds-3 [52.1 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.55.0+ds-3 [33.4 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libwayland-client0 arm64 1.23.0-1+b1 [26.0 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libwayland-cursor0 arm64 1.23.0-1+b1 [11.5 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libwayland-egl1 arm64 1.23.0-1+b1 [5768 B] Get: 163 http://deb.debian.org/debian unstable/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libxfixes3 arm64 1:6.0.0-2+b3 [20.4 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libxcursor1 arm64 1:1.2.2-1+b1 [37.1 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libxinerama1 arm64 2:1.1.4-3+b3 [16.1 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 xkb-data all 2.42-1 [790 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libxkbcommon0 arm64 1.7.0-2 [106 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libxrandr2 arm64 2:1.5.4-1+b2 [36.0 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libgtk-3-common all 3.24.43-4 [4657 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libgtk-3-0t64 arm64 3.24.43-4 [2546 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 175 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libglapi-mesa arm64 24.2.8-1 [48.2 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [241 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libxcb-dri2-0 arm64 1.17.0-2+b1 [107 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 libxshmfence1 arm64 1.3-1+b2 [9076 B] Get: 186 http://deb.debian.org/debian unstable/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b3 [19.2 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 libdrm-radeon1 arm64 2.4.123-1 [21.3 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.6-1 [23.3 MB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libsensors5 arm64 1:3.6.0-10+b1 [34.3 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 mesa-libgallium arm64 24.2.8-1 [7689 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libvulkan1 arm64 1.3.296.0-1 [123 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libwayland-server0 arm64 1.23.0-1+b1 [33.4 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 libgbm1 arm64 24.2.8-1 [42.0 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libgl1-mesa-dri arm64 24.2.8-1 [43.6 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libglx-mesa0 arm64 24.2.8-1 [152 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libasound2-data all 1.2.12-1 [21.0 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libasound2t64 arm64 1.2.12-1+b1 [336 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libxtst6 arm64 2:1.2.3-1.1+b3 [26.0 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre arm64 21.0.6~6ea-1 [193 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 default-jre arm64 2:1.21-76 [1068 B] Get: 209 http://deb.debian.org/debian unstable/main arm64 libfml0 arm64 0.1+git20221215.85f159e-1 [65.6 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libssw0 arm64 1.1-15+b1 [20.0 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libseqlib2 arm64 1.2.0+dfsg-11+b2 [146 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libtabixpp0t64 arm64 1.1.2-2.1+b1 [9504 B] Get: 214 http://deb.debian.org/debian unstable/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4+b2 [4920 B] Get: 215 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b2 [32.4 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libwfa2-0 arm64 2.3.3-4+b1 [55.2 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libvcflib2 arm64 1.0.9+dfsg1-3+b2 [165 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 freebayes arm64 1.3.7-1 [1430 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 223 http://deb.debian.org/debian unstable/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 224 http://deb.debian.org/debian unstable/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 junit5 all 5.10.3-1 [2459 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libantlr4-runtime-java all 4.9.2-2 [317 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 231 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 232 http://deb.debian.org/debian unstable/main arm64 libapfloat-java all 1.14.0-2 [725 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libargs4j-java all 2.33-2 [138 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libasm-java all 9.7.1-1 [391 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 236 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 libciftools-java all 6.0.0-1 [2211 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libcommons-math-java all 2.2-9 [933 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.17.0-1 [488 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 libguice-java all 5.1.0-1 [932 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 261 http://deb.debian.org/debian unstable/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 268 http://deb.debian.org/debian unstable/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 271 http://deb.debian.org/debian unstable/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libsnappy1v5 arm64 1.2.1-1+b1 [28.7 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libsnappy-jni arm64 1.1.10.7-1 [6476 B] Get: 281 http://deb.debian.org/debian unstable/main arm64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libxz-java all 1.9-1 [143 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 librngom-java all 2.3.0.1-11 [292 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 libxsom-java all 2.3.0.1-11 [401 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libtxw2-java all 2.3.0.1-11 [134 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 libcommons-text-java all 1.12.0-1 [222 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libjheaps-java all 0.14-2 [144 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libjgrapht-java all 1.5.2-1 [1610 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libinchi1.07 arm64 1.07.1+dfsg-6 [499 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libjni-inchi-jni arm64 0.8+dfsg-8 [9480 B] Get: 312 http://deb.debian.org/debian unstable/main arm64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 315 http://deb.debian.org/debian unstable/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 318 http://deb.debian.org/debian unstable/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 325 http://deb.debian.org/debian unstable/main arm64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get: 326 http://deb.debian.org/debian unstable/main arm64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libmsgpack-java all 0.9.6-1 [161 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libmmtf-java all 1.0.11-1 [187 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get: 331 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 332 http://deb.debian.org/debian unstable/main arm64 libcharts4j-java all 1.3-4 [162 kB] Get: 333 http://deb.debian.org/debian unstable/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.1-1 [325 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 libdistlib-java all 1.0-5 [72.5 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 343 http://deb.debian.org/debian unstable/main arm64 libxom-java all 1.3.9-1 [174 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 345 http://deb.debian.org/debian unstable/main arm64 libmbedcrypto16 arm64 3.6.2-3 [341 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 libmbedx509-7 arm64 3.6.2-3 [146 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 libmbedtls21 arm64 3.6.2-3 [222 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.0.9+dfsg-2 [1110 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 libncbi-ngs3 arm64 3.0.9+dfsg-7+b1 [143 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 libngs-jni arm64 3.0.9+dfsg-7+b1 [25.8 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 libngs-java arm64 3.0.9+dfsg-7+b1 [112 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 355 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 357 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3 [16.3 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3 [16.1 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 361 http://deb.debian.org/debian unstable/main arm64 libsnp-sites1 arm64 2.5.1-2+b2 [14.1 kB] Get: 362 http://deb.debian.org/debian unstable/main arm64 libtrove3-java all 3.0.3-5 [2146 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 libsnpeff-java all 5.2.e+dfsg-1 [2157 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b3 [51.6 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB] Get: 367 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 369 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 371 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB] Get: 372 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 373 http://deb.debian.org/debian unstable/main arm64 r-cran-littler arm64 0.3.20-2 [102 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 littler all 0.3.20-2 [16.0 kB] Get: 375 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 376 http://deb.debian.org/debian unstable/main arm64 r-cran-rcpp arm64 1.0.13-1-1 [2057 kB] Get: 377 http://deb.debian.org/debian unstable/main arm64 r-cran-plyr arm64 1.8.9-1+b1 [791 kB] Get: 378 http://deb.debian.org/debian unstable/main arm64 r-cran-cli arm64 3.6.3-1 [1340 kB] Get: 379 http://deb.debian.org/debian unstable/main arm64 r-cran-glue arm64 1.8.0-1 [165 kB] Get: 380 http://deb.debian.org/debian unstable/main arm64 r-cran-rlang arm64 1.1.4-1+b1 [1708 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 383 http://deb.debian.org/debian unstable/main arm64 r-cran-isoband arm64 0.2.7-1+b1 [1614 kB] Get: 384 http://deb.debian.org/debian unstable/main arm64 r-cran-mass arm64 7.3-61-1+b1 [1112 kB] Get: 385 http://deb.debian.org/debian unstable/main arm64 r-cran-lattice arm64 0.22-6-1+b1 [1417 kB] Get: 386 http://deb.debian.org/debian unstable/main arm64 r-cran-nlme arm64 3.1.166-1 [2326 kB] Get: 387 http://deb.debian.org/debian unstable/main arm64 r-cran-matrix arm64 1.7-1-1 [4023 kB] Get: 388 http://deb.debian.org/debian unstable/main arm64 r-cran-mgcv arm64 1.9-1-1+b1 [3218 kB] Get: 389 http://deb.debian.org/debian unstable/main arm64 r-cran-farver arm64 2.1.2-1+b1 [1397 kB] Get: 390 http://deb.debian.org/debian unstable/main arm64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 391 http://deb.debian.org/debian unstable/main arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1713 kB] Get: 392 http://deb.debian.org/debian unstable/main arm64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 393 http://deb.debian.org/debian unstable/main arm64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 394 http://deb.debian.org/debian unstable/main arm64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 395 http://deb.debian.org/debian unstable/main arm64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 396 http://deb.debian.org/debian unstable/main arm64 r-cran-scales all 1.3.0-1 [677 kB] Get: 397 http://deb.debian.org/debian unstable/main arm64 r-cran-fansi arm64 1.0.5-1+b1 [626 kB] Get: 398 http://deb.debian.org/debian unstable/main arm64 r-cran-magrittr arm64 2.0.3-1+b1 [203 kB] Get: 399 http://deb.debian.org/debian unstable/main arm64 r-cran-utf8 arm64 1.2.4-1+b1 [133 kB] Get: 400 http://deb.debian.org/debian unstable/main arm64 r-cran-vctrs arm64 0.6.5-1+b1 [1378 kB] Get: 401 http://deb.debian.org/debian unstable/main arm64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 402 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 403 http://deb.debian.org/debian unstable/main arm64 r-cran-tibble arm64 3.2.1+dfsg-2+b1 [425 kB] Get: 404 http://deb.debian.org/debian unstable/main arm64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 405 http://deb.debian.org/debian unstable/main arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 406 http://deb.debian.org/debian unstable/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 407 http://deb.debian.org/debian unstable/main arm64 libvcflib-tools arm64 1.0.9+dfsg1-3+b2 [590 kB] Get: 408 http://deb.debian.org/debian unstable/main arm64 minimap2 arm64 2.27+dfsg-1+b3 [381 kB] Get: 409 http://deb.debian.org/debian unstable/main arm64 sysstat arm64 12.7.5-2+b1 [596 kB] Get: 410 http://deb.debian.org/debian unstable/main arm64 parallel all 20240222+ds-2 [2163 kB] Get: 411 http://deb.debian.org/debian unstable/main arm64 samclip all 0.4.0-4 [20.1 kB] Get: 412 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 413 http://deb.debian.org/debian unstable/main arm64 seqtk arm64 1.4-2+b1 [33.0 kB] Get: 414 http://deb.debian.org/debian unstable/main arm64 snp-sites arm64 2.5.1-2+b2 [14.0 kB] Get: 415 http://deb.debian.org/debian unstable/main arm64 snpeff all 5.2.e+dfsg-1 [7200 B] Get: 416 http://deb.debian.org/debian unstable/main arm64 vt arm64 0.57721+ds-3+b2 [720 kB] Fetched 314 MB in 2s (180 MB/s) Preconfiguring packages ... Selecting previously unselected package libapparmor1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19975 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b3_arm64.deb ... Unpacking libapparmor1:arm64 (3.1.7-1+b3) ... Selecting previously unselected package libsystemd-shared:arm64. Preparing to unpack .../libsystemd-shared_257.1-5_arm64.deb ... Unpacking libsystemd-shared:arm64 (257.1-5) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_257.1-5_arm64.deb ... Unpacking systemd (257.1-5) ... Setting up libapparmor1:arm64 (3.1.7-1+b3) ... Setting up libsystemd-shared:arm64 (257.1-5) ... Setting up systemd (257.1-5) ... 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 ... 20932 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_257.1-5_arm64.deb ... Unpacking systemd-sysv (257.1-5) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../1-libdbus-1-3_1.16.0-1_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.16.0-1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../2-dbus-bin_1.16.0-1_arm64.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:arm64. Preparing to unpack .../4-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../5-dbus-daemon_1.16.0-1_arm64.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_arm64.deb ... Unpacking dbus (1.16.0-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../8-libpython3.12-minimal_3.12.8-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-3) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../9-python3.12-minimal_3.12.8-3_arm64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:arm64 (3.12.8-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... 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 ... 21344 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.8-1_arm64.deb ... Unpacking python3-minimal (3.12.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../04-libffi8_3.4.6-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.6-1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../05-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../06-libcom-err2_1.47.2~rc1-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../07-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../08-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../09-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../10-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../11-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../12-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../13-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../14-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../15-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../16-libpython3.12-stdlib_3.12.8-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../17-python3.12_3.12.8-3_arm64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../18-libpython3-stdlib_3.12.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.8-1) ... Setting up python3-minimal (3.12.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22412 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.8-1_arm64.deb ... Unpacking python3 (3.12.8-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... 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_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... 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_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-3_arm64.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package libpam-systemd:arm64. Preparing to unpack .../012-libpam-systemd_257.1-5_arm64.deb ... Unpacking libpam-systemd:arm64 (257.1-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-13_arm64.deb ... Unpacking bsdextrautils (2.40.2-13) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0046_all.deb ... Moving old data out of the way Unpacking ucf (3.0046) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../017-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../018-libglib2.0-0t64_2.82.4-1_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.82.4-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../019-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../020-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../021-shared-mime-info_2.4-5+b1_arm64.deb ... Unpacking shared-mime-info (2.4-5+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../022-libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../023-libpng16-16t64_1.6.44-3_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-3) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../024-libdeflate0_1.22-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.22-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../025-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../026-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../027-libsharpyuv0_1.4.0-0.1+b1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../028-libwebp7_1.4.0-0.1+b1_arm64.deb ... Unpacking libwebp7:arm64 (1.4.0-0.1+b1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../029-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. Preparing to unpack .../030-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_arm64.deb ... Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1+b1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../031-gtk-update-icon-cache_4.16.7+ds-1_arm64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.16.7+ds-1) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../032-hicolor-icon-theme_0.18-1_all.deb ... Unpacking hicolor-icon-theme (0.18-1) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../033-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 .../034-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../035-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../036-liblcms2-2_2.16-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.16-2) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../037-libnspr4_2%3a4.36-1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.36-1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../038-libnss3_2%3a3.106-1_arm64.deb ... Unpacking libnss3:arm64 (2:3.106-1) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../039-libpcsclite1_2.3.1-1_arm64.deb ... Unpacking libpcsclite1:arm64 (2.3.1-1) ... Selecting previously unselected package openjdk-21-jre-headless:arm64. Preparing to unpack .../040-openjdk-21-jre-headless_21.0.6~6ea-1_arm64.deb ... Unpacking openjdk-21-jre-headless:arm64 (21.0.6~6ea-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../041-default-jre-headless_2%3a1.21-76_arm64.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../042-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package ant-optional. Preparing to unpack .../043-ant-optional_1.10.15-1_all.deb ... Unpacking ant-optional (1.10.15-1) ... Selecting previously unselected package any2fasta. Preparing to unpack .../044-any2fasta_0.4.2-2_all.deb ... Unpacking any2fasta (0.4.2-2) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../045-at-spi2-common_2.54.0-1_all.deb ... Unpacking at-spi2-common (2.54.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../046-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../047-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../048-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../049-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../050-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../051-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../052-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../053-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../054-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../055-libtasn1-6_4.19.0-3+b3_arm64.deb ... Unpacking libtasn1-6:arm64 (4.19.0-3+b3) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../056-libgnutls30t64_3.8.8-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.8-2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../057-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../058-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../059-libldap-2.5-0_2.5.19+dfsg-1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.19+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../060-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../061-libnghttp3-9_1.6.0-2_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.6.0-2) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../062-libngtcp2-16_1.9.1-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.9.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../063-libngtcp2-crypto-gnutls8_1.9.1-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../064-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../065-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../066-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../067-libcurl3t64-gnutls_8.11.1-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.11.1-1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../068-libhtscodecs2_1.6.1-1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../069-libhts3t64_1.20+ds-2_arm64.deb ... Unpacking libhts3t64:arm64 (1.20+ds-2) ... Selecting previously unselected package bcftools. Preparing to unpack .../070-bcftools_1.20-2+b1_arm64.deb ... Unpacking bcftools (1.20-2+b1) ... Selecting previously unselected package bedtools. Preparing to unpack .../071-bedtools_2.31.1+dfsg-2+b1_arm64.deb ... Unpacking bedtools (2.31.1+dfsg-2+b1) ... Selecting previously unselected package bwa. Preparing to unpack .../072-bwa_0.7.18-1_arm64.deb ... Unpacking bwa (0.7.18-1) ... Selecting previously unselected package dbus-user-session. Preparing to unpack .../073-dbus-user-session_1.16.0-1_arm64.deb ... Unpacking dbus-user-session (1.16.0-1) ... Selecting previously unselected package libdconf1:arm64. Preparing to unpack .../074-libdconf1_0.40.0-4+b3_arm64.deb ... Unpacking libdconf1:arm64 (0.40.0-4+b3) ... Selecting previously unselected package dconf-service. Preparing to unpack .../075-dconf-service_0.40.0-4+b3_arm64.deb ... Unpacking dconf-service (0.40.0-4+b3) ... Selecting previously unselected package dconf-gsettings-backend:arm64. Preparing to unpack .../076-dconf-gsettings-backend_0.40.0-4+b3_arm64.deb ... Unpacking dconf-gsettings-backend:arm64 (0.40.0-4+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../077-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../078-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../079-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../080-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../081-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../082-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../083-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../084-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../085-gettext_0.22.5-3_arm64.deb ... Unpacking gettext (0.22.5-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../086-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../087-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../088-debhelper_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package libatk1.0-0t64:arm64. Preparing to unpack .../089-libatk1.0-0t64_2.54.0-1_arm64.deb ... Unpacking libatk1.0-0t64:arm64 (2.54.0-1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../090-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../091-libxdmcp6_1%3a1.1.5-1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../092-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../093-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../094-libx11-6_2%3a1.8.10-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.10-2) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../095-libxext6_2%3a1.3.4-1+b2_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../096-libxi6_2%3a1.8.2-1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8.2-1) ... Selecting previously unselected package libatspi2.0-0t64:arm64. Preparing to unpack .../097-libatspi2.0-0t64_2.54.0-1_arm64.deb ... Unpacking libatspi2.0-0t64:arm64 (2.54.0-1) ... Selecting previously unselected package libatk-bridge2.0-0t64:arm64. Preparing to unpack .../098-libatk-bridge2.0-0t64_2.54.0-1_arm64.deb ... Unpacking libatk-bridge2.0-0t64:arm64 (2.54.0-1) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../099-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../100-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../101-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../102-fontconfig-config_2.15.0-1.1+b1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../103-libfontconfig1_2.15.0-1.1+b1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1+b1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../104-libpixman-1-0_0.44.0-3_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.44.0-3) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../105-libxcb-render0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../106-libxcb-shm0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../107-libxrender1_1%3a0.9.10-1.1+b3_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b3) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../108-libcairo2_1.18.2-2_arm64.deb ... Unpacking libcairo2:arm64 (1.18.2-2) ... Selecting previously unselected package libcairo-gobject2:arm64. Preparing to unpack .../109-libcairo-gobject2_1.18.2-2_arm64.deb ... Unpacking libcairo-gobject2:arm64 (1.18.2-2) ... Selecting previously unselected package libcloudproviders0:arm64. Preparing to unpack .../110-libcloudproviders0_0.3.6-1+b1_arm64.deb ... Unpacking libcloudproviders0:arm64 (0.3.6-1+b1) ... Selecting previously unselected package libcolord2:arm64. Preparing to unpack .../111-libcolord2_1.4.7-1+b2_arm64.deb ... Unpacking libcolord2:arm64 (1.4.7-1+b2) ... Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../112-libavahi-common-data_0.8-15_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-15) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../113-libavahi-common3_0.8-15_arm64.deb ... Unpacking libavahi-common3:arm64 (0.8-15) ... Selecting previously unselected package libavahi-client3:arm64. Preparing to unpack .../114-libavahi-client3_0.8-15_arm64.deb ... Unpacking libavahi-client3:arm64 (0.8-15) ... Selecting previously unselected package libcups2t64:arm64. Preparing to unpack .../115-libcups2t64_2.4.10-2+b1_arm64.deb ... Unpacking libcups2t64:arm64 (2.4.10-2+b1) ... Selecting previously unselected package libepoxy0:arm64. Preparing to unpack .../116-libepoxy0_1.5.10-2_arm64.deb ... Unpacking libepoxy0:arm64 (1.5.10-2) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../117-libfribidi0_1.0.16-1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.16-1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../118-libgraphite2-3_1.3.14-2+b1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../119-libharfbuzz0b_10.1.0-2_arm64.deb ... Unpacking libharfbuzz0b:arm64 (10.1.0-2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../120-fontconfig_2.15.0-1.1+b1_arm64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../121-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../122-libdatrie1_0.2.13-3+b1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3+b1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../123-libthai0_0.1.29-2+b1_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../124-libpango-1.0-0_1.55.0+ds-3_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.55.0+ds-3) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../125-libpangoft2-1.0-0_1.55.0+ds-3_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.55.0+ds-3) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../126-libpangocairo-1.0-0_1.55.0+ds-3_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.55.0+ds-3) ... Selecting previously unselected package libwayland-client0:arm64. Preparing to unpack .../127-libwayland-client0_1.23.0-1+b1_arm64.deb ... Unpacking libwayland-client0:arm64 (1.23.0-1+b1) ... Selecting previously unselected package libwayland-cursor0:arm64. Preparing to unpack .../128-libwayland-cursor0_1.23.0-1+b1_arm64.deb ... Unpacking libwayland-cursor0:arm64 (1.23.0-1+b1) ... Selecting previously unselected package libwayland-egl1:arm64. Preparing to unpack .../129-libwayland-egl1_1.23.0-1+b1_arm64.deb ... Unpacking libwayland-egl1:arm64 (1.23.0-1+b1) ... Selecting previously unselected package libxcomposite1:arm64. Preparing to unpack .../130-libxcomposite1_1%3a0.4.6-1_arm64.deb ... Unpacking libxcomposite1:arm64 (1:0.4.6-1) ... Selecting previously unselected package libxfixes3:arm64. Preparing to unpack .../131-libxfixes3_1%3a6.0.0-2+b3_arm64.deb ... Unpacking libxfixes3:arm64 (1:6.0.0-2+b3) ... Selecting previously unselected package libxcursor1:arm64. Preparing to unpack .../132-libxcursor1_1%3a1.2.2-1+b1_arm64.deb ... Unpacking libxcursor1:arm64 (1:1.2.2-1+b1) ... Selecting previously unselected package libxdamage1:arm64. Preparing to unpack .../133-libxdamage1_1%3a1.1.6-1+b2_arm64.deb ... Unpacking libxdamage1:arm64 (1:1.1.6-1+b2) ... Selecting previously unselected package libxinerama1:arm64. Preparing to unpack .../134-libxinerama1_2%3a1.1.4-3+b3_arm64.deb ... Unpacking libxinerama1:arm64 (2:1.1.4-3+b3) ... Selecting previously unselected package xkb-data. Preparing to unpack .../135-xkb-data_2.42-1_all.deb ... Unpacking xkb-data (2.42-1) ... Selecting previously unselected package libxkbcommon0:arm64. Preparing to unpack .../136-libxkbcommon0_1.7.0-2_arm64.deb ... Unpacking libxkbcommon0:arm64 (1.7.0-2) ... Selecting previously unselected package libxrandr2:arm64. Preparing to unpack .../137-libxrandr2_2%3a1.5.4-1+b2_arm64.deb ... Unpacking libxrandr2:arm64 (2:1.5.4-1+b2) ... Selecting previously unselected package libgtk-3-common. Preparing to unpack .../138-libgtk-3-common_3.24.43-4_all.deb ... Unpacking libgtk-3-common (3.24.43-4) ... Selecting previously unselected package libgtk-3-0t64:arm64. Preparing to unpack .../139-libgtk-3-0t64_3.24.43-4_arm64.deb ... Unpacking libgtk-3-0t64:arm64 (3.24.43-4) ... Selecting previously unselected package libglvnd0:arm64. Preparing to unpack .../140-libglvnd0_1.7.0-1+b2_arm64.deb ... Unpacking libglvnd0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../141-libdrm-common_2.4.123-1_all.deb ... Unpacking libdrm-common (2.4.123-1) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../142-libdrm2_2.4.123-1_arm64.deb ... Unpacking libdrm2:arm64 (2.4.123-1) ... Selecting previously unselected package libglapi-mesa:arm64. Preparing to unpack .../143-libglapi-mesa_24.2.8-1_arm64.deb ... Unpacking libglapi-mesa:arm64 (24.2.8-1) ... Selecting previously unselected package libx11-xcb1:arm64. Preparing to unpack .../144-libx11-xcb1_2%3a1.8.10-2_arm64.deb ... Unpacking libx11-xcb1:arm64 (2:1.8.10-2) ... Selecting previously unselected package libxcb-dri2-0:arm64. Preparing to unpack .../145-libxcb-dri2-0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-dri2-0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-dri3-0:arm64. Preparing to unpack .../146-libxcb-dri3-0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-glx0:arm64. Preparing to unpack .../147-libxcb-glx0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-glx0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-present0:arm64. Preparing to unpack .../148-libxcb-present0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-present0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-randr0:arm64. Preparing to unpack .../149-libxcb-randr0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-randr0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-sync1:arm64. Preparing to unpack .../150-libxcb-sync1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-sync1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-xfixes0:arm64. Preparing to unpack .../151-libxcb-xfixes0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxshmfence1:arm64. Preparing to unpack .../152-libxshmfence1_1.3-1+b2_arm64.deb ... Unpacking libxshmfence1:arm64 (1.3-1+b2) ... Selecting previously unselected package libxxf86vm1:arm64. Preparing to unpack .../153-libxxf86vm1_1%3a1.1.4-1+b3_arm64.deb ... Unpacking libxxf86vm1:arm64 (1:1.1.4-1+b3) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../154-libdrm-amdgpu1_2.4.123-1_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.123-1) ... Selecting previously unselected package libdrm-radeon1:arm64. Preparing to unpack .../155-libdrm-radeon1_2.4.123-1_arm64.deb ... Unpacking libdrm-radeon1:arm64 (2.4.123-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../156-libedit2_3.1-20240808-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240808-1) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../157-libz3-4_4.13.3-1_arm64.deb ... Unpacking libz3-4:arm64 (4.13.3-1) ... Selecting previously unselected package libllvm19:arm64. Preparing to unpack .../158-libllvm19_1%3a19.1.6-1_arm64.deb ... Unpacking libllvm19:arm64 (1:19.1.6-1) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../159-libsensors-config_1%3a3.6.0-10_all.deb ... Unpacking libsensors-config (1:3.6.0-10) ... Selecting previously unselected package libsensors5:arm64. Preparing to unpack .../160-libsensors5_1%3a3.6.0-10+b1_arm64.deb ... Unpacking libsensors5:arm64 (1:3.6.0-10+b1) ... Selecting previously unselected package mesa-libgallium:arm64. Preparing to unpack .../161-mesa-libgallium_24.2.8-1_arm64.deb ... Unpacking mesa-libgallium:arm64 (24.2.8-1) ... Selecting previously unselected package libvulkan1:arm64. Preparing to unpack .../162-libvulkan1_1.3.296.0-1_arm64.deb ... Unpacking libvulkan1:arm64 (1.3.296.0-1) ... Selecting previously unselected package libwayland-server0:arm64. Preparing to unpack .../163-libwayland-server0_1.23.0-1+b1_arm64.deb ... Unpacking libwayland-server0:arm64 (1.23.0-1+b1) ... Selecting previously unselected package libgbm1:arm64. Preparing to unpack .../164-libgbm1_24.2.8-1_arm64.deb ... Unpacking libgbm1:arm64 (24.2.8-1) ... Selecting previously unselected package libgl1-mesa-dri:arm64. Preparing to unpack .../165-libgl1-mesa-dri_24.2.8-1_arm64.deb ... Unpacking libgl1-mesa-dri:arm64 (24.2.8-1) ... Selecting previously unselected package libglx-mesa0:arm64. Preparing to unpack .../166-libglx-mesa0_24.2.8-1_arm64.deb ... Unpacking libglx-mesa0:arm64 (24.2.8-1) ... Selecting previously unselected package libglx0:arm64. Preparing to unpack .../167-libglx0_1.7.0-1+b2_arm64.deb ... Unpacking libglx0:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libgl1:arm64. Preparing to unpack .../168-libgl1_1.7.0-1+b2_arm64.deb ... Unpacking libgl1:arm64 (1.7.0-1+b2) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../169-libasound2-data_1.2.12-1_all.deb ... Unpacking libasound2-data (1.2.12-1) ... Selecting previously unselected package libasound2t64:arm64. Preparing to unpack .../170-libasound2t64_1.2.12-1+b1_arm64.deb ... Unpacking libasound2t64:arm64 (1.2.12-1+b1) ... Selecting previously unselected package libgif7:arm64. Preparing to unpack .../171-libgif7_5.2.2-1+b1_arm64.deb ... Unpacking libgif7:arm64 (5.2.2-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../172-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package libxtst6:arm64. Preparing to unpack .../173-libxtst6_2%3a1.2.3-1.1+b3_arm64.deb ... Unpacking libxtst6:arm64 (2:1.2.3-1.1+b3) ... Selecting previously unselected package openjdk-21-jre:arm64. Preparing to unpack .../174-openjdk-21-jre_21.0.6~6ea-1_arm64.deb ... Unpacking openjdk-21-jre:arm64 (21.0.6~6ea-1) ... Selecting previously unselected package default-jre. Preparing to unpack .../175-default-jre_2%3a1.21-76_arm64.deb ... Unpacking default-jre (2:1.21-76) ... Selecting previously unselected package libfml0:arm64. Preparing to unpack .../176-libfml0_0.1+git20221215.85f159e-1_arm64.deb ... Unpacking libfml0:arm64 (0.1+git20221215.85f159e-1) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../177-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package libssw0:arm64. Preparing to unpack .../178-libssw0_1.1-15+b1_arm64.deb ... Unpacking libssw0:arm64 (1.1-15+b1) ... Selecting previously unselected package libseqlib2:arm64. Preparing to unpack .../179-libseqlib2_1.2.0+dfsg-11+b2_arm64.deb ... Unpacking libseqlib2:arm64 (1.2.0+dfsg-11+b2) ... Selecting previously unselected package libtabixpp0t64:arm64. Preparing to unpack .../180-libtabixpp0t64_1.1.2-2.1+b1_arm64.deb ... Unpacking libtabixpp0t64:arm64 (1.1.2-2.1+b1) ... Selecting previously unselected package libdisorder0:arm64. Preparing to unpack .../181-libdisorder0_0.0.2+git20130809.8062ee1-4+b2_arm64.deb ... Unpacking libdisorder0:arm64 (0.0.2+git20130809.8062ee1-4+b2) ... Selecting previously unselected package libfastahack0:arm64. Preparing to unpack .../182-libfastahack0_1.0.0+dfsg-11+b2_arm64.deb ... Unpacking libfastahack0:arm64 (1.0.0+dfsg-11+b2) ... Selecting previously unselected package libsmithwaterman0:arm64. Preparing to unpack .../183-libsmithwaterman0_0.0+git20160702.2610e25-12+b2_arm64.deb ... Unpacking libsmithwaterman0:arm64 (0.0+git20160702.2610e25-12+b2) ... Selecting previously unselected package libwfa2-0:arm64. Preparing to unpack .../184-libwfa2-0_2.3.3-4+b1_arm64.deb ... Unpacking libwfa2-0:arm64 (2.3.3-4+b1) ... Selecting previously unselected package libvcflib2:arm64. Preparing to unpack .../185-libvcflib2_1.0.9+dfsg1-3+b2_arm64.deb ... Unpacking libvcflib2:arm64 (1.0.9+dfsg1-3+b2) ... Selecting previously unselected package freebayes. Preparing to unpack .../186-freebayes_1.3.7-1_arm64.deb ... Unpacking freebayes (1.3.7-1) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../187-libhamcrest-java_2.2-2_all.deb ... Unpacking libhamcrest-java (2.2-2) ... Selecting previously unselected package junit4. Preparing to unpack .../188-junit4_4.13.2-5_all.deb ... Unpacking junit4 (4.13.2-5) ... Selecting previously unselected package libapiguardian-java. Preparing to unpack .../189-libapiguardian-java_1.1.2-1_all.deb ... Unpacking libapiguardian-java (1.1.2-1) ... Selecting previously unselected package libopentest4j-java. Preparing to unpack .../190-libopentest4j-java_1.2.0-4_all.deb ... Unpacking libopentest4j-java (1.2.0-4) ... Selecting previously unselected package libopentest4j-reporting-java. Preparing to unpack .../191-libopentest4j-reporting-java_0.1.0-M1-2_all.deb ... Unpacking libopentest4j-reporting-java (0.1.0-M1-2) ... Selecting previously unselected package libpicocli-java. Preparing to unpack .../192-libpicocli-java_4.6.2-2_all.deb ... Unpacking libpicocli-java (4.6.2-2) ... Selecting previously unselected package libunivocity-parsers-java. Preparing to unpack .../193-libunivocity-parsers-java_2.9.1-1_all.deb ... Unpacking libunivocity-parsers-java (2.9.1-1) ... Selecting previously unselected package junit5. Preparing to unpack .../194-junit5_5.10.3-1_all.deb ... Unpacking junit5 (5.10.3-1) ... Selecting previously unselected package libactivation-java. Preparing to unpack .../195-libactivation-java_1.2.0-2_all.deb ... Unpacking libactivation-java (1.2.0-2) ... Selecting previously unselected package libantlr4-runtime-java. Preparing to unpack .../196-libantlr4-runtime-java_4.9.2-2_all.deb ... Unpacking libantlr4-runtime-java (4.9.2-2) ... Selecting previously unselected package libaopalliance-java. Preparing to unpack .../197-libaopalliance-java_20070526-7_all.deb ... Unpacking libaopalliance-java (20070526-7) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../198-libapache-pom-java_33-2_all.deb ... Unpacking libapache-pom-java (33-2) ... Selecting previously unselected package libapfloat-java. Preparing to unpack .../199-libapfloat-java_1.14.0-2_all.deb ... Unpacking libapfloat-java (1.14.0-2) ... Selecting previously unselected package libargs4j-java. Preparing to unpack .../200-libargs4j-java_2.33-2_all.deb ... Unpacking libargs4j-java (2.33-2) ... Selecting previously unselected package libasm-java. Preparing to unpack .../201-libasm-java_9.7.1-1_all.deb ... Unpacking libasm-java (9.7.1-1) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../202-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../203-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../204-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../205-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... Selecting previously unselected package libgeronimo-annotation-1.3-spec-java. Preparing to unpack .../206-libgeronimo-annotation-1.3-spec-java_1.3-1_all.deb ... Unpacking libgeronimo-annotation-1.3-spec-java (1.3-1) ... Selecting previously unselected package libgoogle-gson-java. Preparing to unpack .../207-libgoogle-gson-java_2.10.1-1_all.deb ... Unpacking libgoogle-gson-java (2.10.1-1) ... Selecting previously unselected package libciftools-java. Preparing to unpack .../208-libciftools-java_6.0.0-1_all.deb ... Unpacking libciftools-java (6.0.0-1) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../209-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-codec-java. Preparing to unpack .../210-libcommons-codec-java_1.17.1-1_all.deb ... Unpacking libcommons-codec-java (1.17.1-1) ... Selecting previously unselected package libcommons-math-java. Preparing to unpack .../211-libcommons-math-java_2.2-9_all.deb ... Unpacking libcommons-math-java (2.2-9) ... Selecting previously unselected package liberror-prone-java. Preparing to unpack .../212-liberror-prone-java_2.18.0-1_all.deb ... Unpacking liberror-prone-java (2.18.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../213-libjsr305-java_0.1~+svn49-11_all.deb ... Unpacking libjsr305-java (0.1~+svn49-11) ... Selecting previously unselected package libguava-java. Preparing to unpack .../214-libguava-java_32.0.1-1_all.deb ... Unpacking libguava-java (32.0.1-1) ... Selecting previously unselected package libitext5-java. Preparing to unpack .../215-libitext5-java_5.5.13.3-4_all.deb ... Unpacking libitext5-java (5.5.13.3-4) ... Selecting previously unselected package libjackson2-annotations-java. Preparing to unpack .../216-libjackson2-annotations-java_2.14.0-1_all.deb ... Unpacking libjackson2-annotations-java (2.14.0-1) ... Selecting previously unselected package libjackson2-core-java. Preparing to unpack .../217-libjackson2-core-java_2.14.1-1_all.deb ... Unpacking libjackson2-core-java (2.14.1-1) ... Selecting previously unselected package libjackson2-databind-java. Preparing to unpack .../218-libjackson2-databind-java_2.14.0-1_all.deb ... Unpacking libjackson2-databind-java (2.14.0-1) ... Selecting previously unselected package libjaxb-api-java. Preparing to unpack .../219-libjaxb-api-java_2.3.1-1_all.deb ... Unpacking libjaxb-api-java (2.3.1-1) ... Selecting previously unselected package libjaxen-java. Preparing to unpack .../220-libjaxen-java_1.1.6-5_all.deb ... Unpacking libjaxen-java (1.1.6-5) ... Selecting previously unselected package libdom4j-java. Preparing to unpack .../221-libdom4j-java_2.1.4-1_all.deb ... Unpacking libdom4j-java (2.1.4-1) ... Selecting previously unselected package libcommons-io-java. Preparing to unpack .../222-libcommons-io-java_2.17.0-1_all.deb ... Unpacking libcommons-io-java (2.17.0-1) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../223-libslf4j-java_1.7.32-1_all.deb ... Unpacking libslf4j-java (1.7.32-1) ... Selecting previously unselected package libmaven-shared-utils-java. Preparing to unpack .../224-libmaven-shared-utils-java_3.4.2-1_all.deb ... Unpacking libmaven-shared-utils-java (3.4.2-1) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../225-libcommons-cli-java_1.6.0-1_all.deb ... Unpacking libcommons-cli-java (1.6.0-1) ... Selecting previously unselected package libguice-java. Preparing to unpack .../226-libguice-java_5.1.0-1_all.deb ... Unpacking libguice-java (5.1.0-1) ... Selecting previously unselected package libmaven-parent-java. Preparing to unpack .../227-libmaven-parent-java_43-2_all.deb ... Unpacking libmaven-parent-java (43-2) ... Selecting previously unselected package libcommons-lang3-java. Preparing to unpack .../228-libcommons-lang3-java_3.17.0-1_all.deb ... Unpacking libcommons-lang3-java (3.17.0-1) ... Selecting previously unselected package libplexus-utils2-java. Preparing to unpack .../229-libplexus-utils2-java_3.4.2-1_all.deb ... Unpacking libplexus-utils2-java (3.4.2-1) ... Selecting previously unselected package libwagon-provider-api-java. Preparing to unpack .../230-libwagon-provider-api-java_3.5.3-1_all.deb ... Unpacking libwagon-provider-api-java (3.5.3-1) ... Selecting previously unselected package libmaven-resolver-java. Preparing to unpack .../231-libmaven-resolver-java_1.9.22-1_all.deb ... Unpacking libmaven-resolver-java (1.9.22-1) ... Selecting previously unselected package libplexus-cipher-java. Preparing to unpack .../232-libplexus-cipher-java_2.0-1_all.deb ... Unpacking libplexus-cipher-java (2.0-1) ... Selecting previously unselected package libplexus-classworlds-java. Preparing to unpack .../233-libplexus-classworlds-java_2.7.0-1_all.deb ... Unpacking libplexus-classworlds-java (2.7.0-1) ... Selecting previously unselected package libplexus-component-annotations-java. Preparing to unpack .../234-libplexus-component-annotations-java_2.1.1-1_all.deb ... Unpacking libplexus-component-annotations-java (2.1.1-1) ... Selecting previously unselected package libplexus-interpolation-java. Preparing to unpack .../235-libplexus-interpolation-java_1.27-1_all.deb ... Unpacking libplexus-interpolation-java (1.27-1) ... Selecting previously unselected package libplexus-sec-dispatcher-java. Preparing to unpack .../236-libplexus-sec-dispatcher-java_2.0-3_all.deb ... Unpacking libplexus-sec-dispatcher-java (2.0-3) ... Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java. Preparing to unpack .../237-libgeronimo-interceptor-3.0-spec-java_1.0.1-4_all.deb ... Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Selecting previously unselected package libcdi-api-java. Preparing to unpack .../238-libcdi-api-java_1.2-4_all.deb ... Unpacking libcdi-api-java (1.2-4) ... Selecting previously unselected package libsisu-inject-java. Preparing to unpack .../239-libsisu-inject-java_0.3.5-1_all.deb ... Unpacking libsisu-inject-java (0.3.5-1) ... Selecting previously unselected package libsisu-plexus-java. Preparing to unpack .../240-libsisu-plexus-java_0.3.5-1_all.deb ... Unpacking libsisu-plexus-java (0.3.5-1) ... Selecting previously unselected package libmaven3-core-java. Preparing to unpack .../241-libmaven3-core-java_3.9.9-1_all.deb ... Unpacking libmaven3-core-java (3.9.9-1) ... Selecting previously unselected package libmaven-shared-io-java. Preparing to unpack .../242-libmaven-shared-io-java_3.0.0-4_all.deb ... Unpacking libmaven-shared-io-java (3.0.0-4) ... Selecting previously unselected package libmaven-file-management-java. Preparing to unpack .../243-libmaven-file-management-java_3.0.0-1_all.deb ... Unpacking libmaven-file-management-java (3.0.0-1) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../244-libcommons-compress-java_1.27.1-2_all.deb ... Unpacking libcommons-compress-java (1.27.1-2) ... Selecting previously unselected package libplexus-io-java. Preparing to unpack .../245-libplexus-io-java_3.3.1-2_all.deb ... Unpacking libplexus-io-java (3.3.1-2) ... Selecting previously unselected package libsnappy1v5:arm64. Preparing to unpack .../246-libsnappy1v5_1.2.1-1+b1_arm64.deb ... Unpacking libsnappy1v5:arm64 (1.2.1-1+b1) ... Selecting previously unselected package libsnappy-jni. Preparing to unpack .../247-libsnappy-jni_1.1.10.7-1_arm64.deb ... Unpacking libsnappy-jni (1.1.10.7-1) ... Selecting previously unselected package libsnappy-java. Preparing to unpack .../248-libsnappy-java_1.1.10.7-1_all.deb ... Unpacking libsnappy-java (1.1.10.7-1) ... Selecting previously unselected package libxz-java. Preparing to unpack .../249-libxz-java_1.9-1_all.deb ... Unpacking libxz-java (1.9-1) ... Selecting previously unselected package libplexus-archiver-java. Preparing to unpack .../250-libplexus-archiver-java_4.6.1-1_all.deb ... Unpacking libplexus-archiver-java (4.6.1-1) ... Selecting previously unselected package libhttpcore-java. Preparing to unpack .../251-libhttpcore-java_4.4.16-1_all.deb ... Unpacking libhttpcore-java (4.4.16-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../252-libcommons-logging-java_1.3.0-1_all.deb ... Unpacking libcommons-logging-java (1.3.0-1) ... Selecting previously unselected package libhttpclient-java. Preparing to unpack .../253-libhttpclient-java_4.5.14-1_all.deb ... Unpacking libhttpclient-java (4.5.14-1) ... Selecting previously unselected package libjsoup-java. Preparing to unpack .../254-libjsoup-java_1.15.3-1_all.deb ... Unpacking libjsoup-java (1.15.3-1) ... Selecting previously unselected package libwagon-http-java. Preparing to unpack .../255-libwagon-http-java_3.5.3-1_all.deb ... Unpacking libwagon-http-java (3.5.3-1) ... Selecting previously unselected package libistack-commons-java. Preparing to unpack .../256-libistack-commons-java_3.0.6-5_all.deb ... Unpacking libistack-commons-java (3.0.6-5) ... Selecting previously unselected package libcodemodel-java. Preparing to unpack .../257-libcodemodel-java_2.6+jaxb2.3.0.1-11_all.deb ... Unpacking libcodemodel-java (2.6+jaxb2.3.0.1-11) ... Selecting previously unselected package librelaxng-datatype-java. Preparing to unpack .../258-librelaxng-datatype-java_1.0+ds1-3.1_all.deb ... Unpacking librelaxng-datatype-java (1.0+ds1-3.1) ... Selecting previously unselected package librngom-java. Preparing to unpack .../259-librngom-java_2.3.0.1-11_all.deb ... Unpacking librngom-java (2.3.0.1-11) ... Selecting previously unselected package libxsom-java. Preparing to unpack .../260-libxsom-java_2.3.0.1-11_all.deb ... Unpacking libxsom-java (2.3.0.1-11) ... Selecting previously unselected package libtxw2-java. Preparing to unpack .../261-libtxw2-java_2.3.0.1-11_all.deb ... Unpacking libtxw2-java (2.3.0.1-11) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Preparing to unpack .../262-libxml-commons-resolver1.1-java_1.2-11_all.deb ... Unpacking libxml-commons-resolver1.1-java (1.2-11) ... Selecting previously unselected package libdtd-parser-java. Preparing to unpack .../263-libdtd-parser-java_1.2-1_all.deb ... Unpacking libdtd-parser-java (1.2-1) ... Selecting previously unselected package libstax-ex-java. Preparing to unpack .../264-libstax-ex-java_1.7.8-3_all.deb ... Unpacking libstax-ex-java (1.7.8-3) ... Selecting previously unselected package libstreambuffer-java. Preparing to unpack .../265-libstreambuffer-java_1.5.4-1.1_all.deb ... Unpacking libstreambuffer-java (1.5.4-1.1) ... Selecting previously unselected package libfastinfoset-java. Preparing to unpack .../266-libfastinfoset-java_1.2.12-3_all.deb ... Unpacking libfastinfoset-java (1.2.12-3) ... Selecting previously unselected package libjaxb-java. Preparing to unpack .../267-libjaxb-java_2.3.0.1-11_all.deb ... Unpacking libjaxb-java (2.3.0.1-11) ... Selecting previously unselected package libmaven-archiver-java. Preparing to unpack .../268-libmaven-archiver-java_3.6.2-1_all.deb ... Unpacking libmaven-archiver-java (3.6.2-1) ... Selecting previously unselected package libmaven-jar-plugin-java. Preparing to unpack .../269-libmaven-jar-plugin-java_3.3.0-2_all.deb ... Unpacking libmaven-jar-plugin-java (3.3.0-2) ... Selecting previously unselected package libcommons-text-java. Preparing to unpack .../270-libcommons-text-java_1.12.0-1_all.deb ... Unpacking libcommons-text-java (1.12.0-1) ... Selecting previously unselected package libfastutil-java. Preparing to unpack .../271-libfastutil-java_8.5.15+dfsg-1_all.deb ... Unpacking libfastutil-java (8.5.15+dfsg-1) ... Selecting previously unselected package libjheaps-java. Preparing to unpack .../272-libjheaps-java_0.14-2_all.deb ... Unpacking libjheaps-java (0.14-2) ... Selecting previously unselected package libxml-commons-external-java. Preparing to unpack .../273-libxml-commons-external-java_1.4.01-6_all.deb ... Unpacking libxml-commons-external-java (1.4.01-6) ... Selecting previously unselected package libxerces2-java. Preparing to unpack .../274-libxerces2-java_2.12.2-1_all.deb ... Unpacking libxerces2-java (2.12.2-1) ... Selecting previously unselected package libjgraphx-java. Preparing to unpack .../275-libjgraphx-java_2.1.0.7-5_all.deb ... Unpacking libjgraphx-java (2.1.0.7-5) ... Selecting previously unselected package libjgrapht-java. Preparing to unpack .../276-libjgrapht-java_1.5.2-1_all.deb ... Unpacking libjgrapht-java (1.5.2-1) ... Selecting previously unselected package libinchi1.07. Preparing to unpack .../277-libinchi1.07_1.07.1+dfsg-6_arm64.deb ... Unpacking libinchi1.07 (1.07.1+dfsg-6) ... Selecting previously unselected package libjni-inchi-jni. Preparing to unpack .../278-libjni-inchi-jni_0.8+dfsg-8_arm64.deb ... Unpacking libjni-inchi-jni (0.8+dfsg-8) ... Selecting previously unselected package libcommons-exec-java. Preparing to unpack .../279-libcommons-exec-java_1.3-2_all.deb ... Unpacking libcommons-exec-java (1.3-2) ... Selecting previously unselected package libexec-maven-plugin-java. Preparing to unpack .../280-libexec-maven-plugin-java_3.1.0-2_all.deb ... Unpacking libexec-maven-plugin-java (3.1.0-2) ... Selecting previously unselected package libmaven-shared-incremental-java. Preparing to unpack .../281-libmaven-shared-incremental-java_1.1-6_all.deb ... Unpacking libmaven-shared-incremental-java (1.1-6) ... Selecting previously unselected package libcommons-lang-java. Preparing to unpack .../282-libcommons-lang-java_2.6-10_all.deb ... Unpacking libcommons-lang-java (2.6-10) ... Selecting previously unselected package libxbean-reflect-java. Preparing to unpack .../283-libxbean-reflect-java_4.5-9_all.deb ... Unpacking libxbean-reflect-java (4.5-9) ... Selecting previously unselected package libplexus-container-default-java. Preparing to unpack .../284-libplexus-container-default-java_2.1.1-1_all.deb ... Unpacking libplexus-container-default-java (2.1.1-1) ... Selecting previously unselected package libplexus-compiler-java. Preparing to unpack .../285-libplexus-compiler-java_2.13.0-1_all.deb ... Unpacking libplexus-compiler-java (2.13.0-1) ... Selecting previously unselected package libqdox2-java. Preparing to unpack .../286-libqdox2-java_2.0.3-1_all.deb ... Unpacking libqdox2-java (2.0.3-1) ... Selecting previously unselected package libplexus-languages-java. Preparing to unpack .../287-libplexus-languages-java_1.1.1-2_all.deb ... Unpacking libplexus-languages-java (1.1.1-2) ... Selecting previously unselected package libmaven-compiler-plugin-java. Preparing to unpack .../288-libmaven-compiler-plugin-java_3.13.0-1_all.deb ... Unpacking libmaven-compiler-plugin-java (3.13.0-1) ... Selecting previously unselected package liblog4j1.2-java. Preparing to unpack .../289-liblog4j1.2-java_1.2.17-11_all.deb ... Unpacking liblog4j1.2-java (1.2.17-11) ... Selecting previously unselected package libjni-inchi-java. Preparing to unpack .../290-libjni-inchi-java_0.8+dfsg-8_all.deb ... Unpacking libjni-inchi-java (0.8+dfsg-8) ... Selecting previously unselected package libnaga-java. Preparing to unpack .../291-libnaga-java_3.0+svn80-5_all.deb ... Unpacking libnaga-java (3.0+svn80-5) ... Selecting previously unselected package libjmol-java. Preparing to unpack .../292-libjmol-java_16.2.33+dfsg-1_all.deb ... Unpacking libjmol-java (16.2.33+dfsg-1) ... Selecting previously unselected package libjson-simple-java. Preparing to unpack .../293-libjson-simple-java_2.3.0-1_all.deb ... Unpacking libjson-simple-java (2.3.0-1) ... Selecting previously unselected package libmsgpack-java. Preparing to unpack .../294-libmsgpack-java_0.9.6-1_all.deb ... Unpacking libmsgpack-java (0.9.6-1) ... Selecting previously unselected package libmmtf-java. Preparing to unpack .../295-libmmtf-java_1.0.11-1_all.deb ... Unpacking libmmtf-java (1.0.11-1) ... Selecting previously unselected package libvecmath-java. Preparing to unpack .../296-libvecmath-java_1.5.2-7_all.deb ... Unpacking libvecmath-java (1.5.2-7) ... Selecting previously unselected package libbiojava6-java. Preparing to unpack .../297-libbiojava6-java_6.1.0+dfsg-5_all.deb ... Unpacking libbiojava6-java (6.1.0+dfsg-5) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../298-libblas3_3.12.0-4_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-4) ... Selecting previously unselected package libcharts4j-java. Preparing to unpack .../299-libcharts4j-java_1.3-4_all.deb ... Unpacking libcharts4j-java (1.3-4) ... Selecting previously unselected package libcommons-collections3-java. Preparing to unpack .../300-libcommons-collections3-java_3.2.2-3_all.deb ... Unpacking libcommons-collections3-java (3.2.2-3) ... Selecting previously unselected package libcommons-beanutils-java. Preparing to unpack .../301-libcommons-beanutils-java_1.9.4-2_all.deb ... Unpacking libcommons-beanutils-java (1.9.4-2) ... Selecting previously unselected package libcommons-collections4-java. Preparing to unpack .../302-libcommons-collections4-java_4.4-2_all.deb ... Unpacking libcommons-collections4-java (4.4-2) ... Selecting previously unselected package libcommons-jexl2-java. Preparing to unpack .../303-libcommons-jexl2-java_2.1.1-6_all.deb ... Unpacking libcommons-jexl2-java (2.1.1-6) ... Selecting previously unselected package libcommons-math3-java. Preparing to unpack .../304-libcommons-math3-java_3.6.1-3_all.deb ... Unpacking libcommons-math3-java (3.6.1-3) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../305-libcurl4t64_8.11.1-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.11.1-1) ... Selecting previously unselected package libdistlib-java. Preparing to unpack .../306-libdistlib-java_1.0-5_all.deb ... Unpacking libdistlib-java (1.0-5) ... Selecting previously unselected package libezmorph-java. Preparing to unpack .../307-libezmorph-java_1.0.6-4_all.deb ... Unpacking libezmorph-java (1.0.6-4) ... Selecting previously unselected package libfreemarker-java. Preparing to unpack .../308-libfreemarker-java_2.3.32-2_all.deb ... Unpacking libfreemarker-java (2.3.32-2) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../309-libgfortran5_14.2.0-12_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-12) ... Selecting previously unselected package libxom-java. Preparing to unpack .../310-libxom-java_1.3.9-1_all.deb ... Unpacking libxom-java (1.3.9-1) ... Selecting previously unselected package libjson-java. Preparing to unpack .../311-libjson-java_3.1.0+dfsg-2_all.deb ... Unpacking libjson-java (3.1.0+dfsg-2) ... Selecting previously unselected package libmbedcrypto16:arm64. Preparing to unpack .../312-libmbedcrypto16_3.6.2-3_arm64.deb ... Unpacking libmbedcrypto16:arm64 (3.6.2-3) ... Selecting previously unselected package libmbedx509-7:arm64. Preparing to unpack .../313-libmbedx509-7_3.6.2-3_arm64.deb ... Unpacking libmbedx509-7:arm64 (3.6.2-3) ... Selecting previously unselected package libmbedtls21:arm64. Preparing to unpack .../314-libmbedtls21_3.6.2-3_arm64.deb ... Unpacking libmbedtls21:arm64 (3.6.2-3) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../315-ncbi-vdb-data_3.0.9+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.0.9+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:arm64. Preparing to unpack .../316-libncbi-vdb3_3.0.9+dfsg-2_arm64.deb ... Unpacking libncbi-vdb3:arm64 (3.0.9+dfsg-2) ... Selecting previously unselected package libncbi-ngs3:arm64. Preparing to unpack .../317-libncbi-ngs3_3.0.9+dfsg-7+b1_arm64.deb ... Unpacking libncbi-ngs3:arm64 (3.0.9+dfsg-7+b1) ... Selecting previously unselected package libngs-jni:arm64. Preparing to unpack .../318-libngs-jni_3.0.9+dfsg-7+b1_arm64.deb ... Unpacking libngs-jni:arm64 (3.0.9+dfsg-7+b1) ... Selecting previously unselected package libngs-java:arm64. Preparing to unpack .../319-libngs-java_3.0.9+dfsg-7+b1_arm64.deb ... Unpacking libngs-java:arm64 (3.0.9+dfsg-7+b1) ... Selecting previously unselected package librhino-java. Preparing to unpack .../320-librhino-java_1.7.15-1_all.deb ... Unpacking librhino-java (1.7.15-1) ... Selecting previously unselected package libhtsjdk-java. Preparing to unpack .../321-libhtsjdk-java_4.1.3+dfsg-2_all.deb ... Unpacking libhtsjdk-java (4.1.3+dfsg-2) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../322-libice6_2%3a1.1.1-1_arm64.deb ... Unpacking libice6:arm64 (2:1.1.1-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../323-liblapack3_3.12.0-4_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-4) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../324-libncurses6_6.5-2+b1_arm64.deb ... Unpacking libncurses6:arm64 (6.5-2+b1) ... Selecting previously unselected package libpaper2:arm64. Preparing to unpack .../325-libpaper2_2.2.5-0.3_arm64.deb ... Unpacking libpaper2:arm64 (2.2.5-0.3) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../326-libpaper-utils_2.2.5-0.3_arm64.deb ... Unpacking libpaper-utils (2.2.5-0.3) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../327-libsm6_2%3a1.2.4-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.4-1) ... Selecting previously unselected package libsnp-sites1:arm64. Preparing to unpack .../328-libsnp-sites1_2.5.1-2+b2_arm64.deb ... Unpacking libsnp-sites1:arm64 (2.5.1-2+b2) ... Selecting previously unselected package libtrove3-java. Preparing to unpack .../329-libtrove3-java_3.0.3-5_all.deb ... Unpacking libtrove3-java (3.0.3-5) ... Selecting previously unselected package libsnpeff-java. Preparing to unpack .../330-libsnpeff-java_5.2.e+dfsg-1_all.deb ... Unpacking libsnpeff-java (5.2.e+dfsg-1) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../331-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../332-libxft2_2.3.6-1+b3_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b3) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../333-libxss1_1%3a1.2.3-1+b2_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b2) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../334-libtk8.6_8.6.15-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.15-1) ... Selecting previously unselected package zip. Preparing to unpack .../335-zip_3.0-14+b1_arm64.deb ... Unpacking zip (3.0-14+b1) ... Selecting previously unselected package unzip. Preparing to unpack .../336-unzip_6.0-28+b1_arm64.deb ... Unpacking unzip (6.0-28+b1) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../337-xdg-utils_1.2.1-2_all.deb ... Unpacking xdg-utils (1.2.1-2) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../338-libxt6t64_1%3a1.2.1-1.2+b1_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../339-r-base-core_4.4.2-1_arm64.deb ... Unpacking r-base-core (4.4.2-1) ... Selecting previously unselected package r-cran-littler. Preparing to unpack .../340-r-cran-littler_0.3.20-2_arm64.deb ... Unpacking r-cran-littler (0.3.20-2) ... Selecting previously unselected package littler. Preparing to unpack .../341-littler_0.3.20-2_all.deb ... Unpacking littler (0.3.20-2) ... Selecting previously unselected package r-cran-pkgkitten. Preparing to unpack .../342-r-cran-pkgkitten_0.2.4-1_all.deb ... Unpacking r-cran-pkgkitten (0.2.4-1) ... Selecting previously unselected package r-cran-rcpp. Preparing to unpack .../343-r-cran-rcpp_1.0.13-1-1_arm64.deb ... Unpacking r-cran-rcpp (1.0.13-1-1) ... Selecting previously unselected package r-cran-plyr. Preparing to unpack .../344-r-cran-plyr_1.8.9-1+b1_arm64.deb ... Unpacking r-cran-plyr (1.8.9-1+b1) ... Selecting previously unselected package r-cran-cli. Preparing to unpack .../345-r-cran-cli_3.6.3-1_arm64.deb ... Unpacking r-cran-cli (3.6.3-1) ... Selecting previously unselected package r-cran-glue. Preparing to unpack .../346-r-cran-glue_1.8.0-1_arm64.deb ... Unpacking r-cran-glue (1.8.0-1) ... Selecting previously unselected package r-cran-rlang. Preparing to unpack .../347-r-cran-rlang_1.1.4-1+b1_arm64.deb ... Unpacking r-cran-rlang (1.1.4-1+b1) ... Selecting previously unselected package r-cran-lifecycle. Preparing to unpack .../348-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... Selecting previously unselected package r-cran-gtable. Preparing to unpack .../349-r-cran-gtable_0.3.6+dfsg-1_all.deb ... Unpacking r-cran-gtable (0.3.6+dfsg-1) ... Selecting previously unselected package r-cran-isoband. Preparing to unpack .../350-r-cran-isoband_0.2.7-1+b1_arm64.deb ... Unpacking r-cran-isoband (0.2.7-1+b1) ... Selecting previously unselected package r-cran-mass. Preparing to unpack .../351-r-cran-mass_7.3-61-1+b1_arm64.deb ... Unpacking r-cran-mass (7.3-61-1+b1) ... Selecting previously unselected package r-cran-lattice. Preparing to unpack .../352-r-cran-lattice_0.22-6-1+b1_arm64.deb ... Unpacking r-cran-lattice (0.22-6-1+b1) ... Selecting previously unselected package r-cran-nlme. Preparing to unpack .../353-r-cran-nlme_3.1.166-1_arm64.deb ... Unpacking r-cran-nlme (3.1.166-1) ... Selecting previously unselected package r-cran-matrix. Preparing to unpack .../354-r-cran-matrix_1.7-1-1_arm64.deb ... Unpacking r-cran-matrix (1.7-1-1) ... Selecting previously unselected package r-cran-mgcv. Preparing to unpack .../355-r-cran-mgcv_1.9-1-1+b1_arm64.deb ... Unpacking r-cran-mgcv (1.9-1-1+b1) ... Selecting previously unselected package r-cran-farver. Preparing to unpack .../356-r-cran-farver_2.1.2-1+b1_arm64.deb ... Unpacking r-cran-farver (2.1.2-1+b1) ... Selecting previously unselected package r-cran-labeling. Preparing to unpack .../357-r-cran-labeling_0.4.3-1_all.deb ... Unpacking r-cran-labeling (0.4.3-1) ... Selecting previously unselected package r-cran-colorspace. Preparing to unpack .../358-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... Selecting previously unselected package r-cran-munsell. Preparing to unpack .../359-r-cran-munsell_0.5.1-1_all.deb ... Unpacking r-cran-munsell (0.5.1-1) ... Selecting previously unselected package r-cran-r6. Preparing to unpack .../360-r-cran-r6_2.5.1-1_all.deb ... Unpacking r-cran-r6 (2.5.1-1) ... Selecting previously unselected package r-cran-rcolorbrewer. Preparing to unpack .../361-r-cran-rcolorbrewer_1.1-3-1_all.deb ... Unpacking r-cran-rcolorbrewer (1.1-3-1) ... Selecting previously unselected package r-cran-viridislite. Preparing to unpack .../362-r-cran-viridislite_0.4.2-2_all.deb ... Unpacking r-cran-viridislite (0.4.2-2) ... Selecting previously unselected package r-cran-scales. Preparing to unpack .../363-r-cran-scales_1.3.0-1_all.deb ... Unpacking r-cran-scales (1.3.0-1) ... Selecting previously unselected package r-cran-fansi. Preparing to unpack .../364-r-cran-fansi_1.0.5-1+b1_arm64.deb ... Unpacking r-cran-fansi (1.0.5-1+b1) ... Selecting previously unselected package r-cran-magrittr. Preparing to unpack .../365-r-cran-magrittr_2.0.3-1+b1_arm64.deb ... Unpacking r-cran-magrittr (2.0.3-1+b1) ... Selecting previously unselected package r-cran-utf8. Preparing to unpack .../366-r-cran-utf8_1.2.4-1+b1_arm64.deb ... Unpacking r-cran-utf8 (1.2.4-1+b1) ... Selecting previously unselected package r-cran-vctrs. Preparing to unpack .../367-r-cran-vctrs_0.6.5-1+b1_arm64.deb ... Unpacking r-cran-vctrs (0.6.5-1+b1) ... Selecting previously unselected package r-cran-pillar. Preparing to unpack .../368-r-cran-pillar_1.9.0+dfsg-1_all.deb ... Unpacking r-cran-pillar (1.9.0+dfsg-1) ... Selecting previously unselected package r-cran-pkgconfig. Preparing to unpack .../369-r-cran-pkgconfig_2.0.3-2_all.deb ... Unpacking r-cran-pkgconfig (2.0.3-2) ... Selecting previously unselected package r-cran-tibble. Preparing to unpack .../370-r-cran-tibble_3.2.1+dfsg-2+b1_arm64.deb ... Unpacking r-cran-tibble (3.2.1+dfsg-2+b1) ... Selecting previously unselected package r-cran-withr. Preparing to unpack .../371-r-cran-withr_3.0.2+dfsg-1_all.deb ... Unpacking r-cran-withr (3.0.2+dfsg-1) ... Selecting previously unselected package r-cran-ggplot2. Preparing to unpack .../372-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... Selecting previously unselected package r-cran-gridbase. Preparing to unpack .../373-r-cran-gridbase_0.4-7-5_all.deb ... Unpacking r-cran-gridbase (0.4-7-5) ... Selecting previously unselected package libvcflib-tools. Preparing to unpack .../374-libvcflib-tools_1.0.9+dfsg1-3+b2_arm64.deb ... Unpacking libvcflib-tools (1.0.9+dfsg1-3+b2) ... Selecting previously unselected package minimap2. Preparing to unpack .../375-minimap2_2.27+dfsg-1+b3_arm64.deb ... Unpacking minimap2 (2.27+dfsg-1+b3) ... Selecting previously unselected package sysstat. Preparing to unpack .../376-sysstat_12.7.5-2+b1_arm64.deb ... Unpacking sysstat (12.7.5-2+b1) ... Selecting previously unselected package parallel. Preparing to unpack .../377-parallel_20240222+ds-2_all.deb ... Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20240222+ds-2) ... Selecting previously unselected package samclip. Preparing to unpack .../378-samclip_0.4.0-4_all.deb ... Unpacking samclip (0.4.0-4) ... Selecting previously unselected package samtools. Preparing to unpack .../379-samtools_1.20-3+b1_arm64.deb ... Unpacking samtools (1.20-3+b1) ... Selecting previously unselected package seqtk. Preparing to unpack .../380-seqtk_1.4-2+b1_arm64.deb ... Unpacking seqtk (1.4-2+b1) ... Selecting previously unselected package snp-sites. Preparing to unpack .../381-snp-sites_2.5.1-2+b2_arm64.deb ... Unpacking snp-sites (2.5.1-2+b2) ... Selecting previously unselected package snpeff. Preparing to unpack .../382-snpeff_5.2.e+dfsg-1_all.deb ... Unpacking snpeff (5.2.e+dfsg-1) ... Selecting previously unselected package vt. Preparing to unpack .../383-vt_0.57721+ds-3+b2_arm64.deb ... Unpacking vt (0.57721+ds-3+b2) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libdisorder0:arm64 (0.0.2+git20130809.8062ee1-4+b2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libfastutil-java (8.5.15+dfsg-1) ... Setting up libjackson2-annotations-java (2.14.0-1) ... Setting up libwfa2-0:arm64 (2.3.3-4+b1) ... Setting up libdtd-parser-java (1.2-1) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libslf4j-java (1.7.32-1) ... Setting up systemd-sysv (257.1-5) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up libxcb-xfixes0:arm64 (1.17.0-2+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up seqtk (1.4-2+b1) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.40.2-13) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up java-common (0.76) ... Setting up libdatrie1:arm64 (0.2.13-3+b1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libjheaps-java (0.14-2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libvecmath-java (1.5.2-7) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up bwa (0.7.18-1) ... Setting up libglvnd0:arm64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up minimap2 (2.27+dfsg-1+b3) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libxcb-glx0:arm64 (1.17.0-2+b1) ... Setting up unzip (6.0-28+b1) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libedit2:arm64 (3.1-20240808-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Setting up libmagic1t64:arm64 (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+23.1) ... 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:arm64 (0.0+git20160702.2610e25-12+b2) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... 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 (4.9.2-2) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libjson-simple-java (2.3.0-1) ... Setting up libunivocity-parsers-java (2.9.1-1) ... Setting up libfml0:arm64 (0.1+git20221215.85f159e-1) ... Setting up libfastahack0:arm64 (1.0.0+dfsg-11+b2) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up samclip (0.4.0-4) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libsnappy1v5:arm64 (1.2.1-1+b1) ... Setting up libcharts4j-java (1.3-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Feb 3 03:30:48 UTC 2026. Universal Time is now: Tue Feb 3 03:30:48 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libasound2-data (1.2.12-1) ... Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-14+b1) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libasound2t64:arm64 (1.2.12-1+b1) ... Setting up libjpeg62-turbo:arm64 (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:arm64 (1.5.10-2) ... Setting up libnspr4:arm64 (2:4.36-1) ... Setting up libxcb-sync1:arm64 (1.17.0-2+b1) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:arm64 (0.8-15) ... Setting up libncurses6:arm64 (6.5-2+b1) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:arm64 (1.16.0-1) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:arm64 (1.6.44-3) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:arm64 (2.3.1-1) ... Setting up libsensors5:arm64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:arm64 (24.2.8-1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-12) ... Setting up libvulkan1:arm64 (1.3.296.0-1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libapfloat-java (1.14.0-2) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up libxcb-dri2-0:arm64 (1.17.0-2+b1) ... Setting up libgif7:arm64 (5.2.2-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... 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:arm64 (1.3-1+b2) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.54.0-1) ... Setting up libcommons-math-java (2.2-9) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:arm64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.0-1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up libjackson2-core-java (2.14.1-1) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libsnp-sites1:arm64 (2.5.1-2+b2) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libwayland-egl1:arm64 (1.23.0-1+b1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmbedcrypto16:arm64 (3.6.2-3) ... Setting up libpaper2:arm64 (2.2.5-0.3) ... Setting up libssh2-1t64:arm64 (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+ds1-3.1) ... Setting up openssl (3.3.2-2) ... Setting up libinchi1.07 (1.07.1+dfsg-6) ... 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:arm64 (1:0.4.6-1) ... Setting up libssw0:arm64 (1.1-15+b1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (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+b1) ... Setting up dbus-bin (1.16.0-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libxkbcommon0:arm64 (1.7.0-2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libwayland-client0:arm64 (1.23.0-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:arm64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libllvm19:arm64 (1:19.1.6-1) ... Setting up libwayland-server0:arm64 (1.23.0-1+b1) ... Setting up libx11-xcb1:arm64 (2:1.8.10-2) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-3) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b2) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... 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:arm64 (0.8-15) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libnss3:arm64 (2:3.106-1) ... 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) ... Setting up libxom-java (1.3.9-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b3) ... 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:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:arm64 (2.82.4-1) ... Setting up libmbedx509-7:arm64 (3.6.2-3) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b3) ... 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+b1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libxrandr2:arm64 (2:1.5.4-1+b2) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0046) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:arm64 (3.6.2-3) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up librngom-java (2.3.0.1-11) ... Setting up libdrm2:arm64 (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:arm64 (1.23.0-1+b1) ... Setting up libpam-systemd:arm64 (257.1-5) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (10.1.0-2) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1+b1) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... 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:arm64 (2:1.2.4-1) ... Setting up sysstat (12.7.5-2+b1) ... 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:arm64 (0.8-15) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up gtk-update-icon-cache (4.16.7+ds-1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.6-1+b3) ... Setting up libatk1.0-0t64:arm64 (2.54.0-1) ... Setting up openjdk-21-jre-headless:arm64 (21.0.6~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:arm64 (2.4.123-1) ... Setting up libxtst6:arm64 (2:1.2.3-1.1+b3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.15-1) ... Setting up libdistlib-java (1.0-5) ... Setting up libxcursor1:arm64 (1:1.2.2-1+b1) ... Setting up libpango-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:arm64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:arm64 (0.3.6-1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libldap-2.5-0:arm64 (2.5.19+dfsg-1) ... Setting up libcolord2:arm64 (1.4.7-1+b2) ... Setting up libdconf1:arm64 (0.40.0-4+b3) ... 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:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:arm64 (2.54.0-1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b1) ... Setting up parallel (20240222+ds-2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:arm64 (1.18.2-2) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libpangoft2-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:arm64 (1.55.0+ds-3) ... Setting up libncbi-ngs3:arm64 (3.0.9+dfsg-7+b1) ... Setting up libatk-bridge2.0-0t64:arm64 (2.54.0-1) ... Setting up mesa-libgallium:arm64 (24.2.8-1) ... Setting up libngs-jni:arm64 (3.0.9+dfsg-7+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-3) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:arm64 (8.11.1-1) ... Setting up libgbm1:arm64 (24.2.8-1) ... Setting up python3.12 (3.12.8-3) ... Setting up libgl1-mesa-dri:arm64 (24.2.8-1) ... Setting up libcurl3t64-gnutls:arm64 (8.11.1-1) ... Setting up debhelper (13.23) ... Setting up dconf-service (0.40.0-4+b3) ... 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+b1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1+b1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libhts3t64:arm64 (1.20+ds-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:arm64 (3.0.9+dfsg-7+b1) ... 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+b1) ... Setting up libseqlib2:arm64 (1.2.0+dfsg-11+b2) ... Setting up libpython3-stdlib:arm64 (3.12.8-1) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up r-cran-rlang (1.1.4-1+b1) ... Setting up libglx-mesa0:arm64 (24.2.8-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up vt (0.57721+ds-3+b2) ... Setting up libglx0:arm64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:arm64 (0.40.0-4+b3) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up bcftools (1.20-2+b1) ... Setting up r-cran-fansi (1.0.5-1+b1) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up r-cran-mass (7.3-61-1+b1) ... Setting up python3 (3.12.8-1) ... 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 (1.20-3+b1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1+b1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libgl1:arm64 (1.7.0-1+b2) ... Setting up r-cran-plyr (1.8.9-1+b1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1+b1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1+b1) ... Setting up libtabixpp0t64:arm64 (1.1.2-2.1+b1) ... Setting up r-cran-vctrs (0.6.5-1+b1) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2+b1) ... Setting up libvcflib2:arm64 (1.0.9+dfsg1-3+b2) ... Setting up libgtk-3-0t64:arm64 (3.24.43-4) ... Setting up r-cran-scales (1.3.0-1) ... Setting up freebayes (1.3.7-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libvcflib-tools (1.0.9+dfsg1-3+b2) ... 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 (3.0.0-1) ... 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 (2.40-4) ... Processing triggers for systemd (257.1-5) ... 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:arm64 (21.0.6~6ea-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.e+dfsg-1) ... Setting up snpeff (5.2.e+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/17200/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/17200/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 arm64 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 [17:31:08] This is snippy 4.6.0 [17:31:08] Written by Torsten Seemann [17:31:08] Obtained from https://github.com/tseemann/snippy [17:31:08] Detected operating system: linux [17:31:08] Enabling bundled linux tools. [17:31:08] Found bwa - /usr/bin/bwa [17:31:08] Found bcftools - /usr/bin/bcftools [17:31:08] Found samtools - /usr/bin/samtools [17:31:08] Found java - /usr/bin/java [17:31:08] Found snpEff - /usr/bin/snpEff [17:31:08] Found samclip - /usr/bin/samclip [17:31:08] Found seqtk - /usr/bin/seqtk [17:31:08] Found parallel - /usr/bin/parallel [17:31:08] Found freebayes - /usr/bin/freebayes [17:31:08] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [17:31:08] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [17:31:08] Found vcfstreamsort - /usr/bin/vcfstreamsort [17:31:08] Found vcfuniq - /usr/bin/vcfuniq [17:31:08] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [17:31:08] Found gzip - /usr/bin/gzip [17:31:08] Found vt - /usr/bin/vt [17:31:08] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [17:31:08] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [17:31:08] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [17:31:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [17:31:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [17:31:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [17:31:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [17:31:08] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [17:31:08] Treating reference as 'fasta' format. [17:31:08] Will use 2 CPU cores. [17:31:08] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq [17:31:08] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq [17:31:08] Used --force, will overwrite existing S1 [17:31:08] Changing working directory: S1 [17:31:08] Creating reference folder: reference [17:31:08] Extracting FASTA and GFF from reference. [17:31:08] Wrote 3 sequences to ref.fa [17:31:08] Wrote 0 features to ref.gff [17:31:08] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [17:31:08] Using BAM RG (Read Group) ID: S1 [17:31:08] Running: samtools faidx reference/ref.fa 2>> snps.log [17:31:08] Running: bwa index reference/ref.fa 2>> snps.log [17:31:08] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [17:31:08] Running: ln -sf reference/ref.fa . 2>> snps.log [17:31:08] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [17:31:08] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [17:31:08] 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 1.395 CPU sec, 0.700 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: 0.852 sec; CPU: 1.461 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. [17:31:10] Running: samtools index snps.bam 2>> snps.log [17:31:10] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [17:31:10] 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 [17:31:11] 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 [17:31:11] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [17:31:11] 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 [17:31:12] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [17:31:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [17:31:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log [17:31:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [17:31:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [17:31:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [17:31:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [17:31:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [17:31:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [17:31:12] Marked 749 heterozygous sites with 'n' [17:31:12] Creating extra output files: BED GFF CSV TXT HTML [17:31:12] Identified 261 variants. [17:31:12] Result folder: S1 [17:31:12] Result files: [17:31:12] * S1/snps.aligned.fa [17:31:12] * S1/snps.bam [17:31:12] * S1/snps.bam.bai [17:31:12] * S1/snps.bed [17:31:12] * S1/snps.consensus.fa [17:31:12] * S1/snps.consensus.subs.fa [17:31:12] * S1/snps.csv [17:31:12] * S1/snps.filt.vcf [17:31:12] * S1/snps.gff [17:31:12] * S1/snps.html [17:31:12] * S1/snps.log [17:31:12] * S1/snps.raw.vcf [17:31:12] * S1/snps.subs.vcf [17:31:12] * S1/snps.tab [17:31:12] * S1/snps.txt [17:31:12] * S1/snps.vcf [17:31:12] * S1/snps.vcf.gz [17:31:12] * S1/snps.vcf.gz.csi [17:31:12] Walltime used: 4 seconds [17:31:12] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues [17:31:12] 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 [17:31:12] This is snippy 4.6.0 [17:31:12] Written by Torsten Seemann [17:31:12] Obtained from https://github.com/tseemann/snippy [17:31:12] Detected operating system: linux [17:31:12] Enabling bundled linux tools. [17:31:12] Found bwa - /usr/bin/bwa [17:31:12] Found bcftools - /usr/bin/bcftools [17:31:12] Found samtools - /usr/bin/samtools [17:31:12] Found java - /usr/bin/java [17:31:12] Found snpEff - /usr/bin/snpEff [17:31:12] Found samclip - /usr/bin/samclip [17:31:12] Found seqtk - /usr/bin/seqtk [17:31:12] Found parallel - /usr/bin/parallel [17:31:12] Found freebayes - /usr/bin/freebayes [17:31:12] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [17:31:12] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [17:31:12] Found vcfstreamsort - /usr/bin/vcfstreamsort [17:31:12] Found vcfuniq - /usr/bin/vcfuniq [17:31:12] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [17:31:12] Found gzip - /usr/bin/gzip [17:31:12] Found vt - /usr/bin/vt [17:31:12] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [17:31:12] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [17:31:12] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [17:31:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [17:31:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [17:31:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [17:31:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [17:31:13] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [17:31:13] Treating reference as 'fasta' format. [17:31:13] Will use 2 CPU cores. [17:31:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq [17:31:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq [17:31:13] Used --force, will overwrite existing S2 [17:31:13] Changing working directory: S2 [17:31:13] Creating reference folder: reference [17:31:13] Extracting FASTA and GFF from reference. [17:31:13] Wrote 3 sequences to ref.fa [17:31:13] Wrote 0 features to ref.gff [17:31:13] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [17:31:13] Using BAM RG (Read Group) ID: S2 [17:31:13] Running: samtools faidx reference/ref.fa 2>> snps.log [17:31:13] Running: bwa index reference/ref.fa 2>> snps.log [17:31:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [17:31:13] Running: ln -sf reference/ref.fa . 2>> snps.log [17:31:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [17:31:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [17:31:13] 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 1.375 CPU sec, 0.690 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: 0.840 sec; CPU: 1.441 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. [17:31:14] Running: samtools index snps.bam 2>> snps.log [17:31:14] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [17:31:14] 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 [17:31:16] 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 [17:31:16] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [17:31:16] 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 [17:31:16] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [17:31:16] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [17:31:16] Running: bcftools index -f snps.vcf.gz 2>> snps.log [17:31:16] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [17:31:16] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [17:31:16] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [17:31:16] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [17:31:16] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [17:31:16] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [17:31:16] Marked 841 heterozygous sites with 'n' [17:31:16] Creating extra output files: BED GFF CSV TXT HTML [17:31:16] Identified 246 variants. [17:31:16] Result folder: S2 [17:31:16] Result files: [17:31:16] * S2/snps.aligned.fa [17:31:16] * S2/snps.bam [17:31:16] * S2/snps.bam.bai [17:31:16] * S2/snps.bed [17:31:16] * S2/snps.consensus.fa [17:31:16] * S2/snps.consensus.subs.fa [17:31:16] * S2/snps.csv [17:31:16] * S2/snps.filt.vcf [17:31:16] * S2/snps.gff [17:31:16] * S2/snps.html [17:31:16] * S2/snps.log [17:31:16] * S2/snps.raw.vcf [17:31:16] * S2/snps.subs.vcf [17:31:16] * S2/snps.tab [17:31:16] * S2/snps.txt [17:31:16] * S2/snps.vcf [17:31:16] * S2/snps.vcf.gz [17:31:16] * S2/snps.vcf.gz.csi [17:31:16] Walltime used: 4 seconds [17:31:16] Wishing you a life free of homopolymer errors. [17:31:16] 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 [17:31:17] This is snippy 4.6.0 [17:31:17] Written by Torsten Seemann [17:31:17] Obtained from https://github.com/tseemann/snippy [17:31:17] Detected operating system: linux [17:31:17] Enabling bundled linux tools. [17:31:17] Found bwa - /usr/bin/bwa [17:31:17] Found bcftools - /usr/bin/bcftools [17:31:17] Found samtools - /usr/bin/samtools [17:31:17] Found java - /usr/bin/java [17:31:17] Found snpEff - /usr/bin/snpEff [17:31:17] Found samclip - /usr/bin/samclip [17:31:17] Found seqtk - /usr/bin/seqtk [17:31:17] Found parallel - /usr/bin/parallel [17:31:17] Found freebayes - /usr/bin/freebayes [17:31:17] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [17:31:17] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [17:31:17] Found vcfstreamsort - /usr/bin/vcfstreamsort [17:31:17] Found vcfuniq - /usr/bin/vcfuniq [17:31:17] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [17:31:17] Found gzip - /usr/bin/gzip [17:31:17] Found vt - /usr/bin/vt [17:31:17] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [17:31:17] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [17:31:17] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [17:31:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [17:31:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [17:31:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [17:31:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [17:31:17] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [17:31:17] Treating reference as 'fasta' format. [17:31:17] Will use 2 CPU cores. [17:31:17] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq [17:31:17] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq [17:31:17] Used --force, will overwrite existing S3 [17:31:17] Changing working directory: S3 [17:31:17] Creating reference folder: reference [17:31:17] Extracting FASTA and GFF from reference. [17:31:17] Wrote 3 sequences to ref.fa [17:31:17] Wrote 0 features to ref.gff [17:31:17] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [17:31:17] Using BAM RG (Read Group) ID: S3 [17:31:17] Running: samtools faidx reference/ref.fa 2>> snps.log [17:31:17] Running: bwa index reference/ref.fa 2>> snps.log [17:31:17] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [17:31:17] Running: ln -sf reference/ref.fa . 2>> snps.log [17:31:17] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [17:31:17] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [17:31:17] 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 1.467 CPU sec, 0.737 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: 0.890 sec; CPU: 1.533 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. [17:31:19] Running: samtools index snps.bam 2>> snps.log [17:31:19] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [17:31:19] 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 [17:31:20] 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 [17:31:20] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [17:31:20] 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 [17:31:20] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [17:31:20] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [17:31:20] Running: bcftools index -f snps.vcf.gz 2>> snps.log [17:31:20] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [17:31:20] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [17:31:20] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [17:31:20] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [17:31:20] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [17:31:21] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [17:31:21] Marked 846 heterozygous sites with 'n' [17:31:21] Creating extra output files: BED GFF CSV TXT HTML [17:31:21] Identified 254 variants. [17:31:21] Result folder: S3 [17:31:21] Result files: [17:31:21] * S3/snps.aligned.fa [17:31:21] * S3/snps.bam [17:31:21] * S3/snps.bam.bai [17:31:21] * S3/snps.bed [17:31:21] * S3/snps.consensus.fa [17:31:21] * S3/snps.consensus.subs.fa [17:31:21] * S3/snps.csv [17:31:21] * S3/snps.filt.vcf [17:31:21] * S3/snps.gff [17:31:21] * S3/snps.html [17:31:21] * S3/snps.log [17:31:21] * S3/snps.raw.vcf [17:31:21] * S3/snps.subs.vcf [17:31:21] * S3/snps.tab [17:31:21] * S3/snps.txt [17:31:21] * S3/snps.vcf [17:31:21] * S3/snps.vcf.gz [17:31:21] * S3/snps.vcf.gz.csi [17:31:21] Walltime used: 4 seconds [17:31:21] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md [17:31:21] 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 [17:31:21] This is snippy 4.6.0 [17:31:21] Written by Torsten Seemann [17:31:21] Obtained from https://github.com/tseemann/snippy [17:31:21] Detected operating system: linux [17:31:21] Enabling bundled linux tools. [17:31:21] Found bwa - /usr/bin/bwa [17:31:21] Found bcftools - /usr/bin/bcftools [17:31:21] Found samtools - /usr/bin/samtools [17:31:21] Found java - /usr/bin/java [17:31:21] Found snpEff - /usr/bin/snpEff [17:31:21] Found samclip - /usr/bin/samclip [17:31:21] Found seqtk - /usr/bin/seqtk [17:31:21] Found parallel - /usr/bin/parallel [17:31:21] Found freebayes - /usr/bin/freebayes [17:31:21] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [17:31:21] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [17:31:21] Found vcfstreamsort - /usr/bin/vcfstreamsort [17:31:21] Found vcfuniq - /usr/bin/vcfuniq [17:31:21] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [17:31:21] Found gzip - /usr/bin/gzip [17:31:21] Found vt - /usr/bin/vt [17:31:21] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [17:31:21] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report [17:31:21] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [17:31:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [17:31:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [17:31:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [17:31:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [17:31:21] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna [17:31:21] Treating reference as 'fasta' format. [17:31:21] Will use 2 CPU cores. [17:31:21] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq [17:31:21] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq [17:31:21] Used --force, will overwrite existing S4 [17:31:21] Changing working directory: S4 [17:31:21] Creating reference folder: reference [17:31:21] Extracting FASTA and GFF from reference. [17:31:21] Wrote 3 sequences to ref.fa [17:31:21] Wrote 0 features to ref.gff [17:31:21] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [17:31:21] Using BAM RG (Read Group) ID: S4 [17:31:21] Running: samtools faidx reference/ref.fa 2>> snps.log [17:31:21] Running: bwa index reference/ref.fa 2>> snps.log [17:31:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [17:31:22] Running: ln -sf reference/ref.fa . 2>> snps.log [17:31:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [17:31:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [17:31:22] 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 1.478 CPU sec, 0.742 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: 0.841 sec; CPU: 1.543 sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. [17:31:23] Running: samtools index snps.bam 2>> snps.log [17:31:23] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [17:31:23] 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 [17:31:25] 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 [17:31:25] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [17:31:25] 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 [17:31:25] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [17:31:25] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [17:31:25] Running: bcftools index -f snps.vcf.gz 2>> snps.log [17:31:25] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [17:31:25] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [17:31:25] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [17:31:25] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [17:31:25] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [17:31:25] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [17:31:25] Marked 799 heterozygous sites with 'n' [17:31:25] Creating extra output files: BED GFF CSV TXT HTML [17:31:25] Identified 257 variants. [17:31:25] Result folder: S4 [17:31:25] Result files: [17:31:25] * S4/snps.aligned.fa [17:31:25] * S4/snps.bam [17:31:25] * S4/snps.bam.bai [17:31:25] * S4/snps.bed [17:31:25] * S4/snps.consensus.fa [17:31:25] * S4/snps.consensus.subs.fa [17:31:25] * S4/snps.csv [17:31:25] * S4/snps.filt.vcf [17:31:25] * S4/snps.gff [17:31:25] * S4/snps.html [17:31:25] * S4/snps.log [17:31:25] * S4/snps.raw.vcf [17:31:25] * S4/snps.subs.vcf [17:31:25] * S4/snps.tab [17:31:25] * S4/snps.txt [17:31:25] * S4/snps.vcf [17:31:25] * S4/snps.vcf.gz [17:31:25] * S4/snps.vcf.gz.csi [17:31:25] Walltime used: 4 seconds [17:31:25] Questionable SNP? Try the --report option to see the alignments. [17:31:25] 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 The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md 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 The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md 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_arm64.buildinfo dpkg-genchanges --build=binary -O../snippy_4.6.0+dfsg-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/17200/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/17200/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/17200 and its subdirectories I: Current time: Tue Feb 3 17:31:31 +14 2026 I: pbuilder-time-stamp: 1770089491