I: pbuilder: network access will be disabled during build
I: Current time: Fri Feb 28 09:04:25 +14 2025
I: pbuilder-time-stamp: 1740683065
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/4002399/tmp/hooks/D01_modify_environment starting
debug: Running on ionos11-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb 27 19:04 /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/4002399/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/4002399/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=amd64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=x86_64
  HOST_ARCH=amd64
  IFS=' 	
  '
  INVOCATION_ID=a89a1eb191db499bbbcded63464b2e95
  LANG=C
  LANGUAGE=et_EE:et
  LC_ALL=C
  MACHTYPE=x86_64-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=4002399
  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.uQjFAbFN/pbuilderrc_3Bn4 --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.uQjFAbFN/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc'
  SUDO_GID=111
  SUDO_UID=106
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://46.16.76.132:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/4002399/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), 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 ... 19779 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on any2fasta; however:
  Package any2fasta is not installed.
 pbuilder-satisfydepends-dummy depends on bcftools; however:
  Package bcftools is not installed.
 pbuilder-satisfydepends-dummy depends on bedtools; however:
  Package bedtools is not installed.
 pbuilder-satisfydepends-dummy depends on bwa; however:
  Package bwa is not installed.
 pbuilder-satisfydepends-dummy depends on freebayes; however:
  Package freebayes is not installed.
 pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however:
  Package libbio-perl-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libvcflib-tools; however:
  Package libvcflib-tools is not installed.
 pbuilder-satisfydepends-dummy depends on minimap2; however:
  Package minimap2 is not installed.
 pbuilder-satisfydepends-dummy depends on parallel; however:
  Package parallel is not installed.
 pbuilder-satisfydepends-dummy depends on samtools; however:
  Package samtools is not installed.
 pbuilder-satisfydepends-dummy depends on samclip; however:
  Package samclip is not installed.
 pbuilder-satisfydepends-dummy depends on seqtk; however:
  Package seqtk is not installed.
 pbuilder-satisfydepends-dummy depends on snp-sites; however:
  Package snp-sites is not installed.
 pbuilder-satisfydepends-dummy depends on snpeff; however:
  Package snpeff is not installed.
 pbuilder-satisfydepends-dummy depends on vt; however:
  Package vt is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  adwaita-icon-theme{a} ant{a} ant-optional{a} any2fasta{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bedtools{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} freebayes{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapfloat-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbio-perl-perl{a} libbiojava6-java{a} libblas3{a} libbrotli1{a} libcairo-gobject2{a} libcairo2{a} libcdi-api-java{a} libcharts4j-java{a} libciftools-java{a} libcloudproviders0{a} libcodemodel-java{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcups2t64{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-stag-perl{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdisorder0{a} libdistlib-java{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} 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} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libice6{a} libicu72{a} libidn2-0{a} libinchi1.07{a} libio-string-perl{a} libistack-commons-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjson-java{a} libjson-simple-java{a} libjsoncpp26{a} libjsoup-java{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} liblog4j1.2-java{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-jar-plugin-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmmtf-java{a} libmsgpack-java{a} libnaga-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib2{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsmithwaterman0{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsnp-sites1{a} libsnpeff-java{a} libssh2-1t64{a} libssw0{a} libstax-ex-java{a} libstreambuffer-java{a} libsystemd-shared{a} libtabixpp0t64{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtrove3-java{a} libtxw2-java{a} libuchardet0{a} libunistring5{a} libunivocity-parsers-java{a} libvcflib-tools{a} libvcflib2{a} libvecmath-java{a} libvulkan1{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwfa2-0{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxom-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxss1{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} littler{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} minimap2{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} parallel{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} samclip{a} samtools{a} sensible-utils{a} seqtk{a} shared-mime-info{a} snp-sites{a} snpeff{a} sysstat{a} systemd{a} systemd-sysv{a} tzdata{a} ucf{a} unzip{a} vt{a} x11-common{a} xdg-utils{a} xkb-data{a} zip{a} 
The following packages are RECOMMENDED but will NOT be installed:
  alsa-topology-conf alsa-ucm-conf at-spi2-core bioperl-run chrony curl fonts-dejavu-extra krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libatk-wrapper-java-jni libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libfile-mimeinfo-perl libgd-perl libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libgtk-3-bin libhtml-parser-perl libhtml-tableextract-perl libjansi-java libkmod2 libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libnet-dbus-perl libnss-systemd libpostscript-perl librsvg2-common libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libx11-protocol-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl linux-sysctl-defaults lynx mesa-vulkan-drivers ntpsec openntpd perl-tk psmisc publicsuffix python3-gffutils python3-matplotlib r-base-dev r-cran-abind r-cran-bench r-cran-bit64 r-cran-blob r-cran-brio r-cran-callr r-cran-covr r-cran-crayon r-cran-dbi r-cran-diagrammer r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-evaluate r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-here r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lobstr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-multcomp r-cran-mvtnorm r-cran-nanotime r-cran-palmerpenguins r-cran-pkgbuild r-cran-pkgdown r-cran-pkgload r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-purrr r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-survival r-cran-svglite r-cran-testthat r-cran-tidyr r-cran-tidyverse r-cran-unitizer r-cran-units r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended systemd-cryptsetup systemd-timesyncd wget x11-utils x11-xserver-utils xdg-user-dirs 
0 packages upgraded, 416 newly installed, 0 to remove and 0 not upgraded.
Need to get 326 MB of archives. After unpacking 963 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 257.3-1 [2138 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 4.1.0~beta5-2+b1 [43.7 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 systemd amd64 257.3-1 [3092 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 257.3-1 [61.4 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.16.0-1 [70.5 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-1 [28.1 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 257.3-1 [293 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 42 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0050 [42.7 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.4-1 [1512 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.17.5+ds-3 [51.5 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 48~beta-3 [504 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B]
Get: 62 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.108-1 [1393 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B]
Get: 68 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.15-1 [2163 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 ant-optional all 1.10.15-1 [456 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 any2fasta all 0.4.2-2 [6232 B]
Get: 71 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.55.2-1 [170 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.21-1 [784 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.55.2-1 [51.4 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.55.2-1 [77.0 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.55.2-1 [68.1 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-16 [112 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB]
Get: 147 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB]
Get: 148 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB]
Get: 149 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 150 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 151 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get: 152 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2 [463 kB]
Get: 153 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 154 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 155 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 156 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB]
Get: 157 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB]
Get: 158 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB]
Get: 159 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.1-3 [26.8 kB]
Get: 160 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.1-3 [11.9 kB]
Get: 161 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.1-3 [5860 B]
Get: 162 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB]
Get: 163 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB]
Get: 164 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB]
Get: 165 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB]
Get: 166 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB]
Get: 167 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB]
Get: 168 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB]
Get: 169 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB]
Get: 170 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.48-4 [4873 kB]
Get: 171 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.48-4 [2767 kB]
Get: 172 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB]
Get: 173 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B]
Get: 174 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB]
Get: 175 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB]
Get: 176 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB]
Get: 177 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB]
Get: 178 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB]
Get: 179 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB]
Get: 180 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB]
Get: 181 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB]
Get: 182 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB]
Get: 183 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB]
Get: 184 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB]
Get: 185 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 186 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB]
Get: 187 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get: 188 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB]
Get: 189 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB]
Get: 190 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB]
Get: 191 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B]
Get: 192 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 25.0.0-1 [9620 kB]
Get: 193 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB]
Get: 194 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 25.0.0-1 [43.9 kB]
Get: 195 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB]
Get: 196 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 25.0.0-1 [45.5 kB]
Get: 197 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 25.0.0-1 [142 kB]
Get: 198 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.13-1 [21.1 kB]
Get: 201 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB]
Get: 202 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB]
Get: 203 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 204 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB]
Get: 205 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [205 kB]
Get: 206 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B]
Get: 207 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB]
Get: 208 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 209 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB]
Get: 210 http://deb.debian.org/debian unstable/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b3 [172 kB]
Get: 211 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB]
Get: 212 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B]
Get: 213 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB]
Get: 214 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB]
Get: 215 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4+b2 [60.9 kB]
Get: 216 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.12+dfsg-1 [233 kB]
Get: 217 http://deb.debian.org/debian unstable/main amd64 freebayes amd64 1.3.9-1 [1523 kB]
Get: 218 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB]
Get: 219 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-5 [350 kB]
Get: 220 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B]
Get: 221 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B]
Get: 222 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get: 223 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB]
Get: 224 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get: 225 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.3-1 [2459 kB]
Get: 226 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 227 http://deb.debian.org/debian unstable/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB]
Get: 228 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get: 229 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B]
Get: 230 http://deb.debian.org/debian unstable/main amd64 libapfloat-java all 1.14.0-2 [725 kB]
Get: 231 http://deb.debian.org/debian unstable/main amd64 libargs4j-java all 2.33-2 [138 kB]
Get: 232 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7.1-1 [391 kB]
Get: 233 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B]
Get: 234 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get: 235 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB]
Get: 236 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 237 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 238 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get: 239 http://deb.debian.org/debian unstable/main amd64 libciftools-java all 6.0.0-1 [2211 kB]
Get: 240 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 241 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB]
Get: 242 http://deb.debian.org/debian unstable/main amd64 libcommons-math-java all 2.2-9 [933 kB]
Get: 243 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 244 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB]
Get: 245 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB]
Get: 246 http://deb.debian.org/debian unstable/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB]
Get: 247 http://deb.debian.org/debian unstable/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB]
Get: 248 http://deb.debian.org/debian unstable/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB]
Get: 249 http://deb.debian.org/debian unstable/main amd64 libjackson2-databind-java all 2.14.0+ds-1 [1532 kB]
Get: 250 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 251 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-5 [214 kB]
Get: 252 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB]
Get: 253 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.18.0-1 [509 kB]
Get: 254 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 255 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB]
Get: 256 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get: 257 http://deb.debian.org/debian unstable/main amd64 libguice-java all 5.1.0-1 [932 kB]
Get: 258 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 43-2 [6252 B]
Get: 259 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB]
Get: 260 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 261 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 262 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB]
Get: 263 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 264 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 265 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 266 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB]
Get: 267 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 268 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B]
Get: 269 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-4 [55.3 kB]
Get: 270 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB]
Get: 271 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB]
Get: 272 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB]
Get: 273 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 274 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB]
Get: 275 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB]
Get: 276 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 277 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB]
Get: 278 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B]
Get: 279 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB]
Get: 280 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB]
Get: 281 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 282 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 283 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 284 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 285 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 286 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get: 287 http://deb.debian.org/debian unstable/main amd64 libistack-commons-java all 3.0.6-5 [145 kB]
Get: 288 http://deb.debian.org/debian unstable/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB]
Get: 289 http://deb.debian.org/debian unstable/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB]
Get: 290 http://deb.debian.org/debian unstable/main amd64 librngom-java all 2.3.0.1-11 [292 kB]
Get: 291 http://deb.debian.org/debian unstable/main amd64 libxsom-java all 2.3.0.1-11 [401 kB]
Get: 292 http://deb.debian.org/debian unstable/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB]
Get: 293 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 294 http://deb.debian.org/debian unstable/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB]
Get: 295 http://deb.debian.org/debian unstable/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB]
Get: 296 http://deb.debian.org/debian unstable/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB]
Get: 297 http://deb.debian.org/debian unstable/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB]
Get: 298 http://deb.debian.org/debian unstable/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB]
Get: 299 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB]
Get: 300 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get: 301 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.12.0-1 [222 kB]
Get: 302 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB]
Get: 303 http://deb.debian.org/debian unstable/main amd64 libjheaps-java all 0.14-2 [144 kB]
Get: 304 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get: 305 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 306 http://deb.debian.org/debian unstable/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB]
Get: 307 http://deb.debian.org/debian unstable/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB]
Get: 308 http://deb.debian.org/debian unstable/main amd64 libinchi1.07 amd64 1.07.3+dfsg-1 [557 kB]
Get: 309 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B]
Get: 310 http://deb.debian.org/debian unstable/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get: 311 http://deb.debian.org/debian unstable/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB]
Get: 312 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B]
Get: 313 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 314 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-9 [132 kB]
Get: 315 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 316 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB]
Get: 317 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get: 318 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
Get: 319 http://deb.debian.org/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB]
Get: 320 http://deb.debian.org/debian unstable/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB]
Get: 321 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB]
Get: 322 http://deb.debian.org/debian unstable/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB]
Get: 323 http://deb.debian.org/debian unstable/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB]
Get: 324 http://deb.debian.org/debian unstable/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB]
Get: 325 http://deb.debian.org/debian unstable/main amd64 libmsgpack-java all 0.9.6-1 [161 kB]
Get: 326 http://deb.debian.org/debian unstable/main amd64 libmmtf-java all 1.0.11-1 [187 kB]
Get: 327 http://deb.debian.org/debian unstable/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB]
Get: 328 http://deb.debian.org/debian unstable/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB]
Get: 329 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 330 http://deb.debian.org/debian unstable/main amd64 libcharts4j-java all 1.3-4 [162 kB]
Get: 331 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get: 332 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB]
Get: 333 http://deb.debian.org/debian unstable/main amd64 libcommons-collections4-java all 4.4-2 [682 kB]
Get: 334 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 335 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB]
Get: 336 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 337 http://deb.debian.org/debian unstable/main amd64 libdistlib-java all 1.0-5 [72.5 kB]
Get: 338 http://deb.debian.org/debian unstable/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB]
Get: 339 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB]
Get: 340 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 341 http://deb.debian.org/debian unstable/main amd64 libxom-java all 1.3.9-1 [174 kB]
Get: 342 http://deb.debian.org/debian unstable/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB]
Get: 343 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB]
Get: 344 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB]
Get: 345 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB]
Get: 346 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB]
Get: 347 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB]
Get: 348 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b2 [156 kB]
Get: 349 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b2 [25.9 kB]
Get: 350 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.0.9+dfsg-7+b2 [112 kB]
Get: 351 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.15-1 [1382 kB]
Get: 352 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB]
Get: 353 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get: 354 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 355 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-1 [105 kB]
Get: 356 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB]
Get: 357 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB]
Get: 358 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB]
Get: 359 http://deb.debian.org/debian unstable/main amd64 libsnp-sites1 amd64 2.5.1-2+b2 [14.8 kB]
Get: 360 http://deb.debian.org/debian unstable/main amd64 libtrove3-java all 3.0.3-5 [2146 kB]
Get: 361 http://deb.debian.org/debian unstable/main amd64 libsnpeff-java all 5.2.f+dfsg-1 [2156 kB]
Get: 362 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get: 363 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 364 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get: 365 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB]
Get: 366 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get: 367 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get: 368 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB]
Get: 369 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 370 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 371 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB]
Get: 372 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB]
Get: 373 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB]
Get: 374 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-2 [16.0 kB]
Get: 375 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB]
Get: 376 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB]
Get: 377 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
Get: 378 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB]
Get: 379 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB]
Get: 380 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.5-1 [1712 kB]
Get: 381 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
Get: 382 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB]
Get: 383 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB]
Get: 384 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB]
Get: 385 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB]
Get: 386 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.167-1 [2331 kB]
Get: 387 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-2-1 [4155 kB]
Get: 388 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB]
Get: 389 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB]
Get: 390 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB]
Get: 391 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB]
Get: 392 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB]
Get: 393 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.6.1-1 [106 kB]
Get: 394 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get: 395 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB]
Get: 396 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB]
Get: 397 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB]
Get: 398 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB]
Get: 399 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB]
Get: 400 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB]
Get: 401 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
Get: 402 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get: 403 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB]
Get: 404 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB]
Get: 405 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB]
Get: 406 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB]
Get: 407 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.12+dfsg-1 [608 kB]
Get: 408 http://deb.debian.org/debian unstable/main amd64 minimap2 amd64 2.27+dfsg-1+b3 [391 kB]
Get: 409 http://deb.debian.org/debian unstable/main amd64 sysstat amd64 12.7.5-2 [623 kB]
Get: 410 http://deb.debian.org/debian unstable/main amd64 parallel all 20240222+ds-2 [2163 kB]
Get: 411 http://deb.debian.org/debian unstable/main amd64 samclip all 0.4.0-4 [20.1 kB]
Get: 412 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.21-1 [667 kB]
Get: 413 http://deb.debian.org/debian unstable/main amd64 seqtk amd64 1.4-2 [34.6 kB]
Get: 414 http://deb.debian.org/debian unstable/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB]
Get: 415 http://deb.debian.org/debian unstable/main amd64 snpeff all 5.2.f+dfsg-1 [7244 B]
Get: 416 http://deb.debian.org/debian unstable/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB]
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Setting up libbrotli1:amd64 (1.1.0-2+b7) ...
Setting up libedit2:amd64 (3.1-20250104-1) ...
Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ...
Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up libpicocli-java (4.6.2-2) ...
Setting up libasm-java (9.7.1-1) ...
Setting up x11-common (1:7.7+24) ...
Running in chroot, ignoring request.

Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libsensors-config (1:3.6.0-10) ...
Setting up libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12+b2) ...
Setting up libnghttp2-14:amd64 (1.64.0-1) ...
Setting up libdeflate0:amd64 (1.23-1+b1) ...
Setting up liblog4j1.2-java (1.2.17-11) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up xkb-data (2.42-1) ...
Setting up libplexus-component-annotations-java (2.1.1-1) ...
Setting up any2fasta (0.4.2-2) ...
Setting up libantlr4-runtime-java (4.9.2-3) ...
Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ...
Setting up libcom-err2:amd64 (1.47.2-1) ...
Setting up file (1:5.45-3+b1) ...
Setting up libjson-simple-java (2.3.0-2) ...
Setting up libunivocity-parsers-java (2.9.1-1) ...
Setting up libtext-wrapi18n-perl (0.06-10) ...
Setting up libfml0:amd64 (0.1+git20221215.85f159e-1) ...
Setting up libfastahack0:amd64 (1.0.0+dfsg-11+b2) ...
Setting up libjbig0:amd64 (2.1-6.1+b2) ...
Setting up samclip (0.4.0-4) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up libsnappy1v5:amd64 (1.2.1-1+b1) ...
Setting up libcharts4j-java (1.3-4) ...
Setting up libkrb5support0:amd64 (1.21.3-4) ...
Setting up libexec-maven-plugin-java (3.1.0-2) ...
Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ...
Setting up tzdata (2025a-2) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Thu Feb 27 19:07:58 UTC 2025.
Universal Time is now:  Thu Feb 27 19:07:58 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up libxcb-present0:amd64 (1.17.0-2+b1) ...
Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ...
Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ...
Setting up libcommons-collections3-java (3.2.2-3) ...
Setting up libasound2-data (1.2.13-1) ...
Setting up libio-string-perl (1.08-4) ...
Setting up zip (3.0-14) ...
Setting up librhino-java (1.7.15-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:amd64 (4.13.3-1) ...
Setting up libblas3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libasound2t64:amd64 (1.2.13-1+b1) ...
Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ...
Setting up libjaxen-java (1.1.6-5) ...
Setting up libapiguardian-java (1.1.2-1) ...
Setting up libx11-data (2:1.8.10-2) ...
Setting up libepoxy0:amd64 (1.5.10-2) ...
Setting up libnspr4:amd64 (2:4.36-1) ...
Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ...
Setting up libjsoncpp26:amd64 (1.9.6-3) ...
Setting up libapache-pom-java (33-2) ...
Setting up libavahi-common-data:amd64 (0.8-16) ...
Setting up libncurses6:amd64 (6.5+20250216-1) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-6) ...
Setting up libdbus-1-3:amd64 (1.16.0-1) ...
Setting up libfribidi0:amd64 (1.0.16-1) ...
Setting up libproc2-0:amd64 (2:4.0.4-7) ...
Setting up libplexus-interpolation-java (1.27-1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libitext5-java (5.5.13.3-4) ...
Setting up libpng16-16t64:amd64 (1.6.47-1) ...
Setting up libxml-commons-resolver1.1-java (1.2-11) ...
Setting up libxz-java (1.9-1) ...
Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libpcsclite1:amd64 (2.3.1-1) ...
Setting up libsensors5:amd64 (1:3.6.0-10+b1) ...
Setting up libk5crypto3:amd64 (1.21.3-4) ...
Setting up libactivation-java (1.2.0-2) ...
Setting up libhamcrest-java (2.2-2) ...
Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ...
Setting up libgfortran5:amd64 (14.2.0-17) ...
Setting up libvulkan1:amd64 (1.4.304.0-1) ...
Setting up autoconf (2.72-3) ...
Setting up libnghttp3-9:amd64 (1.6.0-2) ...
Setting up libapfloat-java (1.14.0-2) ...
Setting up libwebp7:amd64 (1.5.0-0.1) ...
Setting up libgif7:amd64 (5.2.2-1+b1) ...
Setting up libffi8:amd64 (3.4.7-1) ...
Setting up libtrove3-java (3.0.3-5) ...
Setting up dwz (0.15-1+b1) ...
Setting up libdata-stag-perl (0.14-3) ...
Setting up libfreemarker-java (2.3.32-2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libxshmfence1:amd64 (1.3-1+b3) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.55.2-1) ...
Setting up libcommons-math-java (2.2-9) ...
Setting up libtiff6:amd64 (4.5.1+git230720-5) ...
Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ...
Setting up dbus-session-bus-common (1.16.0-1) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libxml-commons-external-java (1.4.01-6) ...
Setting up procps (2:4.0.4-7) ...
Setting up libxbean-reflect-java (4.5-9) ...
Setting up libopentest4j-java (1.2.0-4) ...
Setting up libtasn1-6:amd64 (4.20.0-2) ...
Setting up libjackson2-core-java (2.14.1-1) ...
Setting up libx11-6:amd64 (2:1.8.10-2) ...
Setting up ncbi-vdb-data (3.0.9+dfsg-2) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...
Setting up libsnp-sites1:amd64 (2.5.1-2+b2) ...
Setting up libngtcp2-16:amd64 (1.9.1-1) ...
Setting up libcommons-math3-java (3.6.1-4) ...
Setting up libkrb5-3:amd64 (1.21.3-4) ...
Setting up libwayland-egl1:amd64 (1.23.1-3) ...
Setting up libbio-perl-perl (1.7.8-1) ...
Setting up libmbedcrypto16:amd64 (3.6.2-3) ...
Setting up libpaper2:amd64 (2.2.5-0.3+b1) ...
Setting up libssh2-1t64:amd64 (1.11.1-1) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up dbus-system-bus-common (1.16.0-1) ...
warn: The home dir /nonexistent you specified can't be accessed: No such file or directory

useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
Setting up librelaxng-datatype-java (1.0+ds1-4) ...
Setting up openssl (3.4.1-1) ...
Setting up libinchi1.07 (1.07.3+dfsg-1) ...
Setting up libdrm-common (2.4.123-1) ...
Setting up libcdi-api-java (1.2-4) ...
Setting up libsnappy-jni (1.1.10.7-1) ...
Setting up libezmorph-java (1.0.6-4) ...
Setting up libxcomposite1:amd64 (1:0.4.6-1) ...
Setting up libssw0:amd64 (1.1-15+b2) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up xdg-utils (1.2.1-2) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up bedtools (2.31.1+dfsg-2) ...
Setting up libldap2:amd64 (2.6.9+dfsg-1) ...
Setting up dbus-bin (1.16.0-1) ...
Setting up libargs4j-java (2.33-2) ...
Setting up libxkbcommon0:amd64 (1.7.0-2) ...
Setting up libnaga-java (3.0+svn80-5) ...
Setting up libwayland-client0:amd64 (1.23.1-3) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libdom4j-java (2.1.4-1) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libllvm19:amd64 (1:19.1.7-1+b1) ...
Setting up libwayland-server0:amd64 (1.23.1-3) ...
Setting up libx11-xcb1:amd64 (2:1.8.10-2) ...
Setting up libice6:amd64 (2:1.1.1-1) ...
Setting up liblapack3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up gettext (0.23.1-1) ...
Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ...
Setting up libplexus-languages-java (1.1.1-2) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ...
Setting up libtool (2.5.4-3) ...
Setting up fontconfig-config (2.15.0-2) ...
Setting up libstax-ex-java (1.7.8-3) ...
Setting up libmaven-parent-java (43-2) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:amd64 (0.8-16) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b3) ...
Setting up libsisu-inject-java (0.3.5-1) ...
Setting up libidn2-0:amd64 (2.3.7-2+b1) ...
Setting up libnss3:amd64 (2:3.108-1) ...
Setting up libciftools-java (6.0.0-1) ...
Setting up dbus-daemon (1.16.0-1) ...
Setting up libpaper-utils (2.2.5-0.3+b1) ...
Setting up libxom-java (1.3.9-1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libjackson2-databind-java (2.14.0+ds-1) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:amd64 (0.1.29-2+b1) ...
Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.5-1) ...
Setting up libglib2.0-0t64:amd64 (2.83.4-1) ...
Setting up libmbedx509-7:amd64 (3.6.2-3) ...
Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ...
Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ...
Setting up dbus (1.16.0-1) ...
Running in chroot, ignoring request.

invoke-rc.d: policy-rc.d denied execution of start.
Setting up shared-mime-info (2.4-5+b2) ...
Setting up libp11-kit0:amd64 (0.25.5-3) ...
Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ...
Setting up libstreambuffer-java (1.5.4-1.1) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ...
Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ...
Setting up libcommons-collections4-java (4.4-2) ...
Setting up ucf (3.0050) ...
Setting up libcommons-lang3-java (3.17.0-1) ...
Setting up libmbedtls21:amd64 (3.6.2-3) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up librngom-java (2.3.0.1-11) ...
Setting up libdrm2:amd64 (2.4.123-1) ...
Setting up libjni-inchi-jni (0.8+dfsg-8) ...
Setting up libjgraphx-java (2.1.0.7-5) ...
Setting up snp-sites (2.5.1-2+b2) ...
Setting up groff-base (1.23.0-7) ...
Setting up libwayland-cursor0:amd64 (1.23.1-3) ...
Setting up libpam-systemd:amd64 (257.3-1) ...
Setting up libcommons-beanutils-java (1.9.4-2) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ...
Setting up libsnappy-java (1.1.10.7-1) ...
Setting up libxss1:amd64 (1:1.2.3-1+b3) ...
Setting up libfontconfig1:amd64 (2.15.0-2) ...
Setting up libxsom-java (2.3.0.1-11) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libcommons-codec-java (1.17.1-1) ...
Setting up libsm6:amd64 (2:1.2.4-1) ...
Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ...
Setting up sysstat (12.7.5-2) ...
Creating config file /etc/default/sysstat with new version
update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode
Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-collect.timer' -> '/usr/lib/systemd/system/sysstat-collect.timer'.

Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-rotate.timer' -> '/usr/lib/systemd/system/sysstat-rotate.timer'.

Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-summary.timer' -> '/usr/lib/systemd/system/sysstat-summary.timer'.

Created symlink '/etc/systemd/system/multi-user.target.wants/sysstat.service' -> '/usr/lib/systemd/system/sysstat.service'.

Setting up libavahi-client3:amd64 (0.8-16) ...
Setting up libpython3-stdlib:amd64 (3.13.2-1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ...
Setting up libgnutls30t64:amd64 (3.8.9-2) ...
Setting up gtk-update-icon-cache (4.17.5+ds-3) ...
Setting up fontconfig (2.15.0-2) ...
Regenerating fonts cache... done.
Setting up libxft2:amd64 (2.3.6-1+b4) ...
Setting up libatk1.0-0t64:amd64 (2.55.2-1) ...
Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxi6:amd64 (2:1.8.2-1) ...
Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ...
Setting up python3.13 (3.13.2-1) ...
Setting up libcommons-io-java (2.18.0-1) ...
Setting up libxtst6:amd64 (2:1.2.5-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libtk8.6:amd64 (8.6.16-1) ...
Setting up libdistlib-java (1.0-5) ...
Setting up libxcursor1:amd64 (1:1.2.3-1) ...
Setting up libpango-1.0-0:amd64 (1.56.1-1) ...
Setting up libdrm-intel1:amd64 (2.4.123-1) ...
Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ...
Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ...
Setting up python3 (3.13.2-1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'.

Setting up libcairo2:amd64 (1.18.2-2) ...
Setting up libcolord2:amd64 (1.4.7-1+b2) ...
Setting up libdconf1:amd64 (0.40.0-5) ...
Setting up dbus-user-session (1.16.0-1) ...
Setting up libmaven-resolver-java (1.9.22-1) ...
Setting up adwaita-icon-theme (48~beta-3) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libatspi2.0-0t64:amd64 (2.55.2-1) ...
Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ...
Setting up parallel (20240222+ds-2) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libcairo-gobject2:amd64 (1.18.2-2) ...
Setting up libmaven-shared-utils-java (3.4.2-1) ...
Setting up libfastinfoset-java (1.2.12-4) ...
Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ...
Setting up libcups2t64:amd64 (2.4.10-2+b1) ...
Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ...
Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ...
Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b2) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.55.2-1) ...
Setting up mesa-libgallium:amd64 (25.0.0-1) ...
Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b2) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libcommons-compress-java (1.27.1-2) ...
Setting up libcurl4t64:amd64 (8.12.1-3) ...
Setting up libgbm1:amd64 (25.0.0-1) ...
Setting up libgl1-mesa-dri:amd64 (25.0.0-1) ...
Setting up libcurl3t64-gnutls:amd64 (8.12.1-3) ...
Setting up debhelper (13.24.1) ...
Setting up dconf-service (0.40.0-5) ...
Setting up r-base-core (4.4.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-labeling (0.4.3-1) ...
Setting up r-cran-lattice (0.22-6-1) ...
Setting up r-cran-nlme (3.1.167-1) ...
Setting up r-cran-farver (2.1.2-1) ...
Setting up r-cran-viridislite (0.4.2-2) ...
Setting up libhts3t64:amd64 (1.21+ds-1) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libngs-java:amd64 (3.0.9+dfsg-7+b2) ...
Setting up r-cran-r6 (2.6.1-1) ...
Setting up r-cran-pkgkitten (0.2.4-1) ...
Setting up r-cran-magrittr (2.0.3-1) ...
Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b3) ...
Setting up r-cran-littler (0.3.20-2) ...
Setting up r-cran-rcpp (1.0.14-1) ...
Setting up r-cran-rlang (1.1.5-1) ...
Setting up libglx-mesa0:amd64 (25.0.0-1) ...
Setting up r-cran-gridbase (0.4-7-5) ...
Setting up littler (0.3.20-2) ...
Setting up vt (0.57721+ds-3+b1) ...
Setting up libglx0:amd64 (1.7.0-1+b2) ...
Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ...
Setting up r-cran-withr (3.0.2+dfsg-1) ...
Setting up bcftools (1.21-1) ...
Setting up r-cran-fansi (1.0.5-1) ...
Setting up libmaven-archiver-java (3.6.2-1) ...
Setting up r-cran-mass (7.3-64-1) ...
Setting up r-cran-glue (1.8.0-1) ...
Setting up r-cran-cli (3.6.3-1) ...
Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
Setting up samtools (1.21-1) ...
Setting up r-cran-pkgconfig (2.0.3-2) ...
Setting up r-cran-utf8 (1.2.4-1) ...
Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
Setting up libgl1:amd64 (1.7.0-1+b2) ...
Setting up r-cran-plyr (1.8.9-1) ...
Setting up r-cran-rcolorbrewer (1.1-3-1) ...
Setting up r-cran-isoband (0.2.7-1) ...
Setting up r-cran-gtable (0.3.6+dfsg-1) ...
Setting up r-cran-matrix (1.7-2-1) ...
Setting up r-cran-mgcv (1.9-1-1) ...
Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ...
Setting up r-cran-vctrs (0.6.5-1) ...
Setting up libgtk-3-common (3.24.48-4) ...
Setting up r-cran-pillar (1.10.1+dfsg-1) ...
Setting up r-cran-munsell (0.5.1-1) ...
Setting up r-cran-tibble (3.2.1+dfsg-3) ...
Setting up libvcflib2:amd64 (1.0.12+dfsg-1) ...
Setting up libgtk-3-0t64:amd64 (3.24.48-4) ...
Setting up r-cran-scales (1.3.0-1) ...
Setting up freebayes (1.3.9-1) ...
Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
Setting up libvcflib-tools (1.0.12+dfsg-1) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libguava-java (32.0.1-1) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up libguice-java (5.1.0-1) ...
Setting up libmaven3-core-java (3.9.9-1) ...
Setting up libmaven-shared-incremental-java (1.1-6) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up libplexus-compiler-java (2.13.0-1) ...
Setting up libmaven-compiler-plugin-java (3.13.0-1) ...
Setting up libjni-inchi-java (0.8+dfsg-8) ...
Setting up libmaven-file-management-java (3.0.0-2) ...
Setting up libjmol-java (16.2.33+dfsg-1) ...
Setting up libmaven-jar-plugin-java (3.3.0-2) ...
Setting up libcommons-text-java (1.12.0-1) ...
Setting up libmsgpack-java (0.9.6-1) ...
Setting up libmmtf-java (1.0.11-1) ...
Setting up libjgrapht-java (1.5.2-1) ...
Processing triggers for libc-bin (2.40-7) ...
Processing triggers for systemd (257.3-1) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureSign_Root_CA12.pem
Adding debian:SecureSign_Root_CA14.pem
Adding debian:SecureSign_Root_CA15.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_CYBER_Root_CA.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up openjdk-21-jre:amd64 (21.0.6+7-1) ...
Setting up ant (1.10.15-1) ...
Setting up junit4 (4.13.2-5) ...
Setting up default-jre-headless (2:1.21-76) ...
Setting up default-jre (2:1.21-76) ...
Setting up ant-optional (1.10.15-1) ...
Setting up junit5 (5.10.3-1) ...
Setting up libjson-java (3.1.0+dfsg-2) ...
Setting up libhtsjdk-java (4.1.3+dfsg-2) ...
Setting up libistack-commons-java (3.0.6-5) ...
Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ...
Setting up libtxw2-java (2.3.0.1-11) ...
Setting up libjaxb-java (2.3.0.1-11) ...
Setting up libbiojava6-java (6.1.0+dfsg-5) ...
Setting up libsnpeff-java (5.2.f+dfsg-1) ...
Setting up snpeff (5.2.f+dfsg-1) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20240118) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/4002399/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/4002399/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 <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg'
cd test && /usr/bin/make
make[2]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg/test'
mkdir -p S1
wgsim -S 1 \
         -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
         example.fna S1/R1.fq S1/R2.fq > S1/dwgsim.tab
[wgsim] seed = 1
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 3 sequences, total length: 317336
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq
[09:08:23] This is snippy 4.6.0
[09:08:23] Written by Torsten Seemann
[09:08:23] Obtained from https://github.com/tseemann/snippy
[09:08:23] Detected operating system: linux
[09:08:23] Enabling bundled linux tools.
[09:08:23] Found bwa - /usr/bin/bwa
[09:08:23] Found bcftools - /usr/bin/bcftools
[09:08:23] Found samtools - /usr/bin/samtools
[09:08:23] Found java - /usr/bin/java
[09:08:23] Found snpEff - /usr/bin/snpEff
[09:08:23] Found samclip - /usr/bin/samclip
[09:08:23] Found seqtk - /usr/bin/seqtk
[09:08:23] Found parallel - /usr/bin/parallel
[09:08:23] Found freebayes - /usr/bin/freebayes
[09:08:23] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[09:08:23] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[09:08:23] Found vcfstreamsort - /usr/bin/vcfstreamsort
[09:08:23] Found vcfuniq - /usr/bin/vcfuniq
[09:08:23] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[09:08:23] Found gzip - /usr/bin/gzip
[09:08:23] Found vt - /usr/bin/vt
[09:08:23] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[09:08:23] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[09:08:23] Checking version: samtools --version is >= 1.7 - ok, have 1.21
[09:08:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
[09:08:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[09:08:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[09:08:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[09:08:23] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
[09:08:23] Treating reference as 'fasta' format.
[09:08:23] Will use 2 CPU cores.
[09:08:23] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq
[09:08:23] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq
[09:08:23] Used --force, will overwrite existing S1
[09:08:23] Changing working directory: S1
[09:08:23] Creating reference folder: reference
[09:08:23] Extracting FASTA and GFF from reference.
[09:08:23] Wrote 3 sequences to ref.fa
[09:08:23] Wrote 0 features to ref.gff
[09:08:23] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[09:08:23] Using BAM RG (Read Group) ID: S1
[09:08:23] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:08:23] Running: bwa index reference/ref.fa 2>> snps.log
[09:08:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:08:24] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:08:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:08:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:08:24] Running: bwa mem  -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11587, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 199, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 369)
[M::mem_pestat] mean and std.dev: (199.53, 48.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 437)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 2.470 CPU sec, 1.238 real sec
[main] Version: 0.7.18-r1243-dirty
[samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978
[samclip] Header contained 6 lines
[samclip] Done.
[main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq
[main] Real time: 1.406 sec; CPU: 2.533 sec
[09:08:25] Running: samtools index snps.bam 2>> snps.log
[09:08:25] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[09:08:26] 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
[09:08:27] 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

[09:08:27] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[09:08:27] 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
[09:08:28] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[09:08:28] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[09:08:28] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[09:08:28] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[09:08:28] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[09:08:28] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[09:08:28] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[09:08:28] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[09:08:28] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[09:08:28] Marked 749 heterozygous sites with 'n'
[09:08:28] Creating extra output files: BED GFF CSV TXT HTML
[09:08:28] Identified 261 variants.
[09:08:28] Result folder: S1
[09:08:28] Result files:
[09:08:28] * S1/snps.aligned.fa
[09:08:28] * S1/snps.bam
[09:08:28] * S1/snps.bam.bai
[09:08:28] * S1/snps.bed
[09:08:28] * S1/snps.consensus.fa
[09:08:28] * S1/snps.consensus.subs.fa
[09:08:28] * S1/snps.csv
[09:08:28] * S1/snps.filt.vcf
[09:08:28] * S1/snps.gff
[09:08:28] * S1/snps.html
[09:08:28] * S1/snps.log
[09:08:28] * S1/snps.raw.vcf
[09:08:28] * S1/snps.subs.vcf
[09:08:28] * S1/snps.tab
[09:08:28] * S1/snps.txt
[09:08:28] * S1/snps.vcf
[09:08:28] * S1/snps.vcf.gz
[09:08:28] * S1/snps.vcf.gz.csi
[09:08:28] Walltime used: 5 seconds
[09:08:28] Questionable SNP? Try the --report option to see the alignments.
[09:08:28] 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
[09:08:29] This is snippy 4.6.0
[09:08:29] Written by Torsten Seemann
[09:08:29] Obtained from https://github.com/tseemann/snippy
[09:08:29] Detected operating system: linux
[09:08:29] Enabling bundled linux tools.
[09:08:29] Found bwa - /usr/bin/bwa
[09:08:29] Found bcftools - /usr/bin/bcftools
[09:08:29] Found samtools - /usr/bin/samtools
[09:08:29] Found java - /usr/bin/java
[09:08:29] Found snpEff - /usr/bin/snpEff
[09:08:29] Found samclip - /usr/bin/samclip
[09:08:29] Found seqtk - /usr/bin/seqtk
[09:08:29] Found parallel - /usr/bin/parallel
[09:08:29] Found freebayes - /usr/bin/freebayes
[09:08:29] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[09:08:29] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[09:08:29] Found vcfstreamsort - /usr/bin/vcfstreamsort
[09:08:29] Found vcfuniq - /usr/bin/vcfuniq
[09:08:29] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[09:08:29] Found gzip - /usr/bin/gzip
[09:08:29] Found vt - /usr/bin/vt
[09:08:29] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[09:08:29] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[09:08:29] Checking version: samtools --version is >= 1.7 - ok, have 1.21
[09:08:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
[09:08:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[09:08:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[09:08:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[09:08:29] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
[09:08:29] Treating reference as 'fasta' format.
[09:08:29] Will use 2 CPU cores.
[09:08:29] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq
[09:08:29] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq
[09:08:29] Used --force, will overwrite existing S2
[09:08:29] Changing working directory: S2
[09:08:29] Creating reference folder: reference
[09:08:29] Extracting FASTA and GFF from reference.
[09:08:29] Wrote 3 sequences to ref.fa
[09:08:29] Wrote 0 features to ref.gff
[09:08:29] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[09:08:29] Using BAM RG (Read Group) ID: S2
[09:08:29] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:08:29] Running: bwa index reference/ref.fa 2>> snps.log
[09:08:29] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:08:29] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:08:29] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:08:29] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:08:29] Running: bwa mem  -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 199, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 366)
[M::mem_pestat] mean and std.dev: (199.27, 48.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 433)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 2.418 CPU sec, 1.217 real sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD:[samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987
[samclip] Header contained 6 lines
[samclip] Done.
 bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq
[main] Real time: 1.388 sec; CPU: 2.497 sec
[09:08:31] Running: samtools index snps.bam 2>> snps.log
[09:08:31] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[09:08:31] 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
[09:08:33] 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

[09:08:33] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[09:08:33] 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
[09:08:33] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[09:08:33] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[09:08:33] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[09:08:33] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[09:08:33] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[09:08:33] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[09:08:33] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[09:08:33] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[09:08:33] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[09:08:34] Marked 841 heterozygous sites with 'n'
[09:08:34] Creating extra output files: BED GFF CSV TXT HTML
[09:08:34] Identified 246 variants.
[09:08:34] Result folder: S2
[09:08:34] Result files:
[09:08:34] * S2/snps.aligned.fa
[09:08:34] * S2/snps.bam
[09:08:34] * S2/snps.bam.bai
[09:08:34] * S2/snps.bed
[09:08:34] * S2/snps.consensus.fa
[09:08:34] * S2/snps.consensus.subs.fa
[09:08:34] * S2/snps.csv
[09:08:34] * S2/snps.filt.vcf
[09:08:34] * S2/snps.gff
[09:08:34] * S2/snps.html
[09:08:34] * S2/snps.log
[09:08:34] * S2/snps.raw.vcf
[09:08:34] * S2/snps.subs.vcf
[09:08:34] * S2/snps.tab
[09:08:34] * S2/snps.txt
[09:08:34] * S2/snps.vcf
[09:08:34] * S2/snps.vcf.gz
[09:08:34] * S2/snps.vcf.gz.csi
[09:08:34] Walltime used: 5 seconds
[09:08:34] Wishing you a life free of homopolymer errors.
[09:08:34] 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
[09:08:34] This is snippy 4.6.0
[09:08:34] Written by Torsten Seemann
[09:08:34] Obtained from https://github.com/tseemann/snippy
[09:08:34] Detected operating system: linux
[09:08:34] Enabling bundled linux tools.
[09:08:34] Found bwa - /usr/bin/bwa
[09:08:34] Found bcftools - /usr/bin/bcftools
[09:08:34] Found samtools - /usr/bin/samtools
[09:08:34] Found java - /usr/bin/java
[09:08:34] Found snpEff - /usr/bin/snpEff
[09:08:34] Found samclip - /usr/bin/samclip
[09:08:34] Found seqtk - /usr/bin/seqtk
[09:08:34] Found parallel - /usr/bin/parallel
[09:08:34] Found freebayes - /usr/bin/freebayes
[09:08:34] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[09:08:34] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[09:08:34] Found vcfstreamsort - /usr/bin/vcfstreamsort
[09:08:34] Found vcfuniq - /usr/bin/vcfuniq
[09:08:34] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[09:08:34] Found gzip - /usr/bin/gzip
[09:08:34] Found vt - /usr/bin/vt
[09:08:34] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[09:08:34] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[09:08:35] Checking version: samtools --version is >= 1.7 - ok, have 1.21
[09:08:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
[09:08:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[09:08:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[09:08:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[09:08:35] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
[09:08:35] Treating reference as 'fasta' format.
[09:08:35] Will use 2 CPU cores.
[09:08:35] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq
[09:08:35] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq
[09:08:35] Used --force, will overwrite existing S3
[09:08:35] Changing working directory: S3
[09:08:35] Creating reference folder: reference
[09:08:35] Extracting FASTA and GFF from reference.
[09:08:35] Wrote 3 sequences to ref.fa
[09:08:35] Wrote 0 features to ref.gff
[09:08:35] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[09:08:35] Using BAM RG (Read Group) ID: S3
[09:08:35] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:08:35] Running: bwa index reference/ref.fa 2>> snps.log
[09:08:35] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:08:35] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:08:35] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:08:35] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:08:35] Running: bwa mem  -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368)
[M::mem_pestat] mean and std.dev: (198.46, 48.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 436)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 2.491 CPU sec, 1.248 real sec
[main] Version: 0.7.18-r1243-dirty
[samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970
[samclip] Header contained 6 lines
[samclip] Done.
[main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq
[main] Real time: 1.443 sec; CPU: 2.553 sec
[09:08:37] Running: samtools index snps.bam 2>> snps.log
[09:08:37] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[09:08:37] 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
[09:08:39] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
normalize v0.5

options:     input VCF file                                  -
         [o] output VCF file                                 -
         [w] sorting window size                             10000
         [m] no fail on masked reference inconsistency       false
         [n] no fail on reference inconsistency              false
         [q] quiet                                           false
         [d] debug                                           false
         [r] reference FASTA file                            reference/ref.fa


stats: biallelic
          no. left trimmed                      : 11
          no. right trimmed                     : 30
          no. left and right trimmed            : 1
          no. right trimmed and left aligned    : 0
          no. left aligned                      : 0

       total no. biallelic normalized           : 42

       multiallelic
          no. left trimmed                      : 0
          no. right trimmed                     : 0
          no. left and right trimmed            : 0
          no. right trimmed and left aligned    : 0
          no. left aligned                      : 0

       total no. multiallelic normalized        : 0

       total no. variants normalized            : 42
       total no. variants observed              : 254
       total no. reference observed             : 0

Time elapsed: 0.01s

[09:08:39] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[09:08:39] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[09:08:40] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[09:08:40] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[09:08:40] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[09:08:40] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[09:08:40] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[09:08:40] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[09:08:41] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[09:08:41] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[09:08:41] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[09:08:41] Marked 846 heterozygous sites with 'n'
[09:08:41] Creating extra output files: BED GFF CSV TXT HTML
[09:08:41] Identified 254 variants.
[09:08:41] Result folder: S3
[09:08:41] Result files:
[09:08:41] * S3/snps.aligned.fa
[09:08:41] * S3/snps.bam
[09:08:41] * S3/snps.bam.bai
[09:08:41] * S3/snps.bed
[09:08:41] * S3/snps.consensus.fa
[09:08:41] * S3/snps.consensus.subs.fa
[09:08:41] * S3/snps.csv
[09:08:41] * S3/snps.filt.vcf
[09:08:41] * S3/snps.gff
[09:08:41] * S3/snps.html
[09:08:41] * S3/snps.log
[09:08:41] * S3/snps.raw.vcf
[09:08:41] * S3/snps.subs.vcf
[09:08:41] * S3/snps.tab
[09:08:41] * S3/snps.txt
[09:08:41] * S3/snps.vcf
[09:08:41] * S3/snps.vcf.gz
[09:08:41] * S3/snps.vcf.gz.csi
[09:08:41] Walltime used: 7 seconds
[09:08:41] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md
[09:08:41] 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
[09:08:42] This is snippy 4.6.0
[09:08:42] Written by Torsten Seemann
[09:08:42] Obtained from https://github.com/tseemann/snippy
[09:08:42] Detected operating system: linux
[09:08:42] Enabling bundled linux tools.
[09:08:42] Found bwa - /usr/bin/bwa
[09:08:42] Found bcftools - /usr/bin/bcftools
[09:08:42] Found samtools - /usr/bin/samtools
[09:08:42] Found java - /usr/bin/java
[09:08:42] Found snpEff - /usr/bin/snpEff
[09:08:42] Found samclip - /usr/bin/samclip
[09:08:42] Found seqtk - /usr/bin/seqtk
[09:08:42] Found parallel - /usr/bin/parallel
[09:08:42] Found freebayes - /usr/bin/freebayes
[09:08:42] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[09:08:42] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[09:08:42] Found vcfstreamsort - /usr/bin/vcfstreamsort
[09:08:42] Found vcfuniq - /usr/bin/vcfuniq
[09:08:42] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[09:08:42] Found gzip - /usr/bin/gzip
[09:08:42] Found vt - /usr/bin/vt
[09:08:42] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[09:08:42] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[09:08:42] Checking version: samtools --version is >= 1.7 - ok, have 1.21
[09:08:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
[09:08:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[09:08:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[09:08:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[09:08:42] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
[09:08:42] Treating reference as 'fasta' format.
[09:08:42] Will use 2 CPU cores.
[09:08:42] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq
[09:08:42] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq
[09:08:42] Used --force, will overwrite existing S4
[09:08:42] Changing working directory: S4
[09:08:42] Creating reference folder: reference
[09:08:42] Extracting FASTA and GFF from reference.
[09:08:42] Wrote 3 sequences to ref.fa
[09:08:42] Wrote 0 features to ref.gff
[09:08:42] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[09:08:42] Using BAM RG (Read Group) ID: S4
[09:08:42] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:08:42] Running: bwa index reference/ref.fa 2>> snps.log
[09:08:44] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:08:44] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:08:44] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:08:44] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:08:44] Running: bwa mem  -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11573, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 198, 230)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (35, 360)
[M::mem_pestat] mean and std.dev: (198.20, 48.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 425)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 2.378 CPU sec, 1.463 real sec
[main] Version: 0.7.18-r1243-dirty
[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974
[samclip] Header contained 6 lines
[samclip] Done.
[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: 1.713 sec; CPU: 2.450 sec
[09:08:47] Running: samtools index snps.bam 2>> snps.log
[09:08:47] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[09:08:47] 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
[09:08:49] 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

[09:08:49] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[09:08:49] 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
[09:08:50] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[09:08:50] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[09:08:50] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[09:08:50] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[09:08:50] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[09:08:50] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[09:08:50] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[09:08:50] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[09:08:50] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[09:08:50] Marked 799 heterozygous sites with 'n'
[09:08:50] Creating extra output files: BED GFF CSV TXT HTML
[09:08:50] Identified 257 variants.
[09:08:50] Result folder: S4
[09:08:50] Result files:
[09:08:50] * S4/snps.aligned.fa
[09:08:50] * S4/snps.bam
[09:08:50] * S4/snps.bam.bai
[09:08:50] * S4/snps.bed
[09:08:50] * S4/snps.consensus.fa
[09:08:50] * S4/snps.consensus.subs.fa
[09:08:50] * S4/snps.csv
[09:08:50] * S4/snps.filt.vcf
[09:08:50] * S4/snps.gff
[09:08:50] * S4/snps.html
[09:08:50] * S4/snps.log
[09:08:50] * S4/snps.raw.vcf
[09:08:50] * S4/snps.subs.vcf
[09:08:50] * S4/snps.tab
[09:08:50] * S4/snps.txt
[09:08:50] * S4/snps.vcf
[09:08:50] * S4/snps.vcf.gz
[09:08:50] * S4/snps.vcf.gz.csi
[09:08:50] Walltime used: 8 seconds
[09:08:50] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues
[09:08:50] 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
Found a bug? Post it at http://github.com/tseemann/snippy/issues
Done.
This is snippy-core 4.6.0
Obtained from http://github.com/tseemann/snippy
Enabling bundled tools for linux
Found any2fasta - /usr/bin/any2fasta
Found samtools - /usr/bin/samtools
Found minimap2 - /usr/bin/minimap2
Found bedtools - /usr/bin/bedtools
Found snp-sites - /usr/bin/snp-sites
Saving reference FASTA: core-mask.ref.fa
This is any2fasta 0.4.2
Opening 'example.fna'
Detected FASTA format
Read 5294 lines from 'example.fna'
Wrote 3 sequences from FASTA file.
Processed 1 files.
Done.
Loaded 3 sequences totalling 317336 bp.
Loading mask bed file: example.bed
Will mask 8 regions totalling 3101 bp ~ 0.98%
0	S1	snp=239	del=23	ins=23	het=749	unaligned=9643
1	S2	snp=230	del=15	ins=11	het=841	unaligned=9428
2	S3	snp=226	del=28	ins=14	het=846	unaligned=9376
3	S4	snp=227	del=32	ins=14	het=799	unaligned=9707
Opening: core-mask.tab
Opening: core-mask.vcf
Processing contig: LBB_contig000001
Processing contig: LBB_contig000002
Processing contig: LBB_contig000003
Masking alignment at 8 regions
Generating core-mask.full.aln
Creating TSV file: core-mask.txt
Running: snp-sites -c -o core-mask.aln core-mask.full.aln
Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues
Done.
wc -l S?/snps.tab
  262 S1/snps.tab
  247 S2/snps.tab
  255 S3/snps.tab
  258 S4/snps.tab
 1022 total
make[2]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg/test'
make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/snippy-4.6.0+dfsg'
dh_install
sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile
make[1]: Leaving directory '/build/reproducible-path/snippy-4.6.0+dfsg'
   dh_installdocs
   dh_installchangelogs
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'snippy' in '../snippy_4.6.0+dfsg-5_all.deb'.
dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-5_all.deb'.
 dpkg-genbuildinfo --build=binary -O../snippy_4.6.0+dfsg-5_amd64.buildinfo
 dpkg-genchanges --build=binary -O../snippy_4.6.0+dfsg-5_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/4002399/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/4002399/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/4002399 and its subdirectories
I: Current time: Fri Feb 28 09:08:59 +14 2025
I: pbuilder-time-stamp: 1740683339