sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | snippy 4.6.0+dfsg-5 (amd64) Wed, 22 Jan 2025 14:35:26 +0000 | +==============================================================================+ Package: snippy Version: 4.6.0+dfsg-5 Source Version: 4.6.0+dfsg-5 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Wed, 22 Jan 2025 14:35:27 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-5 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-5 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Wed, 22 Jan 2025 14:35:27 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Get:3 http://deb.debian.org/debian unstable InRelease [205 kB] Get:4 http://localhost:3142/debian sid InRelease [205 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [144 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [147 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [147 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [144 kB] Fetched 829 kB in 7s (123 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2494 kB of archives. After this operation, 4096 B disk space will be freed. Get:1 http://deb.debian.org/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.24 [1114 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 apt amd64 2.9.24 [1380 kB] Fetched 2494 kB in 0s (124 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Fetch source files Wed, 22 Jan 2025 14:35:36 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/snippy_4.6.0+dfsg-5.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 22 Jan 2025 14:35:37 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt, build-essential Filtered Build-Depends: debhelper-compat (= 13), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/snippy-j9oUAE/resolver-8xFjKk/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/snippy-j9oUAE/resolver-8xFjKk/apt_archive ./ InRelease Get:2 copy:/build/snippy-j9oUAE/resolver-8xFjKk/apt_archive ./ Release [609 B] Ign:3 copy:/build/snippy-j9oUAE/resolver-8xFjKk/apt_archive ./ Release.gpg Get:4 copy:/build/snippy-j9oUAE/resolver-8xFjKk/apt_archive ./ Sources [916 B] Get:5 copy:/build/snippy-j9oUAE/resolver-8xFjKk/apt_archive ./ Packages [790 B] Fetched 2315 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adwaita-icon-theme ant ant-optional any2fasta at-spi2-common autoconf automake autopoint autotools-dev bcftools bedtools bsdextrautils bwa ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service debhelper default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono freebayes gettext gettext-base groff-base gtk-update-icon-cache hicolor-icon-theme intltool-debian java-common junit4 junit5 libactivation-java libantlr4-runtime-java libaopalliance-java libapache-pom-java libapfloat-java libapiguardian-java libapparmor1 libarchive-zip-perl libargs4j-java libasm-java libasound2-data libasound2t64 libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libcairo-gobject2 libcairo2 libcdi-api-java libcharts4j-java libciftools-java libcloudproviders0 libcodemodel-java libcolord2 libcom-err2 libcommons-beanutils-java libcommons-cli-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-exec-java libcommons-io-java libcommons-jexl2-java libcommons-lang-java libcommons-lang3-java libcommons-logging-java libcommons-math-java libcommons-math3-java libcommons-parent-java libcommons-text-java libcups2t64 libcurl3t64-gnutls libcurl4t64 libdata-stag-perl libdatrie1 libdbus-1-3 libdconf1 libdebhelper-perl libdeflate0 libdisorder0 libdistlib-java libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libdtd-parser-java libedit2 libelf1t64 libepoxy0 liberror-prone-java libexec-maven-plugin-java libexpat1 libezmorph-java libfastahack0 libfastinfoset-java libfastutil-java libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libguice-java libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libice6 libicu72 libinchi1.07 libio-string-perl libistack-commons-java libitext5-java libjackson2-annotations-java libjackson2-core-java libjackson2-databind-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjgrapht-java libjgraphx-java libjheaps-java libjmol-java libjni-inchi-java libjni-inchi-jni libjpeg62-turbo libjson-java libjson-simple-java libjsoncpp26 libjsoup-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libllvm19 liblog4j1.2-java libmagic-mgc libmagic1t64 libmaven-archiver-java libmaven-compiler-plugin-java libmaven-file-management-java libmaven-jar-plugin-java libmaven-parent-java libmaven-resolver-java libmaven-shared-incremental-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmmtf-java libmsgpack-java libnaga-java libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnspr4 libnss3 libopentest4j-java libopentest4j-reporting-java libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libpicocli-java libpipeline1 libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-compiler-java libplexus-component-annotations-java libplexus-container-default-java libplexus-interpolation-java libplexus-io-java libplexus-languages-java libplexus-sec-dispatcher-java libplexus-utils2-java libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqdox2-java librelaxng-datatype-java librhino-java librngom-java librtmp1 libsensors-config libsensors5 libseqlib2 libsharpyuv0 libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6 libsmithwaterman0 libsnappy-java libsnappy-jni libsnappy1v5 libsnp-sites1 libsnpeff-java libssh2-1t64 libssw0 libstax-ex-java libstreambuffer-java libsystemd-shared libtabixpp0t64 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtool libtrove3-java libtxw2-java libuchardet0 libunivocity-parsers-java libvcflib-tools libvcflib2 libvecmath-java libvulkan1 libwagon-http-java libwagon-provider-api-java libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6 libxbean-reflect-java libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxom-java libxrandr2 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6t64 libxtst6 libxxf86vm1 libxz-java libz3-4 littler m4 man-db media-types mesa-libgallium minimap2 mount ncbi-vdb-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parallel po-debconf procps python3 python3-minimal python3.13 python3.13-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr samclip samtools sensible-utils seqtk shared-mime-info snp-sites snpeff sysstat systemd systemd-sysv tzdata ucf unzip vt x11-common xdg-utils xkb-data zip Suggested packages: adwaita-icon-theme-legacy ant-doc default-jdk | java-compiler | java-sdk antlr javacc junit jython libbcel-java libbsf-java libcommons-net-java libmail-java libjaxp1.3-java libjdepend-java libjsch-java liboro-java libregexp-java libxalan2-java autoconf-archive gnu-standards autoconf-doc python3-numpy texlive-latex-recommended dh-make gettext-doc libasprintf-dev libgettextpo-dev groff alsa-utils libasound2-plugins libatinject-jsr330-api-java-doc bioperl libxml-sax-expatxs-perl libbiojava6-java-doc libel-api-java colord libcommons-collections3-java-doc libcommons-collections4-java-doc libcommons-lang-java-doc libavalon-framework-java libexcalibur-logkit-java cups-common libdistlib-java-doc libmsv-java libxpp2-java libxpp3-java libjdom1-java low-memory-monitor libgoogle-gson-java-doc krb5-doc krb5-user gvfs picard-tools libbcpkix-java libbcprov-java libxml-security-java libjackson2-annotations-java-doc libjmol-java-doc libjson-simple-doc libjsoup-java-doc libjsr305-java-doc liblcms2-utils liblog4j1.2-java-doc libmaven-file-management-java-doc liblogback-java libmmtf-java-doc libngs-java-doc libcryptsetup12 libtss2-rc0t64 pciutils pcscd libeclipse-jdt-core-java libplexus-utils2-java-doc rhino lm-sensors testng libsnpeff-java-doc libarchive13t64 libbpf1 libdw1t64 libfido2-1 libip4tc2 libpwquality1 libqrencode4 tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma libxerces2-java-doc libxml-commons-resolver1.1-java-doc libxom-java-doc m4-doc apparmor less www-browser nfs-common libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic csh fish ksh tcsh zsh libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-knitr r-cran-magick r-cran-rmarkdown r-cran-sf r-cran-getopt r-cran-testthat r-cran-inline cwltool vcfanno isag systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved systemd-repart libtss2-tcti-device0 polkitd Recommended packages: librsvg2-common python3-gffutils python3-matplotlib curl | wget | lynx alsa-ucm-conf alsa-topology-conf at-spi2-core bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-libxml-perl libwww-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libarchive-cpio-perl libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgtk-3-bin krb5-locales libjansi-java libgpm2 publicsuffix libkmod2 libltdl-dev mesa-vulkan-drivers | vulkan-icd libatk-wrapper-java-jni fonts-dejavu-extra libmail-sendmail-perl psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-dbi r-cran-rsqlite r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-bit64 r-cran-diagrammer r-cran-formattable r-cran-lubridate r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-abind r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-fs r-cran-usethis r-cran-dichromat r-cran-hms r-cran-bench r-cran-blob r-cran-brio r-cran-evaluate r-cran-here r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-generics r-cran-pkgdown r-cran-zeallot systemd-timesyncd | time-daemon systemd-cryptsetup libnss-systemd libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: adwaita-icon-theme ant ant-optional any2fasta at-spi2-common autoconf automake autopoint autotools-dev bcftools bedtools bsdextrautils bwa ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service debhelper default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono freebayes gettext gettext-base groff-base gtk-update-icon-cache hicolor-icon-theme intltool-debian java-common junit4 junit5 libactivation-java libantlr4-runtime-java libaopalliance-java libapache-pom-java libapfloat-java libapiguardian-java libapparmor1 libarchive-zip-perl libargs4j-java libasm-java libasound2-data libasound2t64 libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libcairo-gobject2 libcairo2 libcdi-api-java libcharts4j-java libciftools-java libcloudproviders0 libcodemodel-java libcolord2 libcom-err2 libcommons-beanutils-java libcommons-cli-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-exec-java libcommons-io-java libcommons-jexl2-java libcommons-lang-java libcommons-lang3-java libcommons-logging-java libcommons-math-java libcommons-math3-java libcommons-parent-java libcommons-text-java libcups2t64 libcurl3t64-gnutls libcurl4t64 libdata-stag-perl libdatrie1 libdbus-1-3 libdconf1 libdebhelper-perl libdeflate0 libdisorder0 libdistlib-java libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libdtd-parser-java libedit2 libelf1t64 libepoxy0 liberror-prone-java libexec-maven-plugin-java libexpat1 libezmorph-java libfastahack0 libfastinfoset-java libfastutil-java libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libguice-java libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libice6 libicu72 libinchi1.07 libio-string-perl libistack-commons-java libitext5-java libjackson2-annotations-java libjackson2-core-java libjackson2-databind-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjgrapht-java libjgraphx-java libjheaps-java libjmol-java libjni-inchi-java libjni-inchi-jni libjpeg62-turbo libjson-java libjson-simple-java libjsoncpp26 libjsoup-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libllvm19 liblog4j1.2-java libmagic-mgc libmagic1t64 libmaven-archiver-java libmaven-compiler-plugin-java libmaven-file-management-java libmaven-jar-plugin-java libmaven-parent-java libmaven-resolver-java libmaven-shared-incremental-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmmtf-java libmsgpack-java libnaga-java libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnspr4 libnss3 libopentest4j-java libopentest4j-reporting-java libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libpicocli-java libpipeline1 libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-compiler-java libplexus-component-annotations-java libplexus-container-default-java libplexus-interpolation-java libplexus-io-java libplexus-languages-java libplexus-sec-dispatcher-java libplexus-utils2-java libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqdox2-java librelaxng-datatype-java librhino-java librngom-java librtmp1 libsensors-config libsensors5 libseqlib2 libsharpyuv0 libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6 libsmithwaterman0 libsnappy-java libsnappy-jni libsnappy1v5 libsnp-sites1 libsnpeff-java libssh2-1t64 libssw0 libstax-ex-java libstreambuffer-java libsystemd-shared libtabixpp0t64 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtool libtrove3-java libtxw2-java libuchardet0 libunivocity-parsers-java libvcflib-tools libvcflib2 libvecmath-java libvulkan1 libwagon-http-java libwagon-provider-api-java libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6 libxbean-reflect-java libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxom-java libxrandr2 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6t64 libxtst6 libxxf86vm1 libxz-java libz3-4 littler m4 man-db media-types mesa-libgallium minimap2 mount ncbi-vdb-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parallel po-debconf procps python3 python3-minimal python3.13 python3.13-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr samclip samtools sbuild-build-depends-main-dummy sensible-utils seqtk shared-mime-info snp-sites snpeff sysstat systemd systemd-sysv tzdata ucf unzip vt x11-common xdg-utils xkb-data zip 0 upgraded, 409 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After this operation, 950 MB of additional disk space will be used. Get:1 copy:/build/snippy-j9oUAE/resolver-8xFjKk/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:2 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.40.4-1 [155 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 257.2-2 [2138 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 3.1.7-1+b3 [42.1 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 systemd amd64 257.2-2 [3092 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 257.2-2 [60.8 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-1 [259 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:23 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 257.2-2 [293 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:40 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:41 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0048 [42.0 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.45-1 [281 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.16.12+ds-1 [50.6 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B] Get:61 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.107-1 [1390 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.6~6ea-1 [41.8 MB] Get:66 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:67 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.15-1 [2163 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 ant-optional all 1.10.15-1 [456 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 any2fasta all 0.4.2-2 [6232 B] Get:70 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.55.0.1-1 [170 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:81 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.20-2 [760 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get:106 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.55.0.1-1 [51.5 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.55.0.1-1 [77.0 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.55.0.1-1 [68.1 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.0-1+b1 [11.7 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.0-1+b1 [5664 B] Get:153 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b3 [20.2 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get:158 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b2 [36.4 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.43-5 [4655 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.43-5 [2755 kB] Get:163 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:165 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.3.3-1 [38.0 kB] Get:167 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get:168 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get:169 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get:170 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get:171 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get:172 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get:173 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:174 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:175 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get:176 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get:177 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:178 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:179 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-1 [26.0 MB] Get:180 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:181 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get:182 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get:183 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get:184 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b3 [8852 B] Get:185 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 24.3.3-1 [9488 kB] Get:186 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.304.0-1 [129 kB] Get:187 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get:188 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.3.3-1 [43.5 kB] Get:189 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.3.3-1 [44.9 kB] Get:190 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.3.3-1 [142 kB] Get:191 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get:192 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get:193 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get:194 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get:195 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get:196 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.2 [216 kB] Get:197 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b3 [25.9 kB] Get:198 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.6~6ea-1 [204 kB] Get:199 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get:200 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get:201 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get:202 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get:203 http://deb.debian.org/debian unstable/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b2 [172 kB] Get:204 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get:205 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get:206 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get:207 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get:208 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4+b1 [61.1 kB] Get:209 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b2 [194 kB] Get:210 http://deb.debian.org/debian unstable/main amd64 freebayes amd64 1.3.7-1 [1488 kB] Get:211 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get:212 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-5 [350 kB] Get:213 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get:214 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get:215 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get:216 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get:217 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get:218 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.3-1 [2459 kB] Get:219 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get:220 http://deb.debian.org/debian unstable/main amd64 libantlr4-runtime-java all 4.9.2-2 [317 kB] Get:221 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get:222 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get:223 http://deb.debian.org/debian unstable/main amd64 libapfloat-java all 1.14.0-2 [725 kB] Get:224 http://deb.debian.org/debian unstable/main amd64 libargs4j-java all 2.33-2 [138 kB] Get:225 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7.1-1 [391 kB] Get:226 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get:227 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:228 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:229 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:230 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get:231 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get:232 http://deb.debian.org/debian unstable/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get:233 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:234 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get:235 http://deb.debian.org/debian unstable/main amd64 libcommons-math-java all 2.2-9 [933 kB] Get:236 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:237 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get:238 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:239 http://deb.debian.org/debian unstable/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get:240 http://deb.debian.org/debian unstable/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get:241 http://deb.debian.org/debian unstable/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get:242 http://deb.debian.org/debian unstable/main amd64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get:243 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get:244 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get:245 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get:246 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.17.0-1 [488 kB] Get:247 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:248 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get:249 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get:250 http://deb.debian.org/debian unstable/main amd64 libguice-java all 5.1.0-1 [932 kB] Get:251 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 43-2 [6252 B] Get:252 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get:253 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get:254 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get:255 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get:256 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get:257 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get:258 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get:259 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get:260 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get:261 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get:262 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get:263 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get:264 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get:265 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get:266 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get:267 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get:268 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get:269 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get:270 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get:271 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get:272 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get:273 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB] Get:274 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get:275 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:276 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:277 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:278 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get:279 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get:280 http://deb.debian.org/debian unstable/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get:281 http://deb.debian.org/debian unstable/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB] Get:282 http://deb.debian.org/debian unstable/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get:283 http://deb.debian.org/debian unstable/main amd64 librngom-java all 2.3.0.1-11 [292 kB] Get:284 http://deb.debian.org/debian unstable/main amd64 libxsom-java all 2.3.0.1-11 [401 kB] Get:285 http://deb.debian.org/debian unstable/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB] Get:286 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get:287 http://deb.debian.org/debian unstable/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get:288 http://deb.debian.org/debian unstable/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get:289 http://deb.debian.org/debian unstable/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get:290 http://deb.debian.org/debian unstable/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB] Get:291 http://deb.debian.org/debian unstable/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB] Get:292 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get:293 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get:294 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.12.0-1 [222 kB] Get:295 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.15+dfsg-1 [20.0 MB] Get:296 http://deb.debian.org/debian unstable/main amd64 libjheaps-java all 0.14-2 [144 kB] Get:297 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get:298 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get:299 http://deb.debian.org/debian unstable/main amd64 libjgraphx-java all 2.1.0.7-5 [809 kB] Get:300 http://deb.debian.org/debian unstable/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get:301 http://deb.debian.org/debian unstable/main amd64 libinchi1.07 amd64 1.07.2+dfsg-1 [556 kB] Get:302 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B] Get:303 http://deb.debian.org/debian unstable/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get:304 http://deb.debian.org/debian unstable/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get:305 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get:306 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get:307 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get:308 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get:309 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get:310 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get:311 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get:312 http://deb.debian.org/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get:313 http://deb.debian.org/debian unstable/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get:314 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB] Get:315 http://deb.debian.org/debian unstable/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get:316 http://deb.debian.org/debian unstable/main amd64 libjmol-java all 16.2.33+dfsg-1 [10.4 MB] Get:317 http://deb.debian.org/debian unstable/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get:318 http://deb.debian.org/debian unstable/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get:319 http://deb.debian.org/debian unstable/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get:320 http://deb.debian.org/debian unstable/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get:321 http://deb.debian.org/debian unstable/main amd64 libbiojava6-java all 6.1.0+dfsg-5 [5359 kB] Get:322 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:323 http://deb.debian.org/debian unstable/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get:324 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get:325 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get:326 http://deb.debian.org/debian unstable/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get:327 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:328 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get:329 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB] Get:330 http://deb.debian.org/debian unstable/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get:331 http://deb.debian.org/debian unstable/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get:332 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get:333 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-14 [837 kB] Get:334 http://deb.debian.org/debian unstable/main amd64 libxom-java all 1.3.9-1 [174 kB] Get:335 http://deb.debian.org/debian unstable/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get:336 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get:337 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get:338 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get:339 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get:340 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get:341 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b1 [157 kB] Get:342 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b1 [25.8 kB] Get:343 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.0.9+dfsg-7+b1 [112 kB] Get:344 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get:345 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get:346 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:347 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:348 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get:349 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3 [16.3 kB] Get:350 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3 [16.1 kB] Get:351 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:352 http://deb.debian.org/debian unstable/main amd64 libsnp-sites1 amd64 2.5.1-2+b2 [14.8 kB] Get:353 http://deb.debian.org/debian unstable/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get:354 http://deb.debian.org/debian unstable/main amd64 libsnpeff-java all 5.2.e+dfsg-1 [2157 kB] Get:355 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:356 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:357 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:358 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get:359 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:360 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:361 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get:362 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get:363 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:364 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get:365 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:366 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get:367 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-2 [16.0 kB] Get:368 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:369 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get:370 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get:371 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:372 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:373 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:374 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:375 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:376 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:377 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB] Get:378 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:379 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get:380 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:381 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:382 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:383 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:384 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:385 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:386 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:387 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:388 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:389 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:390 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:391 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:392 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:393 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:394 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get:395 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:396 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get:397 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:398 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:399 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get:400 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b2 [660 kB] Get:401 http://deb.debian.org/debian unstable/main amd64 minimap2 amd64 2.27+dfsg-1+b2 [391 kB] Get:402 http://deb.debian.org/debian unstable/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get:403 http://deb.debian.org/debian unstable/main amd64 parallel all 20240222+ds-2 [2163 kB] Get:404 http://deb.debian.org/debian unstable/main amd64 samclip all 0.4.0-4 [20.1 kB] Get:405 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:406 http://deb.debian.org/debian unstable/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get:407 http://deb.debian.org/debian unstable/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB] Get:408 http://deb.debian.org/debian unstable/main amd64 snpeff all 5.2.e+dfsg-1 [7200 B] Get:409 http://deb.debian.org/debian unstable/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] Preconfiguring packages ... Fetched 322 MB in 52s (6189 kB/s) Selecting previously unselected package mount. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../mount_2.40.4-1_amd64.deb ... Unpacking mount (2.40.4-1) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_257.2-2_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.2-2) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_3.1.7-1+b3_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b3) ... Setting up libsystemd-shared:amd64 (257.2-2) ... Selecting previously unselected package systemd. (Reading database ... 23084 files and directories currently installed.) Preparing to unpack .../systemd_257.2-2_amd64.deb ... Unpacking systemd (257.2-2) ... Setting up libapparmor1:amd64 (3.1.7-1+b3) ... Setting up mount (2.40.4-1) ... Setting up systemd (257.2-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' → '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... 24026 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_257.2-2_amd64.deb ... Unpacking systemd-sysv (257.2-2) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../1-libdbus-1-3_1.16.0-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.16.0-1) ... Selecting previously unselected package dbus-bin. 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Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.4.0-2_amd64.deb ... Unpacking openssl (3.4.0-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package libpam-systemd:amd64. Preparing to unpack .../012-libpam-systemd_257.2-2_amd64.deb ... Unpacking libpam-systemd:amd64 (257.2-2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.4-1_amd64.deb ... Unpacking bsdextrautils (2.40.4-1) ... 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Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../020-libglib2.0-0t64_2.82.4-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.4-2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../021-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../022-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../023-shared-mime-info_2.4-5+b1_amd64.deb ... Unpacking shared-mime-info (2.4-5+b1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../024-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../025-libpng16-16t64_1.6.45-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.45-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../026-libdeflate0_1.23-1+b1_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-1+b1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../027-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../028-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../029-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../030-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../031-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../032-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../033-gtk-update-icon-cache_4.16.12+ds-1_amd64.deb ... No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. Unpacking gtk-update-icon-cache (4.16.12+ds-1) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../034-hicolor-icon-theme_0.18-1_all.deb ... Unpacking hicolor-icon-theme (0.18-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../335-libxft2_2.3.6-1+b3_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b3) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../336-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../337-libtk8.6_8.6.16-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.16-1) ... Selecting previously unselected package zip. Preparing to unpack .../338-zip_3.0-14_amd64.deb ... Unpacking zip (3.0-14) ... Selecting previously unselected package unzip. 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Selecting previously unselected package r-cran-gridbase. Preparing to unpack .../376-r-cran-gridbase_0.4-7-5_all.deb ... Unpacking r-cran-gridbase (0.4-7-5) ... Selecting previously unselected package libvcflib-tools. Preparing to unpack .../377-libvcflib-tools_1.0.9+dfsg1-3+b2_amd64.deb ... Unpacking libvcflib-tools (1.0.9+dfsg1-3+b2) ... Selecting previously unselected package minimap2. Preparing to unpack .../378-minimap2_2.27+dfsg-1+b2_amd64.deb ... Unpacking minimap2 (2.27+dfsg-1+b2) ... Selecting previously unselected package sysstat. Preparing to unpack .../379-sysstat_12.7.5-2_amd64.deb ... Unpacking sysstat (12.7.5-2) ... Selecting previously unselected package parallel. Preparing to unpack .../380-parallel_20240222+ds-2_all.deb ... Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20240222+ds-2) ... 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libdisorder0:amd64 (0.0.2+git20130809.8062ee1-4+b2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libfastutil-java (8.5.15+dfsg-1) ... Setting up libjackson2-annotations-java (2.14.0-1) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ... Setting up libwfa2-0:amd64 (2.3.3-4+b1) ... Setting up libdtd-parser-java (1.2-1) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libwayland-server0:amd64 (1.23.0-1+b1) ... Setting up libpciaccess0:amd64 (0.17-3+b3) ... Setting up libslf4j-java (1.7.32-1) ... Setting up systemd-sysv (257.2-2) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libicu72:amd64 (72.1-6) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up seqtk (1.4-2) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.40.4-1) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up java-common (0.76) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libjheaps-java (0.14-2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libvecmath-java (1.5.2-7) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up bwa (0.7.18-1) ... Setting up libglvnd0:amd64 (1.7.0-1+b2) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up minimap2 (2.27+dfsg-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 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+23.2) ... Running in chroot, ignoring request. Setting up libsensors-config (1:3.6.0-10) ... Setting up libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12+b2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... 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 (4.9.2-2) ... 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 (2.3.0-1) ... 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 tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 22 14:36:56 UTC 2025. Universal Time is now: Wed Jan 22 14:36:56 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 (1.0.1-4) ... 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 libglib2.0-0t64:amd64 (2.82.4-2) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libasound2t64:amd64 (1.2.13-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... 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 (6.5-2+b1) ... 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 (2:4.0.4-6) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:amd64 (1.6.45-1) ... 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 libglapi-mesa:amd64 (24.3.3-1) ... Setting up libgfortran5:amd64 (14.2.0-14) ... 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 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 (2.55.0.1-1) ... 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 (2:4.0.4-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libopentest4j-java (1.2.0-4) ... 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) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. 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 (1.23.0-1+b1) ... 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) ... 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) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (3.4.0-2) ... Setting up libinchi1.07 (1.07.2+dfsg-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3) ... Setting up libssw0:amd64 (1.1-15+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up dbus-bin (1.16.0-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libxkbcommon0:amd64 (1.7.0-2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libwayland-client0:amd64 (1.23.0-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... 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) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... 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 libatk1.0-0t64:amd64 (2.55.0.1-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.5.4-2) ... Setting up python3.13 (3.13.1-3) ... 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 libcloudproviders0:amd64 (0.3.6-1+b1) ... 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 python3 (3.13.1-2) ... Setting up libnss3:amd64 (2:3.107-1) ... Setting up libciftools-java (6.0.0-1) ... Setting up dbus-daemon (1.16.0-1) ... Setting up libpaper-utils (2.2.5-0.3) ... Setting up libxom-java (1.3.9-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libjackson2-databind-java (2.14.0-1) ... 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 libdconf1:amd64 (0.40.0-5) ... 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 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+b3) ... Setting up dbus (1.16.0-1) ... Running in chroot, ignoring request. Setting up shared-mime-info (2.4-5+b1) ... 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+b2) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up ucf (3.0048) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... 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 (1.23.0-1+b1) ... Setting up libpam-systemd:amd64 (257.2-2) ... 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-1+b1) ... 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 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 libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up gtk-update-icon-cache (4.16.12+ds-1) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b3) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6~6ea-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 libcurl4t64:amd64 (8.11.1-1+b1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b3) ... 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 libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up dbus-user-session (1.16.0-1) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libatspi2.0-0t64:amd64 (2.55.0.1-1) ... 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 libhts3t64:amd64 (1.20+ds-2) ... 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 libseqlib2:amd64 (1.2.0+dfsg-11+b2) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b1) ... Setting up libatk-bridge2.0-0t64:amd64 (2.55.0.1-1) ... Setting up mesa-libgallium:amd64 (24.3.3-1) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libgbm1:amd64 (24.3.3-1) ... Setting up libgl1-mesa-dri:amd64 (24.3.3-1) ... Setting up bcftools (1.20-2) ... Setting up debhelper (13.24.1) ... Setting up dconf-service (0.40.0-5) ... Setting up samtools (1.20-3) ... 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 (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7+b1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up libglx-mesa0:amd64 (24.3.3-1) ... 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 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 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 libvcflib2:amd64 (1.0.9+dfsg1-3+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 (1.7-1-1) ... Setting up freebayes (1.3.7-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up libgtk-3-common (3.24.43-5) ... 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 libgtk-3-0t64:amd64 (3.24.43-5) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libvcflib-tools (1.0.9+dfsg1-3+b2) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libmaven3-core-java (3.9.9-1) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libjni-inchi-java (0.8+dfsg-8) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (16.2.33+dfsg-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.12.0-1) ... Setting up libmsgpack-java (0.9.6-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.2-1) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for systemd (257.2-2) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.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:ANF_Secure_Server_Root_CA.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:Baltimore_CyberTrust_Root.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.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:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CFCA_EV_ROOT.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:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.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: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: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:Entrust.net_Premium_2048_Secure_Server_CA.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:Entrust_Root_Certification_Authority.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.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:GLOBALTRUST_2020.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.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: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:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.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_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:Secure_Global_CA.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:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.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: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:SZAFIR_ROOT_CA2.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TeliaSonera_Root_CA_v1.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: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:TunTrust_Root_CA.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.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:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem done. Setting up openjdk-21-jre:amd64 (21.0.6~6ea-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up ant-optional (1.10.15-1) ... Setting up junit5 (5.10.3-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ... Setting up libtxw2-java (2.3.0.1-11) ... Setting up libjaxb-java (2.3.0.1-11) ... Setting up libbiojava6-java (6.1.0+dfsg-5) ... Setting up libsnpeff-java (5.2.e+dfsg-1) ... Setting up snpeff (5.2.e+dfsg-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... 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. +------------------------------------------------------------------------------+ | Check architectures Wed, 22 Jan 2025 14:37:05 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment Wed, 22 Jan 2025 14:37:05 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 adwaita-icon-theme_47.0-2 ant_1.10.15-1 ant-optional_1.10.15-1 any2fasta_0.4.2-2 apt_2.9.24 at-spi2-common_2.55.0.1-1 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 bcftools_1.20-2 bedtools_2.31.1+dfsg-2 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.4-1 bsdutils_1:2.40.4-1 build-essential_12.12 bwa_0.7.18-1 bzip2_1.0.8-6 ca-certificates_20241223 ca-certificates-java_20240118 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-13_13.3.0-12 cpp-13-x86-64-linux-gnu_13.3.0-12 cpp-14_14.2.0-14 cpp-14-x86-64-linux-gnu_14.2.0-14 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-11 dbus_1.16.0-1 dbus-bin_1.16.0-1 dbus-daemon_1.16.0-1 dbus-session-bus-common_1.16.0-1 dbus-system-bus-common_1.16.0-1 dbus-user-session_1.16.0-1 dconf-gsettings-backend_0.40.0-5 dconf-service_0.40.0-5 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 default-jre_2:1.21-76 default-jre-headless_2:1.21-76 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r-cran-isoband_0.2.7-1 r-cran-labeling_0.4.3-1 r-cran-lattice_0.22-6-1 r-cran-lifecycle_1.0.4+dfsg-1 r-cran-littler_0.3.20-2 r-cran-magrittr_2.0.3-1 r-cran-mass_7.3-64-1 r-cran-matrix_1.7-1-1 r-cran-mgcv_1.9-1-1 r-cran-munsell_0.5.1-1 r-cran-nlme_3.1.166-1 r-cran-pillar_1.10.1+dfsg-1 r-cran-pkgconfig_2.0.3-2 r-cran-pkgkitten_0.2.4-1 r-cran-plyr_1.8.9-1 r-cran-r6_2.5.1-1 r-cran-rcolorbrewer_1.1-3-1 r-cran-rcpp_1.0.14-1 r-cran-rlang_1.1.4-1 r-cran-scales_1.3.0-1 r-cran-tibble_3.2.1+dfsg-3 r-cran-utf8_1.2.4-1 r-cran-vctrs_0.6.5-1 r-cran-viridislite_0.4.2-2 r-cran-withr_3.0.2+dfsg-1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 samclip_0.4.0-4 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 seqtk_1.4-2 shared-mime-info_2.4-5+b1 snp-sites_2.5.1-2+b2 snpeff_5.2.e+dfsg-1 sqv_1.2.1-5 sysstat_12.7.5-2 systemd_257.2-2 systemd-sysv_257.2-2 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 tzdata_2025a-1 ucf_3.0048 unzip_6.0-28 usr-is-merged_39+nmu2 util-linux_2.40.4-1 vt_0.57721+ds-3+b1 x11-common_1:7.7+23.2 xdg-utils_1.2.1-2 xkb-data_2.42-1 xz-utils_5.6.3-1+b1 zip_3.0-14 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Wed, 22 Jan 2025 14:37:05 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: snippy Binary: snippy, snippy-examples Architecture: all Version: 4.6.0+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/tseemann/snippy/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/snippy Vcs-Git: https://salsa.debian.org/med-team/snippy.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), any2fasta , bcftools , bedtools , bwa , freebayes , libbio-perl-perl , libvcflib-tools , minimap2 , parallel , samtools , samclip , seqtk , snp-sites , snpeff , vt Package-List: snippy deb science optional arch=all snippy-examples deb science optional arch=all Checksums-Sha1: 15848811ce5c2056e10ac5b3d34e173119c5f7d3 271400 snippy_4.6.0+dfsg.orig.tar.xz 23674b8c55b8be1479021ca0db27a69252f28af8 5340 snippy_4.6.0+dfsg-5.debian.tar.xz Checksums-Sha256: 96c9dea7aeab6f362100fb1774d3c4377f12c2209a1fdc63b2926de912997524 271400 snippy_4.6.0+dfsg.orig.tar.xz 273a6903a280928fed9a2fdd7aef35ed5581fa6565f958bf635fc1cf6b201b78 5340 snippy_4.6.0+dfsg-5.debian.tar.xz Files: a4eea48e48f44589cb998e609fdd27ea 271400 snippy_4.6.0+dfsg.orig.tar.xz df32178e8bc17e472dfb199ccd7563ff 5340 snippy_4.6.0+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdYYcMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGSkQ/9HOirKl+sfE5asJrJNkByUzvnmnO0QmhN 5efPSe36CaYnfMUA0jMLTBTPeOQwNaLvEOQTw9uUH6pE8L5mGBxCdh1W3/AriQi9 OcNz0YauRxvB113mGwX8r7ngIwlvgv/tTaXaR/t+h+TKxCKrnlVmOtD1Iir1qC8Z 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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 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Wed, 22 Jan 2025 14:37:05 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network snippy_4.6.0+dfsg-5 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network snippy_4.6.0+dfsg-5 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/snippy-j9oUAE/snippy-4.6.0+dfsg SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-d5b2058c-2c7a-47c5-a820-63fcecd66ad4 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building snippy using existing ./snippy_4.6.0+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building snippy in snippy_4.6.0+dfsg-5.debian.tar.xz dpkg-source: info: building snippy in snippy_4.6.0+dfsg-5.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/build/snippy-j9oUAE/snippy-4.6.0+dfsg' cd test && /usr/bin/make make[2]: Entering directory '/build/snippy-j9oUAE/snippy-4.6.0+dfsg/test' mkdir -p S1 wgsim -S 1 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S1/R1.fq S1/R2.fq > S1/dwgsim.tab [wgsim] seed = 1 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq [14:37:06] This is snippy 4.6.0 [14:37:06] Written by Torsten Seemann [14:37:06] Obtained from https://github.com/tseemann/snippy [14:37:06] Detected operating system: linux [14:37:06] Enabling bundled linux tools. [14:37:06] Found bwa - /usr/bin/bwa [14:37:06] Found bcftools - /usr/bin/bcftools [14:37:06] Found samtools - /usr/bin/samtools [14:37:06] Found java - /usr/bin/java [14:37:06] Found snpEff - /usr/bin/snpEff [14:37:06] Found samclip - /usr/bin/samclip [14:37:06] Found seqtk - /usr/bin/seqtk [14:37:06] Found parallel - /usr/bin/parallel [14:37:06] Found freebayes - /usr/bin/freebayes [14:37:06] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:37:06] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:37:06] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:37:06] Found vcfuniq - /usr/bin/vcfuniq [14:37:06] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:37:06] Found gzip - /usr/bin/gzip [14:37:06] Found vt - /usr/bin/vt [14:37:06] Found snippy-vcf_to_tab - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:37:06] Found snippy-vcf_report - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:37:06] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [14:37:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [14:37:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [14:37:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:37:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:37:06] Using reference: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/example.fna [14:37:06] Treating reference as 'fasta' format. [14:37:06] Will use 2 CPU cores. [14:37:06] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S1/R1.fq [14:37:06] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S1/R2.fq [14:37:06] Used --force, will overwrite existing S1 [14:37:06] Changing working directory: S1 [14:37:06] Creating reference folder: reference [14:37:06] Extracting FASTA and GFF from reference. [14:37:06] Wrote 3 sequences to ref.fa [14:37:06] Wrote 0 features to ref.gff [14:37:06] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:37:06] Using BAM RG (Read Group) ID: S1 [14:37:06] Running: samtools faidx reference/ref.fa 2>> snps.log [14:37:06] Running: bwa index reference/ref.fa 2>> snps.log [14:37:06] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:37:06] Running: ln -sf reference/ref.fa . 2>> snps.log [14:37:06] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:37:06] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:37:06] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S1/R1.fq /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11587, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 233) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 369) [M::mem_pestat] mean and std.dev: (199.53, 48.89) [M::mem_pestat] low and high boundaries for proper pairs: (1, 437) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.100 CPU sec, 0.769 real sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S1/R1.fq /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S1/R2.fq [main] Real time: 0.874 sec; CPU: 1.126 sec [14:37:08] Running: samtools index snps.bam 2>> snps.log [14:37:08] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:37:08] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:37:09] 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: 0.00s [14:37:09] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:37:09] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:37:09] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:37:09] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:37:09] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:37:09] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:37:09] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:37:09] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:37:09] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:37:09] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:37:09] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:37:09] Marked 749 heterozygous sites with 'n' [14:37:09] Creating extra output files: BED GFF CSV TXT HTML [14:37:09] Identified 261 variants. [14:37:09] Result folder: S1 [14:37:09] Result files: [14:37:09] * S1/snps.aligned.fa [14:37:09] * S1/snps.bam [14:37:09] * S1/snps.bam.bai [14:37:09] * S1/snps.bed [14:37:09] * S1/snps.consensus.fa [14:37:09] * S1/snps.consensus.subs.fa [14:37:09] * S1/snps.csv [14:37:09] * S1/snps.filt.vcf [14:37:09] * S1/snps.gff [14:37:09] * S1/snps.html [14:37:09] * S1/snps.log [14:37:09] * S1/snps.raw.vcf [14:37:09] * S1/snps.subs.vcf [14:37:09] * S1/snps.tab [14:37:09] * S1/snps.txt [14:37:09] * S1/snps.vcf [14:37:09] * S1/snps.vcf.gz [14:37:09] * S1/snps.vcf.gz.csi [14:37:09] Walltime used: 3 seconds [14:37:09] Did you know? Snippy is a combination of SNP, Skippy, and snappy. [14:37:09] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S2/R1.fq S2/R2.fq > S2/dwgsim.tab [wgsim] seed = 2 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq [14:37:09] This is snippy 4.6.0 [14:37:09] Written by Torsten Seemann [14:37:09] Obtained from https://github.com/tseemann/snippy [14:37:09] Detected operating system: linux [14:37:09] Enabling bundled linux tools. [14:37:09] Found bwa - /usr/bin/bwa [14:37:09] Found bcftools - /usr/bin/bcftools [14:37:09] Found samtools - /usr/bin/samtools [14:37:09] Found java - /usr/bin/java [14:37:09] Found snpEff - /usr/bin/snpEff [14:37:09] Found samclip - /usr/bin/samclip [14:37:09] Found seqtk - /usr/bin/seqtk [14:37:09] Found parallel - /usr/bin/parallel [14:37:09] Found freebayes - /usr/bin/freebayes [14:37:09] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:37:09] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:37:09] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:37:09] Found vcfuniq - /usr/bin/vcfuniq [14:37:09] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:37:09] Found gzip - /usr/bin/gzip [14:37:09] Found vt - /usr/bin/vt [14:37:09] Found snippy-vcf_to_tab - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:37:09] Found snippy-vcf_report - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:37:09] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [14:37:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [14:37:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [14:37:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:37:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:37:09] Using reference: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/example.fna [14:37:09] Treating reference as 'fasta' format. [14:37:09] Will use 2 CPU cores. [14:37:09] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S2/R1.fq [14:37:09] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S2/R2.fq [14:37:09] Used --force, will overwrite existing S2 [14:37:09] Changing working directory: S2 [14:37:09] Creating reference folder: reference [14:37:09] Extracting FASTA and GFF from reference. [14:37:09] Wrote 3 sequences to ref.fa [14:37:09] Wrote 0 features to ref.gff [14:37:09] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:37:09] Using BAM RG (Read Group) ID: S2 [14:37:09] Running: samtools faidx reference/ref.fa 2>> snps.log [14:37:09] Running: bwa index reference/ref.fa 2>> snps.log [14:37:10] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:37:10] Running: ln -sf reference/ref.fa . 2>> snps.log [14:37:10] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:37:10] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:37:10] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S2/R1.fq /build/snippy-j9oUAE/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 [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 24000 sequences (2400000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 366) [M::mem_pestat] mean and std.dev: (199.27, 48.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.079 CPU sec, 0.803 real sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S2/R1.fq /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S2/R2.fq [main] Real time: 0.909 sec; CPU: 1.106 sec [14:37:11] Running: samtools index snps.bam 2>> snps.log [14:37:11] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:37:11] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:37:12] 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: 0.00s [14:37:12] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:37:12] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:37:12] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:37:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:37:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:37:12] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:37:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:37:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:37:12] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:37:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:37:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:37:12] Marked 841 heterozygous sites with 'n' [14:37:12] Creating extra output files: BED GFF CSV TXT HTML [14:37:12] Identified 246 variants. [14:37:12] Result folder: S2 [14:37:12] Result files: [14:37:12] * S2/snps.aligned.fa [14:37:12] * S2/snps.bam [14:37:12] * S2/snps.bam.bai [14:37:12] * S2/snps.bed [14:37:12] * S2/snps.consensus.fa [14:37:12] * S2/snps.consensus.subs.fa [14:37:12] * S2/snps.csv [14:37:12] * S2/snps.filt.vcf [14:37:12] * S2/snps.gff [14:37:12] * S2/snps.html [14:37:12] * S2/snps.log [14:37:12] * S2/snps.raw.vcf [14:37:12] * S2/snps.subs.vcf [14:37:12] * S2/snps.tab [14:37:12] * S2/snps.txt [14:37:12] * S2/snps.vcf [14:37:12] * S2/snps.vcf.gz [14:37:12] * S2/snps.vcf.gz.csi [14:37:12] Walltime used: 3 seconds [14:37:12] May the SNPs be with you. [14:37:12] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S3/R1.fq S3/R2.fq > S3/dwgsim.tab [wgsim] seed = 3 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq [14:37:12] This is snippy 4.6.0 [14:37:12] Written by Torsten Seemann [14:37:12] Obtained from https://github.com/tseemann/snippy [14:37:12] Detected operating system: linux [14:37:12] Enabling bundled linux tools. [14:37:12] Found bwa - /usr/bin/bwa [14:37:12] Found bcftools - /usr/bin/bcftools [14:37:12] Found samtools - /usr/bin/samtools [14:37:12] Found java - /usr/bin/java [14:37:12] Found snpEff - /usr/bin/snpEff [14:37:12] Found samclip - /usr/bin/samclip [14:37:12] Found seqtk - /usr/bin/seqtk [14:37:12] Found parallel - /usr/bin/parallel [14:37:12] Found freebayes - /usr/bin/freebayes [14:37:12] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:37:12] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:37:12] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:37:12] Found vcfuniq - /usr/bin/vcfuniq [14:37:12] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:37:12] Found gzip - /usr/bin/gzip [14:37:12] Found vt - /usr/bin/vt [14:37:12] Found snippy-vcf_to_tab - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:37:12] Found snippy-vcf_report - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:37:12] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [14:37:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [14:37:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [14:37:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:37:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:37:13] Using reference: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/example.fna [14:37:13] Treating reference as 'fasta' format. [14:37:13] Will use 2 CPU cores. [14:37:13] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S3/R1.fq [14:37:13] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S3/R2.fq [14:37:13] Used --force, will overwrite existing S3 [14:37:13] Changing working directory: S3 [14:37:13] Creating reference folder: reference [14:37:13] Extracting FASTA and GFF from reference. [14:37:13] Wrote 3 sequences to ref.fa [14:37:13] Wrote 0 features to ref.gff [14:37:13] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:37:13] Using BAM RG (Read Group) ID: S3 [14:37:13] Running: samtools faidx reference/ref.fa 2>> snps.log [14:37:13] Running: bwa index reference/ref.fa 2>> snps.log [14:37:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:37:13] Running: ln -sf reference/ref.fa . 2>> snps.log [14:37:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:37:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:37:13] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S3/R1.fq /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 24000 sequences (2400000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368) [M::mem_pestat] mean and std.dev: (198.46, 48.83) [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.092 CPU sec, 0.797 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S3/R1.fq /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S3/R2.fq [main] Real time: 0.897 sec; CPU: 1.118 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. [14:37:14] Running: samtools index snps.bam 2>> snps.log [14:37:14] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:37:14] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:37:15] 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: 0.00s [14:37:15] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:37:15] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:37:15] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:37:15] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:37:15] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:37:15] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:37:15] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:37:15] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:37:15] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:37:15] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:37:15] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:37:15] Marked 846 heterozygous sites with 'n' [14:37:15] Creating extra output files: BED GFF CSV TXT HTML [14:37:15] Identified 254 variants. [14:37:15] Result folder: S3 [14:37:15] Result files: [14:37:15] * S3/snps.aligned.fa [14:37:15] * S3/snps.bam [14:37:15] * S3/snps.bam.bai [14:37:15] * S3/snps.bed [14:37:15] * S3/snps.consensus.fa [14:37:15] * S3/snps.consensus.subs.fa [14:37:15] * S3/snps.csv [14:37:15] * S3/snps.filt.vcf [14:37:15] * S3/snps.gff [14:37:15] * S3/snps.html [14:37:15] * S3/snps.log [14:37:15] * S3/snps.raw.vcf [14:37:15] * S3/snps.subs.vcf [14:37:15] * S3/snps.tab [14:37:15] * S3/snps.txt [14:37:15] * S3/snps.vcf [14:37:15] * S3/snps.vcf.gz [14:37:15] * S3/snps.vcf.gz.csi [14:37:15] Walltime used: 3 seconds [14:37:15] Found a bug? Post it at https://github.com/tseemann/snippy/issues [14:37:15] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S4/R1.fq S4/R2.fq > S4/dwgsim.tab [wgsim] seed = 4 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq [14:37:15] This is snippy 4.6.0 [14:37:15] Written by Torsten Seemann [14:37:15] Obtained from https://github.com/tseemann/snippy [14:37:15] Detected operating system: linux [14:37:15] Enabling bundled linux tools. [14:37:15] Found bwa - /usr/bin/bwa [14:37:15] Found bcftools - /usr/bin/bcftools [14:37:15] Found samtools - /usr/bin/samtools [14:37:15] Found java - /usr/bin/java [14:37:15] Found snpEff - /usr/bin/snpEff [14:37:15] Found samclip - /usr/bin/samclip [14:37:16] Found seqtk - /usr/bin/seqtk [14:37:16] Found parallel - /usr/bin/parallel [14:37:16] Found freebayes - /usr/bin/freebayes [14:37:16] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [14:37:16] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [14:37:16] Found vcfstreamsort - /usr/bin/vcfstreamsort [14:37:16] Found vcfuniq - /usr/bin/vcfuniq [14:37:16] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [14:37:16] Found gzip - /usr/bin/gzip [14:37:16] Found vt - /usr/bin/vt [14:37:16] Found snippy-vcf_to_tab - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab [14:37:16] Found snippy-vcf_report - /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_report [14:37:16] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [14:37:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [14:37:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [14:37:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [14:37:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [14:37:16] Using reference: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/example.fna [14:37:16] Treating reference as 'fasta' format. [14:37:16] Will use 2 CPU cores. [14:37:16] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S4/R1.fq [14:37:16] Using read file: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S4/R2.fq [14:37:16] Used --force, will overwrite existing S4 [14:37:16] Changing working directory: S4 [14:37:16] Creating reference folder: reference [14:37:16] Extracting FASTA and GFF from reference. [14:37:16] Wrote 3 sequences to ref.fa [14:37:16] Wrote 0 features to ref.gff [14:37:16] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [14:37:16] Using BAM RG (Read Group) ID: S4 [14:37:16] Running: samtools faidx reference/ref.fa 2>> snps.log [14:37:16] Running: bwa index reference/ref.fa 2>> snps.log [14:37:16] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:37:16] Running: ln -sf reference/ref.fa . 2>> snps.log [14:37:16] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:37:16] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:37:16] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S4/R1.fq /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11573, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 198, 230) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (35, 360) [M::mem_pestat] mean and std.dev: (198.20, 48.15) [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.098 CPU sec, 0.841 real sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S4/R1.fq /build/snippy-j9oUAE/snippy-4.6.0+dfsg/test/S4/R2.fq [main] Real time: 0.941 sec; CPU: 1.127 sec [14:37:17] Running: samtools index snps.bam 2>> snps.log [14:37:17] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [14:37:17] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [14:37:18] 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: 0.00s [14:37:18] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [14:37:18] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [14:37:18] Running: /build/snippy-j9oUAE/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [14:37:18] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [14:37:18] Running: bcftools index -f snps.vcf.gz 2>> snps.log [14:37:18] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [14:37:18] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [14:37:18] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [14:37:18] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [14:37:18] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [14:37:18] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [14:37:19] Marked 799 heterozygous sites with 'n' [14:37:19] Creating extra output files: BED GFF CSV TXT HTML [14:37:19] Identified 257 variants. [14:37:19] Result folder: S4 [14:37:19] Result files: [14:37:19] * S4/snps.aligned.fa [14:37:19] * S4/snps.bam [14:37:19] * S4/snps.bam.bai [14:37:19] * S4/snps.bed [14:37:19] * S4/snps.consensus.fa [14:37:19] * S4/snps.consensus.subs.fa [14:37:19] * S4/snps.csv [14:37:19] * S4/snps.filt.vcf [14:37:19] * S4/snps.gff [14:37:19] * S4/snps.html [14:37:19] * S4/snps.log [14:37:19] * S4/snps.raw.vcf [14:37:19] * S4/snps.subs.vcf [14:37:19] * S4/snps.tab [14:37:19] * S4/snps.txt [14:37:19] * S4/snps.vcf [14:37:19] * S4/snps.vcf.gz [14:37:19] * S4/snps.vcf.gz.csi [14:37:19] Walltime used: 4 seconds [14:37:19] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md [14:37:19] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Will mask 0 regions totalling 0 bp ~ 0.00% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core.tab Opening: core.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln You can mask columns using '--mask BEDFILE --mask-char X' Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core-mask.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Loading mask bed file: example.bed Will mask 8 regions totalling 3101 bp ~ 0.98% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core-mask.tab Opening: core-mask.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Masking alignment at 8 regions Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md Done. wc -l S?/snps.tab 262 S1/snps.tab 247 S2/snps.tab 255 S3/snps.tab 258 S4/snps.tab 1022 total make[2]: Leaving directory '/build/snippy-j9oUAE/snippy-4.6.0+dfsg/test' make[1]: Leaving directory '/build/snippy-j9oUAE/snippy-4.6.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_install make[1]: Entering directory '/build/snippy-j9oUAE/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/snippy-j9oUAE/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 -O../snippy_4.6.0+dfsg-5_amd64.buildinfo dpkg-genchanges -O../snippy_4.6.0+dfsg-5_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-01-22T14:37:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 22 Jan 2025 14:37:21 +0000 | +------------------------------------------------------------------------------+ snippy_4.6.0+dfsg-5_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 10 Dec 2024 16:40:07 +0100 Source: snippy Binary: snippy snippy-examples Architecture: source all Version: 4.6.0+dfsg-5 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: snippy - rapid haploid variant calling and core genome alignment snippy-examples - rapid haploid variant calling and core genome alignment (examples Closes: 1089272 Changes: snippy (4.6.0+dfsg-5) unstable; urgency=medium . * Build with make 4.4.1 Closes: #1089272 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: 6002310c520fcff3385d7465f4ecd27333caf19e 1445 snippy_4.6.0+dfsg-5.dsc 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snippy-examples_4.6.0+dfsg-5_all.deb 6ad10c1afc5fdf8dd4712d3b1d30edbd982f2c0f 26892 snippy_4.6.0+dfsg-5_all.deb Checksums-Sha256: d7b46295d272295a88b077c0790db347e507775910cb0f44d3707716f5cc54d2 1445 snippy_4.6.0+dfsg-5.dsc c8134543767177b42148058c3935ebc162f1ee35fc7b41e9e52f5a66d49e51d5 310484 snippy-examples_4.6.0+dfsg-5_all.deb d7321afb39cd81a6e334006053c013645b8b0b24afc77fe2a20312dd4c4a20ab 26892 snippy_4.6.0+dfsg-5_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 22 Jan 2025 14:37:21 +0000 Build-Path: /build/snippy-j9oUAE/snippy-4.6.0+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), adwaita-icon-theme (= 47.0-2), ant (= 1.10.15-1), ant-optional (= 1.10.15-1), any2fasta (= 0.4.2-2), at-spi2-common (= 2.55.0.1-1), autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), bcftools (= 1.20-2), bedtools (= 2.31.1+dfsg-2), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bwa (= 0.7.18-1), bzip2 (= 1.0.8-6), ca-certificates (= 20241223), ca-certificates-java (= 20240118), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), dbus (= 1.16.0-1), dbus-bin (= 1.16.0-1), dbus-daemon (= 1.16.0-1), dbus-session-bus-common (= 1.16.0-1), dbus-system-bus-common (= 1.16.0-1), dbus-user-session (= 1.16.0-1), dconf-gsettings-backend (= 0.40.0-5), dconf-service (= 0.40.0-5), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), default-jre (= 2:1.21-76), default-jre-headless (= 2:1.21-76), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-1), diffutils (= 1:3.10-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), fontconfig (= 2.15.0-2), fontconfig-config (= 2.15.0-2), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), freebayes (= 1.3.7-1), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-12), gcc-13-base (= 13.3.0-12), gcc-13-x86-64-linux-gnu (= 13.3.0-12), gcc-14 (= 14.2.0-14), gcc-14-base (= 14.2.0-14), gcc-14-x86-64-linux-gnu (= 14.2.0-14), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), grep (= 3.11-4), groff-base (= 1.23.0-7), gtk-update-icon-cache (= 4.16.12+ds-1), gzip (= 1.13-1), hicolor-icon-theme (= 0.18-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), java-common (= 0.76), junit4 (= 4.13.2-5), junit5 (= 5.10.3-1), libacl1 (= 2.3.2-2+b1), libactivation-java (= 1.2.0-2), libantlr4-runtime-java (= 4.9.2-2), libaopalliance-java (= 20070526-7), libapache-pom-java (= 33-2), libapfloat-java (= 1.14.0-2), libapiguardian-java (= 1.1.2-1), libapparmor1 (= 3.1.7-1+b3), libarchive-zip-perl (= 1.68-1), libargs4j-java (= 2.33-2), libasan8 (= 14.2.0-14), libasm-java (= 9.7.1-1), libasound2-data (= 1.2.13-1), libasound2t64 (= 1.2.13-1+b1), libatinject-jsr330-api-java (= 1.0+ds1-6), libatk-bridge2.0-0t64 (= 2.55.0.1-1), libatk1.0-0t64 (= 2.55.0.1-1), libatomic1 (= 14.2.0-14), libatspi2.0-0t64 (= 2.55.0.1-1), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b1), libavahi-client3 (= 0.8-16), libavahi-common-data (= 0.8-16), libavahi-common3 (= 0.8-16), libbinutils (= 2.43.50.20250108-1), libbio-perl-perl (= 1.7.8-1), libbiojava6-java (= 6.1.0+dfsg-5), libblas3 (= 3.12.0-4), libblkid1 (= 2.40.4-1), libbrotli1 (= 1.1.0-2+b6), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-5), libc-dev-bin (= 2.40-5), libc6 (= 2.40-5), libc6-dev (= 2.40-5), libcairo-gobject2 (= 1.18.2-2), libcairo2 (= 1.18.2-2), libcap-ng0 (= 0.8.5-4), libcap2 (= 1:2.66-5+b1), libcc1-0 (= 14.2.0-14), libcdi-api-java (= 1.2-4), libcharts4j-java (= 1.3-4), libciftools-java (= 6.0.0-1), libcloudproviders0 (= 0.3.6-1+b1), libcodemodel-java (= 2.6+jaxb2.3.0.1-11), libcolord2 (= 1.4.7-1+b2), libcom-err2 (= 1.47.2-1), libcommons-beanutils-java (= 1.9.4-2), libcommons-cli-java (= 1.6.0-1), libcommons-codec-java (= 1.17.1-1), libcommons-collections3-java (= 3.2.2-3), libcommons-collections4-java (= 4.4-2), libcommons-compress-java (= 1.27.1-2), libcommons-exec-java (= 1.3-2), libcommons-io-java (= 2.17.0-1), libcommons-jexl2-java (= 2.1.1-6), libcommons-lang-java (= 2.6-10), libcommons-lang3-java (= 3.17.0-1), libcommons-logging-java (= 1.3.0-1), libcommons-math-java (= 2.2-9), libcommons-math3-java (= 3.6.1-4), libcommons-parent-java (= 56-1), libcommons-text-java (= 1.12.0-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.43.50.20250108-1), libctf0 (= 2.43.50.20250108-1), libcups2t64 (= 2.4.10-2+b1), libcurl3t64-gnutls (= 8.11.1-1+b1), libcurl4t64 (= 8.11.1-1+b1), libdata-stag-perl (= 0.14-3), libdatrie1 (= 0.2.13-3+b1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdbus-1-3 (= 1.16.0-1), libdconf1 (= 0.40.0-5), libdebconfclient0 (= 0.277), libdebhelper-perl (= 13.24.1), libdeflate0 (= 1.23-1+b1), libdisorder0 (= 0.0.2+git20130809.8062ee1-4+b2), libdistlib-java (= 1.0-5), libdom4j-java (= 2.1.4-1), libdpkg-perl (= 1.22.14), libdrm-amdgpu1 (= 2.4.123-1), libdrm-common (= 2.4.123-1), libdrm-intel1 (= 2.4.123-1), libdrm-radeon1 (= 2.4.123-1), libdrm2 (= 2.4.123-1), libdtd-parser-java (= 1.2-1), libedit2 (= 3.1-20250104-1), libelf1t64 (= 0.192-4), libepoxy0 (= 1.5.10-2), liberror-prone-java (= 2.18.0-1), libexec-maven-plugin-java (= 3.1.0-2), libexpat1 (= 2.6.4-1), libezmorph-java (= 1.0.6-4), libfastahack0 (= 1.0.0+dfsg-11+b2), libfastinfoset-java (= 1.2.12-4), libfastutil-java (= 8.5.15+dfsg-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.1-1), libfml0 (= 0.1+git20221215.85f159e-1), libfontconfig1 (= 2.15.0-2), libfreemarker-java (= 2.3.32-2), libfreetype6 (= 2.13.3+dfsg-1), libfribidi0 (= 1.0.16-1), libgbm1 (= 24.3.3-1), libgcc-13-dev (= 13.3.0-12), libgcc-14-dev (= 14.2.0-14), libgcc-s1 (= 14.2.0-14), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgdk-pixbuf-2.0-0 (= 2.42.12+dfsg-1+b1), libgdk-pixbuf2.0-common (= 2.42.12+dfsg-1), libgeronimo-annotation-1.3-spec-java (= 1.3-1), libgeronimo-interceptor-3.0-spec-java (= 1.0.1-4), libgfortran5 (= 14.2.0-14), libgif7 (= 5.2.2-1+b1), libgl1 (= 1.7.0-1+b2), libgl1-mesa-dri (= 24.3.3-1), libglapi-mesa (= 24.3.3-1), libglib2.0-0t64 (= 2.82.4-2), libglvnd0 (= 1.7.0-1+b2), libglx-mesa0 (= 24.3.3-1), libglx0 (= 1.7.0-1+b2), libgmp10 (= 2:6.3.0+dfsg-3), libgnutls30t64 (= 3.8.8-2), libgomp1 (= 14.2.0-14), libgoogle-gson-java (= 2.10.1-1), libgprofng0 (= 2.43.50.20250108-1), libgraphite2-3 (= 1.3.14-2+b1), libgssapi-krb5-2 (= 1.21.3-4), libgtk-3-0t64 (= 3.24.43-5), libgtk-3-common (= 3.24.43-5), libguava-java (= 32.0.1-1), libguice-java (= 5.1.0-1), libhamcrest-java (= 2.2-2), libharfbuzz0b (= 10.2.0-1), libhogweed6t64 (= 3.10-1+b1), libhts3t64 (= 1.20+ds-2), libhtscodecs2 (= 1.6.1-1), libhtsjdk-java (= 4.1.3+dfsg-2), libhttpclient-java (= 4.5.14-1), libhttpcore-java (= 4.4.16-1), libhwasan0 (= 14.2.0-14), libice6 (= 2:1.1.1-1), libicu72 (= 72.1-6), libidn2-0 (= 2.3.7-2+b1), libinchi1.07 (= 1.07.2+dfsg-1), libio-string-perl (= 1.08-4), libisl23 (= 0.27-1), libistack-commons-java (= 3.0.6-5), libitext5-java (= 5.5.13.3-4), libitm1 (= 14.2.0-14), libjackson2-annotations-java (= 2.14.0-1), libjackson2-core-java (= 2.14.1-1), libjackson2-databind-java (= 2.14.0-1), libjansson4 (= 2.14-2+b3), libjaxb-api-java (= 2.3.1-1), libjaxb-java (= 2.3.0.1-11), libjaxen-java (= 1.1.6-5), libjbig0 (= 2.1-6.1+b2), libjgrapht-java (= 1.5.2-1), libjgraphx-java (= 2.1.0.7-5), libjheaps-java (= 0.14-2), libjmol-java (= 16.2.33+dfsg-1), libjni-inchi-java (= 0.8+dfsg-8), libjni-inchi-jni (= 0.8+dfsg-8), libjpeg62-turbo (= 1:2.1.5-3+b1), libjson-java (= 3.1.0+dfsg-2), libjson-simple-java (= 2.3.0-1), libjsoncpp26 (= 1.9.6-3), libjsoup-java (= 1.15.3-1), libjsr305-java (= 0.1~+svn49-11), libk5crypto3 (= 1.21.3-4), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-4), libkrb5support0 (= 1.21.3-4), liblapack3 (= 3.12.0-4), liblcms2-2 (= 2.16-2), libldap2 (= 2.6.9+dfsg-1), liblerc4 (= 4.0.0+ds-5), libllvm19 (= 1:19.1.7-1), liblog4j1.2-java (= 1.2.17-11), liblsan0 (= 14.2.0-14), liblzma5 (= 5.6.3-1+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmaven-archiver-java (= 3.6.2-1), libmaven-compiler-plugin-java (= 3.13.0-1), libmaven-file-management-java (= 3.0.0-1), libmaven-jar-plugin-java (= 3.3.0-2), libmaven-parent-java (= 43-2), libmaven-resolver-java (= 1.9.22-1), libmaven-shared-incremental-java (= 1.1-6), libmaven-shared-io-java (= 3.0.0-4), libmaven-shared-utils-java (= 3.4.2-1), libmaven3-core-java (= 3.9.9-1), libmbedcrypto16 (= 3.6.2-3), libmbedtls21 (= 3.6.2-3), libmbedx509-7 (= 3.6.2-3), libmd0 (= 1.1.0-2+b1), libmmtf-java (= 1.0.11-1), libmount1 (= 2.40.4-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libmsgpack-java (= 0.9.6-1), libnaga-java (= 3.0+svn80-5), libncbi-ngs3 (= 3.0.9+dfsg-7+b1), libncbi-vdb3 (= 3.0.9+dfsg-2), libncurses6 (= 6.5-2+b1), libncursesw6 (= 6.5-2+b1), libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libnghttp3-9 (= 1.6.0-2), libngs-java (= 3.0.9+dfsg-7+b1), libngs-jni (= 3.0.9+dfsg-7+b1), libngtcp2-16 (= 1.9.1-1), libngtcp2-crypto-gnutls8 (= 1.9.1-1), libnspr4 (= 2:4.36-1), libnss3 (= 2:3.107-1), libopentest4j-java (= 1.2.0-4), libopentest4j-reporting-java (= 0.1.0-M1-2), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam-systemd (= 257.2-2), libpam0g (= 1.5.3-7+b1), libpango-1.0-0 (= 1.56.1-1), libpangocairo-1.0-0 (= 1.56.1-1), libpangoft2-1.0-0 (= 1.56.1-1), libpaper-utils (= 2.2.5-0.3), libpaper2 (= 2.2.5-0.3), libpciaccess0 (= 0.17-3+b3), libpcre2-8-0 (= 10.44-5), libpcsclite1 (= 2.3.1-1), libperl5.40 (= 5.40.1-1), libpicocli-java (= 4.6.2-2), libpipeline1 (= 1.5.8-1), libpixman-1-0 (= 0.44.0-3), libplexus-archiver-java (= 4.6.1-1), libplexus-cipher-java (= 2.0-1), libplexus-classworlds-java (= 2.7.0-1), libplexus-compiler-java (= 2.13.0-1), libplexus-component-annotations-java (= 2.1.1-1), libplexus-container-default-java (= 2.1.1-1), libplexus-interpolation-java (= 1.27-1), libplexus-io-java (= 3.3.1-2), libplexus-languages-java (= 1.1.1-2), libplexus-sec-dispatcher-java (= 2.0-3), libplexus-utils2-java (= 3.4.2-1), libpng16-16t64 (= 1.6.45-1), libproc2-0 (= 2:4.0.4-6), libpsl5t64 (= 0.21.2-1.1+b1), libpython3-stdlib (= 3.13.1-2), libpython3.13-minimal (= 3.13.1-3), libpython3.13-stdlib (= 3.13.1-3), libqdox2-java (= 2.0.3-1), libquadmath0 (= 14.2.0-14), libreadline8t64 (= 8.2-6), librelaxng-datatype-java (= 1.0+ds1-3.1), librhino-java (= 1.7.15-1), librngom-java (= 2.3.0.1-11), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8+b1), libsasl2-modules-db (= 2.1.28+dfsg1-8+b1), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsemanage-common (= 3.7-2), libsemanage2 (= 3.7-2+b1), libsensors-config (= 1:3.6.0-10), libsensors5 (= 1:3.6.0-10+b1), libsepol2 (= 3.7-1), libseqlib2 (= 1.2.0+dfsg-11+b2), libsframe1 (= 2.43.50.20250108-1), libsharpyuv0 (= 1.5.0-0.1), libsisu-inject-java (= 0.3.5-1), libsisu-plexus-java (= 0.3.5-1), libslf4j-java (= 1.7.32-1), libsm6 (= 2:1.2.4-1), libsmartcols1 (= 2.40.4-1), libsmithwaterman0 (= 0.0+git20160702.2610e25-12+b2), libsnappy-java (= 1.1.10.7-1), libsnappy-jni (= 1.1.10.7-1), libsnappy1v5 (= 1.2.1-1+b1), libsnp-sites1 (= 2.5.1-2+b2), libsnpeff-java (= 5.2.e+dfsg-1), libsqlite3-0 (= 3.46.1-1), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.4.0-2), libssw0 (= 1.1-15+b2), libstax-ex-java (= 1.7.8-3), libstdc++-14-dev (= 14.2.0-14), libstdc++6 (= 14.2.0-14), libstreambuffer-java (= 1.5.4-1.1), libsystemd-shared (= 257.2-2), libsystemd0 (= 257.2-2), libtabixpp0t64 (= 1.1.2-2.1+b1), libtasn1-6 (= 4.19.0-3+b3), libtcl8.6 (= 8.6.16+dfsg-1), libtext-charwidth-perl (= 0.04-11+b4), libtext-wrapi18n-perl (= 0.06-10), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2+b1), libtiff6 (= 4.5.1+git230720-5), libtinfo6 (= 6.5-2+b1), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3+b1), libtk8.6 (= 8.6.16-1), libtool (= 2.5.4-2), libtrove3-java (= 3.0.3-5), libtsan2 (= 14.2.0-14), libtxw2-java (= 2.3.0.1-11), libubsan1 (= 14.2.0-14), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.2-2), libunistring5 (= 1.3-1), libunivocity-parsers-java (= 2.9.1-1), libuuid1 (= 2.40.4-1), libvcflib-tools (= 1.0.9+dfsg1-3+b2), libvcflib2 (= 1.0.9+dfsg1-3+b2), libvecmath-java (= 1.5.2-7), libvulkan1 (= 1.4.304.0-1), libwagon-http-java (= 3.5.3-1), libwagon-provider-api-java (= 3.5.3-1), libwayland-client0 (= 1.23.0-1+b1), libwayland-cursor0 (= 1.23.0-1+b1), libwayland-egl1 (= 1.23.0-1+b1), libwayland-server0 (= 1.23.0-1+b1), libwebp7 (= 1.5.0-0.1), libwfa2-0 (= 2.3.3-4+b1), libx11-6 (= 2:1.8.10-2), libx11-data (= 2:1.8.10-2), libx11-xcb1 (= 2:1.8.10-2), libxau6 (= 1:1.0.11-1), libxbean-reflect-java (= 4.5-9), libxcb-dri3-0 (= 1.17.0-2+b1), libxcb-glx0 (= 1.17.0-2+b1), libxcb-present0 (= 1.17.0-2+b1), libxcb-randr0 (= 1.17.0-2+b1), libxcb-render0 (= 1.17.0-2+b1), libxcb-shm0 (= 1.17.0-2+b1), libxcb-sync1 (= 1.17.0-2+b1), libxcb-xfixes0 (= 1.17.0-2+b1), libxcb1 (= 1.17.0-2+b1), libxcomposite1 (= 1:0.4.6-1), libxcursor1 (= 1:1.2.3-1), libxdamage1 (= 1:1.1.6-1+b2), libxdmcp6 (= 1:1.1.5-1), libxerces2-java (= 2.12.2-1), libxext6 (= 2:1.3.4-1+b3), libxfixes3 (= 1:6.0.0-2+b3), libxft2 (= 2.3.6-1+b3), libxi6 (= 2:1.8.2-1), libxinerama1 (= 2:1.1.4-3+b3), libxkbcommon0 (= 1.7.0-2), libxml-commons-external-java (= 1.4.01-6), libxml-commons-resolver1.1-java (= 1.2-11), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxom-java (= 1.3.9-1), libxrandr2 (= 2:1.5.4-1+b2), libxrender1 (= 1:0.9.10-1.1+b3), libxshmfence1 (= 1.3-1+b3), libxsom-java (= 2.3.0.1-11), libxss1 (= 1:1.2.3-1+b3), libxt6t64 (= 1:1.2.1-1.2+b2), libxtst6 (= 2:1.2.3-1.1+b3), libxxf86vm1 (= 1:1.1.4-1+b4), libxz-java (= 1.9-1), libz3-4 (= 4.13.3-1), libzstd1 (= 1.5.6+dfsg-2), linux-libc-dev (= 6.12.10-1), littler (= 0.3.20-2), login.defs (= 1:4.16.0-7), m4 (= 1.4.19-5), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), mesa-libgallium (= 24.3.3-1), minimap2 (= 2.27+dfsg-1+b2), mount (= 2.40.4-1), ncbi-vdb-data (= 3.0.9+dfsg-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), netbase (= 6.4), openjdk-21-jre (= 21.0.6~6ea-1), openjdk-21-jre-headless (= 21.0.6~6ea-1), openssl (= 3.4.0-2), openssl-provider-legacy (= 3.4.0-2), parallel (= 20240222+ds-2), passwd (= 1:4.16.0-7), patch (= 2.7.6-7), perl (= 5.40.1-1), perl-base (= 5.40.1-1), perl-modules-5.40 (= 5.40.1-1), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-6), python3 (= 3.13.1-2), python3-minimal (= 3.13.1-2), python3.13 (= 3.13.1-3), python3.13-minimal (= 3.13.1-3), r-base-core (= 4.4.2-1), r-cran-cli (= 3.6.3-1), r-cran-colorspace (= 2.1-1+dfsg-1), r-cran-fansi (= 1.0.5-1), r-cran-farver (= 2.1.2-1), r-cran-ggplot2 (= 3.5.1+dfsg-1), r-cran-glue (= 1.8.0-1), r-cran-gridbase (= 0.4-7-5), r-cran-gtable (= 0.3.6+dfsg-1), r-cran-isoband (= 0.2.7-1), r-cran-labeling (= 0.4.3-1), r-cran-lattice (= 0.22-6-1), r-cran-lifecycle (= 1.0.4+dfsg-1), r-cran-littler (= 0.3.20-2), r-cran-magrittr (= 2.0.3-1), r-cran-mass (= 7.3-64-1), r-cran-matrix (= 1.7-1-1), r-cran-mgcv (= 1.9-1-1), r-cran-munsell (= 0.5.1-1), r-cran-nlme (= 3.1.166-1), r-cran-pillar (= 1.10.1+dfsg-1), r-cran-pkgconfig (= 2.0.3-2), r-cran-pkgkitten (= 0.2.4-1), r-cran-plyr (= 1.8.9-1), r-cran-r6 (= 2.5.1-1), r-cran-rcolorbrewer (= 1.1-3-1), r-cran-rcpp (= 1.0.14-1), r-cran-rlang (= 1.1.4-1), r-cran-scales (= 1.3.0-1), r-cran-tibble (= 3.2.1+dfsg-3), r-cran-utf8 (= 1.2.4-1), r-cran-vctrs (= 0.6.5-1), r-cran-viridislite (= 0.4.2-2), r-cran-withr (= 3.0.2+dfsg-1), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), samclip (= 0.4.0-4), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), seqtk (= 1.4-2), shared-mime-info (= 2.4-5+b1), snp-sites (= 2.5.1-2+b2), snpeff (= 5.2.e+dfsg-1), sysstat (= 12.7.5-2), systemd (= 257.2-2), systemd-sysv (= 257.2-2), sysvinit-utils (= 3.13-1), tar (= 1.35+dfsg-3.1), tzdata (= 2025a-1), ucf (= 3.0048), unzip (= 6.0-28), usr-is-merged (= 39+nmu2), util-linux (= 2.40.4-1), vt (= 0.57721+ds-3+b1), x11-common (= 1:7.7+23.2), xdg-utils (= 1.2.1-2), xkb-data (= 2.42-1), xz-utils (= 5.6.3-1+b1), zip (= 3.0-14), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1733845207" +------------------------------------------------------------------------------+ | Package contents Wed, 22 Jan 2025 14:37:21 +0000 | +------------------------------------------------------------------------------+ snippy-examples_4.6.0+dfsg-5_all.deb ------------------------------------ new Debian package, version 2.0. size 310484 bytes: control archive=1068 bytes. 931 bytes, 22 lines control 559 bytes, 7 lines md5sums Package: snippy-examples Source: snippy Version: 4.6.0+dfsg-5 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 313 Recommends: snippy Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/tseemann/snippy/ Description: rapid haploid variant calling and core genome alignment (examples) Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree). . This package contains example data to test snippy. drwxr-xr-x root/root 0 2024-12-10 15:40 ./ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/doc/snippy-examples/ -rw-r--r-- root/root 730 2024-12-10 15:40 ./usr/share/doc/snippy-examples/changelog.Debian.gz -rw-r--r-- root/root 890 2024-12-10 15:40 ./usr/share/doc/snippy-examples/copyright drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/doc/snippy/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/doc/snippy/examples/ -rw-r--r-- root/root 1610 2024-12-10 15:40 ./usr/share/doc/snippy/examples/Makefile -rw-r--r-- root/root 220 2020-03-09 02:53 ./usr/share/doc/snippy/examples/example.bed -rw-r--r-- root/root 95810 2020-03-09 02:53 ./usr/share/doc/snippy/examples/example.fna.gz -rw-r--r-- root/root 208951 2020-03-09 02:53 ./usr/share/doc/snippy/examples/example.gbk.gz -rwxr-xr-x root/root 836 2024-12-10 15:40 ./usr/share/doc/snippy/examples/test_for_working_snpeff_v5.1+ snippy_4.6.0+dfsg-5_all.deb --------------------------- new Debian package, version 2.0. size 26892 bytes: control archive=1292 bytes. 984 bytes, 18 lines control 841 bytes, 13 lines md5sums Package: snippy Version: 4.6.0+dfsg-5 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 100 Depends: perl:any, any2fasta, bcftools, bedtools, bwa, freebayes (>= 1.3.6-2), libbio-perl-perl, libvcflib-tools, minimap2, parallel, samclip, samtools, seqtk, snp-sites, snpeff, vt Section: science Priority: optional Homepage: https://github.com/tseemann/snippy/ Description: rapid haploid variant calling and core genome alignment Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree). drwxr-xr-x root/root 0 2024-12-10 15:40 ./ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/bin/ -rwxr-xr-x root/root 28069 2024-12-10 15:40 ./usr/bin/snippy -rwxr-xr-x root/root 2518 2024-12-10 15:40 ./usr/bin/snippy-clean_full_aln -rwxr-xr-x root/root 15844 2024-12-10 15:40 ./usr/bin/snippy-core -rwxr-xr-x root/root 2311 2024-12-10 15:40 ./usr/bin/snippy-multi -rwxr-xr-x root/root 6632 2024-12-10 15:40 ./usr/bin/snippy-vcf_extract_subs -rwxr-xr-x root/root 3720 2024-12-10 15:40 ./usr/bin/snippy-vcf_report -rwxr-xr-x root/root 5872 2024-12-10 15:40 ./usr/bin/snippy-vcf_to_tab drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/doc/snippy/ -rw-r--r-- root/root 662 2024-12-10 15:40 ./usr/share/doc/snippy/README.Debian -rw-r--r-- root/root 730 2024-12-10 15:40 ./usr/share/doc/snippy/changelog.Debian.gz -rw-r--r-- root/root 890 2024-12-10 15:40 ./usr/share/doc/snippy/copyright drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/doc/snippy/etc/ -rw-r--r-- root/root 4825 2020-03-09 02:53 ./usr/share/doc/snippy/etc/Mtb_NC_000962.3_mask.bed.gz drwxr-xr-x root/root 0 2020-03-09 02:53 ./usr/share/perl5/ drwxr-xr-x root/root 0 2020-03-09 02:53 ./usr/share/perl5/Snippy/ -rw-r--r-- root/root 342 2020-03-09 02:53 ./usr/share/perl5/Snippy/Version.pm drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/snippy/ drwxr-xr-x root/root 0 2024-12-10 15:40 ./usr/share/snippy/etc/ -rw-r--r-- root/root 12107 2020-03-09 02:53 ./usr/share/snippy/etc/snpeff.config +------------------------------------------------------------------------------+ | Post Build Wed, 22 Jan 2025 14:37:22 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 22 Jan 2025 14:37:22 +0000 | +------------------------------------------------------------------------------+ Purging /build/snippy-j9oUAE Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 22 Jan 2025 14:37:23 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 46052 Build-Time: 16 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 88 Job: /srv/debomatic/incoming/snippy_4.6.0+dfsg-5.dsc Machine Architecture: amd64 Package: snippy Package-Time: 115 Source-Version: 4.6.0+dfsg-5 Space: 46052 Status: successful Version: 4.6.0+dfsg-5 -------------------------------------------------------------------------------- Finished at 2025-01-22T14:37:21Z Build needed 00:01:55, 46052k disk space