sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | snippy 4.6.0+dfsg-4 (amd64) Wed, 05 Jun 2024 19:04:17 +0000 | +==============================================================================+ Package: snippy Version: 4.6.0+dfsg-4 Source Version: 4.6.0+dfsg-4 Distribution: sid Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-debomatic-1d3f5b37-61a7-4672-a5ee-61b81b490064' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-4 sid amd64 ---------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-4 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/snippy-dwLnRT/resolver-i5LExE' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [198 kB] Get:2 http://localhost:3142/debian sid InRelease [198 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-05-1405.56-F-2024-06-02-1406.32.pdiff [216 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-05-1405.56-F-2024-06-02-1406.32.pdiff [216 kB] Get:5 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:6 http://localhost:3142/debian sid/main Sources T-2024-06-05-1405.56-F-2024-06-02-1406.32.pdiff [120 kB] Get:6 http://localhost:3142/debian sid/main Sources T-2024-06-05-1405.56-F-2024-06-02-1406.32.pdiff [120 kB] Fetched 860 kB in 9s (98.1 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libgnutls30t64 libmount1 libsmartcols1 libssl3t64 libuuid1 login passwd util-linux 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7097 kB of archives. After this operation, 47.1 kB disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.1-8 [104 kB] Get:2 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.13+dfsg1-5 [590 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libsmartcols1 amd64 2.40.1-8 [137 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.1-8 [34.7 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.1-8 [166 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.1-8 [197 kB] Get:7 http://localhost:3142/debian unstable/main amd64 util-linux amd64 2.40.1-8 [1210 kB] Get:8 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.13+dfsg1-5 [974 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libgnutls30t64 amd64 3.8.5-4 [1437 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libssl3t64 amd64 3.2.2-1 [2246 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7097 kB in 0s (144 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/snippy_4.6.0+dfsg-4.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/snippy-dwLnRT/snippy-4.6.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/snippy-dwLnRT' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ 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, fakeroot 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, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [933 B] Get:5 copy:/<>/apt_archive ./ Packages [800 B] Fetched 2342 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 blt bsdextrautils bwa ca-certificates ca-certificates-java debhelper default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 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 libarchive-zip-perl libargs4j-java libasm-java libasound2-data libasound2t64 libatinject-jsr330-api-java libatk1.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libbsd0 libcairo2 libcdi-api-java libcharts4j-java libciftools-java libcodemodel-java libcom-err2 libcommons-cli-java libcommons-codec-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 libdebhelper-perl libdeflate0 libdisorder0 libdistlib-java libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libdtd-parser-java libedit2 libelf1t64 liberror-prone-java libexec-maven-plugin-java libexpat1 libfakeroot libfastahack0 libfastinfoset-java libfastutil-java libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfontenc1 libfreemarker-java libfreetype6 libfribidi0 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 libgtk2.0-0t64 libgtk2.0-common libguava-java libguice-java libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libice6 libicu72 libimagequant0 libinchi1 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 libjs-jquery libjs-jquery-ui libjson-simple-java libjsoncpp25 libjsoup-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 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 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmjson-java libmmtf-java libmsgpack-java libnaga-java libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libngs-java libngs-jni libnspr4 libnss3 libopenjp2-7 libopentest4j-java libopentest4j-reporting-java libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 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 libpython3.11-minimal libpython3.11-stdlib libqdox2-java libqhull-r8.0 libraqm0 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 libtabixpp0t64 libtcl8.6 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 libwebp7 libwebpdemux2 libwebpmux3 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6 libxbean-reflect-java libxcb-dri2-0 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 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxsom-java libxss1 libxt6t64 libxtst6 libxxf86vm1 libxz-java libz3-4 littler m4 man-db media-types minimap2 ncbi-vdb-data netbase openjdk-17-jre openjdk-17-jre-headless openssl parallel po-debconf procps python-matplotlib-data python3 python3-appdirs python3-argcomplete python3-argh python3-attr python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-gffutils python3-importlib-metadata python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyfaidx python3-pyparsing python3-reportlab python3-rlpycairo python3-scipy python3-simplejson python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3-zipp python3.11 python3.11-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 sgml-base shared-mime-info snp-sites snpeff sysstat tk8.6-blt2.5 tzdata ucf unicode-data unzip vt w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip Suggested packages: 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 texlive-latex-recommended blt-demo dh-make fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 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 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 libcglib-java picard-tools libbcpkix-java libbcprov-java libxml-security-java libjackson2-annotations-java-doc libxom-java libjmol-java-doc libjs-jquery-ui-docs libjson-simple-doc libjsoup-java-doc libjsr305-java-doc liblcms2-utils liblog4j1.2-java-doc libmaven-file-management-java-doc libmaven-shared-incremental-java-doc libmaven-shared-utils-java-doc liblogback-java libmmtf-java-doc libngs-java-doc pciutils pcscd libeclipse-jdt-core-java libplexus-utils2-java-doc rhino lm-sensors testng libsnpeff-java-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma libxerces2-java-doc libxml-commons-resolver1.1-java-doc m4-doc apparmor less www-browser 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-venv python-attr-doc clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.11-venv python3.11-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 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-knitr r-cran-rmarkdown r-cran-viridis r-cran-covr r-cran-magick r-cran-sf r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-testthat r-cran-inline r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms r-cran-htmltools r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr cwltool sgml-base-doc vcfanno isag Recommended packages: librsvg2-common curl | wget | lynx alsa-ucm-conf alsa-topology-conf 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 dbus libarchive-cpio-perl libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgail-common libgtk2.0-bin javascript-common krb5-locales libjansi-java libgpm2 publicsuffix libltdl-dev mesa-vulkan-drivers | vulkan-icd libatk-wrapper-java-jni fonts-dejavu-extra libmail-sendmail-perl psmisc python-biopython-doc ncbi-blast+ python3-pybedtools python3-bs4 python3-cssselect python3-html5lib python3-olefile isympy-common 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-unitizer r-cran-dplyr 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-lubridate r-cran-abind r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms r-cran-stringi r-cran-data.table r-cran-mockr r-cran-formattable r-cran-generics r-cran-pkgdown r-cran-zeallot systemd | cron | cron-daemon 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 blt bsdextrautils bwa ca-certificates ca-certificates-java debhelper default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 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 libarchive-zip-perl libargs4j-java libasm-java libasound2-data libasound2t64 libatinject-jsr330-api-java libatk1.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libbsd0 libcairo2 libcdi-api-java libcharts4j-java libciftools-java libcodemodel-java libcom-err2 libcommons-cli-java libcommons-codec-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 libdebhelper-perl libdeflate0 libdisorder0 libdistlib-java libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libdtd-parser-java libedit2 libelf1t64 liberror-prone-java libexec-maven-plugin-java libexpat1 libfakeroot libfastahack0 libfastinfoset-java libfastutil-java libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfontenc1 libfreemarker-java libfreetype6 libfribidi0 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 libgtk2.0-0t64 libgtk2.0-common libguava-java libguice-java libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libice6 libicu72 libimagequant0 libinchi1 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 libjs-jquery libjs-jquery-ui libjson-simple-java libjsoncpp25 libjsoup-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 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 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmjson-java libmmtf-java libmsgpack-java libnaga-java libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libngs-java libngs-jni libnspr4 libnss3 libopenjp2-7 libopentest4j-java libopentest4j-reporting-java libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 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 libpython3.11-minimal libpython3.11-stdlib libqdox2-java libqhull-r8.0 libraqm0 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 libtabixpp0t64 libtcl8.6 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 libwebp7 libwebpdemux2 libwebpmux3 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6 libxbean-reflect-java libxcb-dri2-0 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 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxsom-java libxss1 libxt6t64 libxtst6 libxxf86vm1 libxz-java libz3-4 littler m4 man-db media-types minimap2 ncbi-vdb-data netbase openjdk-17-jre openjdk-17-jre-headless openssl parallel po-debconf procps python-matplotlib-data python3 python3-appdirs python3-argcomplete python3-argh python3-attr python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-gffutils python3-importlib-metadata python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyfaidx python3-pyparsing python3-reportlab python3-rlpycairo python3-scipy python3-simplejson python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3-zipp python3.11 python3.11-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 sgml-base shared-mime-info snp-sites snpeff sysstat tk8.6-blt2.5 tzdata ucf unicode-data unzip vt w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 0 upgraded, 437 newly installed, 0 to remove and 0 not upgraded. Need to get 380 MB of archives. After this operation, 1207 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B] Get:2 http://localhost:3142/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:4 http://localhost:3142/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get:5 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:6 http://localhost:3142/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://localhost:3142/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://localhost:3142/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get:10 http://localhost:3142/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:12 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:13 http://localhost:3142/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get:15 http://localhost:3142/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get:16 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:17 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.2.2-1 [1364 kB] Get:18 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:21 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:22 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:24 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:25 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-8 [96.0 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:27 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:28 http://localhost:3142/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-2 [1485 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get:33 http://localhost:3142/debian unstable/main amd64 shared-mime-info amd64 2.4-5 [758 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:38 http://localhost:3142/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [139 kB] Get:43 http://localhost:3142/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.42-1 [46.7 kB] Get:44 http://localhost:3142/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get:45 http://localhost:3142/debian unstable/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get:46 http://localhost:3142/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:47 http://localhost:3142/debian unstable/main amd64 java-common all 0.75 [6640 B] Get:48 http://localhost:3142/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libnss3 amd64 2:3.100-1 [1406 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libpcsclite1 amd64 2.2.3-1 [54.9 kB] Get:52 http://localhost:3142/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get:53 http://localhost:3142/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get:54 http://localhost:3142/debian unstable/main amd64 ant all 1.10.14-1 [2162 kB] Get:55 http://localhost:3142/debian unstable/main amd64 ant-optional all 1.10.14-1 [455 kB] Get:56 http://localhost:3142/debian unstable/main amd64 any2fasta all 0.4.2-2 [6232 B] Get:57 http://localhost:3142/debian unstable/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get:58 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:59 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:60 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:61 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:62 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:68 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:72 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.8.0-1 [434 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:77 http://localhost:3142/debian unstable/main amd64 python3-argcomplete all 3.3.0-1 [38.9 kB] Get:78 http://localhost:3142/debian unstable/main amd64 python3-argh all 0.31.2-1 [26.5 kB] Get:79 http://localhost:3142/debian unstable/main amd64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get:80 http://localhost:3142/debian unstable/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get:81 http://localhost:3142/debian unstable/main amd64 python3-importlib-metadata all 7.1.0-1 [19.2 kB] Get:82 http://localhost:3142/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:83 http://localhost:3142/debian unstable/main amd64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get:84 http://localhost:3142/debian unstable/main amd64 python3-simplejson amd64 3.19.2-1+b1 [69.4 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get:87 http://localhost:3142/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:88 http://localhost:3142/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB] Get:89 http://localhost:3142/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:92 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:93 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get:95 http://localhost:3142/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get:96 http://localhost:3142/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:97 http://localhost:3142/debian unstable/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:98 http://localhost:3142/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:99 http://localhost:3142/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:112 http://localhost:3142/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:113 http://localhost:3142/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:114 http://localhost:3142/debian unstable/main amd64 python3-tk amd64 3.12.3-3.1 [113 kB] Get:115 http://localhost:3142/debian unstable/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get:124 http://localhost:3142/debian unstable/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:126 http://localhost:3142/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:128 http://localhost:3142/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:129 http://localhost:3142/debian unstable/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get:130 http://localhost:3142/debian unstable/main amd64 python3-freetype all 2.4.0-2 [78.6 kB] Get:131 http://localhost:3142/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:132 http://localhost:3142/debian unstable/main amd64 python3-reportlab all 4.2.0-2 [1149 kB] Get:133 http://localhost:3142/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get:134 http://localhost:3142/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:135 http://localhost:3142/debian unstable/main amd64 python3-biopython amd64 1.83+dfsg1-3 [1634 kB] Get:136 http://localhost:3142/debian unstable/main amd64 python3-gffutils all 0.13-1 [1041 kB] Get:137 http://localhost:3142/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:139 http://localhost:3142/debian unstable/main amd64 fonts-lyx all 2.4.0-1 [189 kB] Get:140 http://localhost:3142/debian unstable/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get:141 http://localhost:3142/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get:142 http://localhost:3142/debian unstable/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get:143 http://localhost:3142/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:144 http://localhost:3142/debian unstable/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get:145 http://localhost:3142/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:146 http://localhost:3142/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get:147 http://localhost:3142/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:148 http://localhost:3142/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get:149 http://localhost:3142/debian unstable/main amd64 python3-scipy amd64 1.12.0-2 [21.0 MB] Get:150 http://localhost:3142/debian unstable/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:151 http://localhost:3142/debian unstable/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:152 http://localhost:3142/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:153 http://localhost:3142/debian unstable/main amd64 python3-sympy all 1.12.1-1 [3869 kB] Get:154 http://localhost:3142/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:155 http://localhost:3142/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:156 http://localhost:3142/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:157 http://localhost:3142/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get:158 http://localhost:3142/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get:159 http://localhost:3142/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get:160 http://localhost:3142/debian unstable/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b1 [299 kB] Get:161 http://localhost:3142/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:162 http://localhost:3142/debian unstable/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get:163 http://localhost:3142/debian unstable/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get:164 http://localhost:3142/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get:165 http://localhost:3142/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get:166 http://localhost:3142/debian unstable/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get:167 http://localhost:3142/debian unstable/main amd64 bcftools amd64 1.20-1 [760 kB] Get:168 http://localhost:3142/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:169 http://localhost:3142/debian unstable/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get:170 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:171 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:172 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:173 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:174 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:175 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:176 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:177 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:178 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:179 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:180 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:181 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:182 http://localhost:3142/debian unstable/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get:183 http://localhost:3142/debian unstable/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get:184 http://localhost:3142/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get:185 http://localhost:3142/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get:186 http://localhost:3142/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get:187 http://localhost:3142/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get:188 http://localhost:3142/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get:189 http://localhost:3142/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:190 http://localhost:3142/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:191 http://localhost:3142/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:192 http://localhost:3142/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:193 http://localhost:3142/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get:194 http://localhost:3142/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get:195 http://localhost:3142/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get:196 http://localhost:3142/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get:197 http://localhost:3142/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get:198 http://localhost:3142/debian unstable/main amd64 libxcursor1 amd64 1:1.2.2-1 [37.1 kB] Get:199 http://localhost:3142/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get:200 http://localhost:3142/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:201 http://localhost:3142/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get:202 http://localhost:3142/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get:203 http://localhost:3142/debian unstable/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get:204 http://localhost:3142/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get:205 http://localhost:3142/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:206 http://localhost:3142/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:207 http://localhost:3142/debian unstable/main amd64 libglapi-mesa amd64 24.1.0-2 [36.6 kB] Get:208 http://localhost:3142/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get:209 http://localhost:3142/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB] Get:210 http://localhost:3142/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB] Get:211 http://localhost:3142/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB] Get:212 http://localhost:3142/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB] Get:213 http://localhost:3142/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB] Get:214 http://localhost:3142/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB] Get:215 http://localhost:3142/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB] Get:216 http://localhost:3142/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get:217 http://localhost:3142/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:218 http://localhost:3142/debian unstable/main amd64 libvulkan1 amd64 1.3.283.0-1 [125 kB] Get:219 http://localhost:3142/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:220 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get:221 http://localhost:3142/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get:222 http://localhost:3142/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get:223 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get:224 http://localhost:3142/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:225 http://localhost:3142/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get:226 http://localhost:3142/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:227 http://localhost:3142/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10 [34.7 kB] Get:228 http://localhost:3142/debian unstable/main amd64 libgl1-mesa-dri amd64 24.1.0-2 [8638 kB] Get:229 http://localhost:3142/debian unstable/main amd64 libglx-mesa0 amd64 24.1.0-2 [151 kB] Get:230 http://localhost:3142/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get:231 http://localhost:3142/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get:232 http://localhost:3142/debian unstable/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get:233 http://localhost:3142/debian unstable/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get:234 http://localhost:3142/debian unstable/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get:235 http://localhost:3142/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get:236 http://localhost:3142/debian unstable/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB] Get:237 http://localhost:3142/debian unstable/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get:238 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:239 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:240 http://localhost:3142/debian unstable/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB] Get:241 http://localhost:3142/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get:242 http://localhost:3142/debian unstable/main amd64 libssw0 amd64 1.1-14+b1 [21.2 kB] Get:243 http://localhost:3142/debian unstable/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b1 [172 kB] Get:244 http://localhost:3142/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1 [10.1 kB] Get:245 http://localhost:3142/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b1 [4884 B] Get:246 http://localhost:3142/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b1 [27.6 kB] Get:247 http://localhost:3142/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB] Get:248 http://localhost:3142/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4 [60.5 kB] Get:249 http://localhost:3142/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b1 [188 kB] Get:250 http://localhost:3142/debian unstable/main amd64 freebayes amd64 1.3.7-1 [1488 kB] Get:251 http://localhost:3142/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get:252 http://localhost:3142/debian unstable/main amd64 junit4 all 4.13.2-4 [349 kB] Get:253 http://localhost:3142/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get:254 http://localhost:3142/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get:255 http://localhost:3142/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get:256 http://localhost:3142/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get:257 http://localhost:3142/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get:258 http://localhost:3142/debian unstable/main amd64 junit5 all 5.10.1-1 [2458 kB] Get:259 http://localhost:3142/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get:260 http://localhost:3142/debian unstable/main amd64 libantlr4-runtime-java all 4.9.2-2 [317 kB] Get:261 http://localhost:3142/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get:262 http://localhost:3142/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B] Get:263 http://localhost:3142/debian unstable/main amd64 libapfloat-java all 1.13.0-1 [700 kB] Get:264 http://localhost:3142/debian unstable/main amd64 libargs4j-java all 2.33-2 [138 kB] Get:265 http://localhost:3142/debian unstable/main amd64 libasm-java all 9.7-1 [394 kB] Get:266 http://localhost:3142/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get:267 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:268 http://localhost:3142/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:269 http://localhost:3142/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:270 http://localhost:3142/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get:271 http://localhost:3142/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get:272 http://localhost:3142/debian unstable/main amd64 libciftools-java all 6.0.0-1 [2211 kB] Get:273 http://localhost:3142/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:274 http://localhost:3142/debian unstable/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get:275 http://localhost:3142/debian unstable/main amd64 libcommons-math-java all 2.2-8 [926 kB] Get:276 http://localhost:3142/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:277 http://localhost:3142/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get:278 http://localhost:3142/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:279 http://localhost:3142/debian unstable/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get:280 http://localhost:3142/debian unstable/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get:281 http://localhost:3142/debian unstable/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB] Get:282 http://localhost:3142/debian unstable/main amd64 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get:283 http://localhost:3142/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get:284 http://localhost:3142/debian unstable/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get:285 http://localhost:3142/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get:286 http://localhost:3142/debian unstable/main amd64 libcommons-io-java all 2.16.1-1 [480 kB] Get:287 http://localhost:3142/debian unstable/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get:288 http://localhost:3142/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get:289 http://localhost:3142/debian unstable/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get:290 http://localhost:3142/debian unstable/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get:291 http://localhost:3142/debian unstable/main amd64 libmaven-parent-java all 35-1 [6140 B] Get:292 http://localhost:3142/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get:293 http://localhost:3142/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get:294 http://localhost:3142/debian unstable/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get:295 http://localhost:3142/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get:296 http://localhost:3142/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get:297 http://localhost:3142/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get:298 http://localhost:3142/debian unstable/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get:299 http://localhost:3142/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get:300 http://localhost:3142/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get:301 http://localhost:3142/debian unstable/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get:302 http://localhost:3142/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:303 http://localhost:3142/debian unstable/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get:304 http://localhost:3142/debian unstable/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get:305 http://localhost:3142/debian unstable/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get:306 http://localhost:3142/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get:307 http://localhost:3142/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get:308 http://localhost:3142/debian unstable/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get:309 http://localhost:3142/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get:310 http://localhost:3142/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1 [29.1 kB] Get:311 http://localhost:3142/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get:312 http://localhost:3142/debian unstable/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get:313 http://localhost:3142/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB] Get:314 http://localhost:3142/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get:315 http://localhost:3142/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:316 http://localhost:3142/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:317 http://localhost:3142/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:318 http://localhost:3142/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get:319 http://localhost:3142/debian unstable/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get:320 http://localhost:3142/debian unstable/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get:321 http://localhost:3142/debian unstable/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get:322 http://localhost:3142/debian unstable/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get:323 http://localhost:3142/debian unstable/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB] Get:324 http://localhost:3142/debian unstable/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get:325 http://localhost:3142/debian unstable/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get:326 http://localhost:3142/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get:327 http://localhost:3142/debian unstable/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get:328 http://localhost:3142/debian unstable/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get:329 http://localhost:3142/debian unstable/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get:330 http://localhost:3142/debian unstable/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get:331 http://localhost:3142/debian unstable/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get:332 http://localhost:3142/debian unstable/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get:333 http://localhost:3142/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get:334 http://localhost:3142/debian unstable/main amd64 libcommons-text-java all 1.11.0-1 [217 kB] Get:335 http://localhost:3142/debian unstable/main amd64 libfastutil-java all 8.5.12+dfsg-2 [19.6 MB] Get:336 http://localhost:3142/debian unstable/main amd64 libjheaps-java all 0.14-2 [144 kB] Get:337 http://localhost:3142/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get:338 http://localhost:3142/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get:339 http://localhost:3142/debian unstable/main amd64 libjgraphx-java all 2.1.0.7-3 [807 kB] Get:340 http://localhost:3142/debian unstable/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB] Get:341 http://localhost:3142/debian unstable/main amd64 libinchi1 amd64 1.03+dfsg-4+b2 [436 kB] Get:342 http://localhost:3142/debian unstable/main amd64 libjni-inchi-jni amd64 0.8+dfsg-7 [9064 B] Get:343 http://localhost:3142/debian unstable/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get:344 http://localhost:3142/debian unstable/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get:345 http://localhost:3142/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get:346 http://localhost:3142/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get:347 http://localhost:3142/debian unstable/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get:348 http://localhost:3142/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get:349 http://localhost:3142/debian unstable/main amd64 libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get:350 http://localhost:3142/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get:351 http://localhost:3142/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get:352 http://localhost:3142/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get:353 http://localhost:3142/debian unstable/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get:354 http://localhost:3142/debian unstable/main amd64 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get:355 http://localhost:3142/debian unstable/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get:356 http://localhost:3142/debian unstable/main amd64 libjmol-java all 16.2.15+dfsg-1 [8956 kB] Get:357 http://localhost:3142/debian unstable/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get:358 http://localhost:3142/debian unstable/main amd64 libmsgpack-java all 0.9.6-1 [161 kB] Get:359 http://localhost:3142/debian unstable/main amd64 libmmtf-java all 1.0.11-1 [187 kB] Get:360 http://localhost:3142/debian unstable/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get:361 http://localhost:3142/debian unstable/main amd64 libbiojava6-java all 6.1.0+dfsg-4 [5367 kB] Get:362 http://localhost:3142/debian unstable/main amd64 libcharts4j-java all 1.3-4 [162 kB] Get:363 http://localhost:3142/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:364 http://localhost:3142/debian unstable/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get:365 http://localhost:3142/debian unstable/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB] Get:366 http://localhost:3142/debian unstable/main amd64 libdistlib-java all 1.0-5 [72.5 kB] Get:367 http://localhost:3142/debian unstable/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB] Get:368 http://localhost:3142/debian unstable/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:369 http://localhost:3142/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:370 http://localhost:3142/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:371 http://localhost:3142/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:372 http://localhost:3142/debian unstable/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:373 http://localhost:3142/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get:374 http://localhost:3142/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-7+b1 [156 kB] Get:375 http://localhost:3142/debian unstable/main amd64 libngs-jni amd64 3.0.3+dfsg-7+b1 [23.9 kB] Get:376 http://localhost:3142/debian unstable/main amd64 libngs-java amd64 3.0.3+dfsg-7+b1 [111 kB] Get:377 http://localhost:3142/debian unstable/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get:378 http://localhost:3142/debian unstable/main amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1833 kB] Get:379 http://localhost:3142/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:380 http://localhost:3142/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:381 http://localhost:3142/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:382 http://localhost:3142/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:383 http://localhost:3142/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:384 http://localhost:3142/debian unstable/main amd64 libsnp-sites1 amd64 2.5.1-2+b1 [15.4 kB] Get:385 http://localhost:3142/debian unstable/main amd64 libtrove3-java all 3.0.3-5 [2146 kB] Get:386 http://localhost:3142/debian unstable/main amd64 libsnpeff-java all 5.2.b+dfsg-1 [1656 kB] Get:387 http://localhost:3142/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:388 http://localhost:3142/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:389 http://localhost:3142/debian unstable/main amd64 zip amd64 3.0-13 [230 kB] Get:390 http://localhost:3142/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get:391 http://localhost:3142/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:392 http://localhost:3142/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:393 http://localhost:3142/debian unstable/main amd64 r-base-core amd64 4.4.0-2 [28.2 MB] Get:394 http://localhost:3142/debian unstable/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:395 http://localhost:3142/debian unstable/main amd64 littler all 0.3.20-1 [16.0 kB] Get:396 http://localhost:3142/debian unstable/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:397 http://localhost:3142/debian unstable/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] Get:398 http://localhost:3142/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get:399 http://localhost:3142/debian unstable/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:400 http://localhost:3142/debian unstable/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:401 http://localhost:3142/debian unstable/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get:402 http://localhost:3142/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:403 http://localhost:3142/debian unstable/main amd64 r-cran-gtable all 0.3.5+dfsg-1 [222 kB] Get:404 http://localhost:3142/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:405 http://localhost:3142/debian unstable/main amd64 r-cran-mass amd64 7.3-60.2-1 [1111 kB] Get:406 http://localhost:3142/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:407 http://localhost:3142/debian unstable/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get:408 http://localhost:3142/debian unstable/main amd64 r-cran-matrix amd64 1.7-0-3 [4127 kB] Get:409 http://localhost:3142/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:410 http://localhost:3142/debian unstable/main amd64 r-cran-farver amd64 2.1.1-2 [1405 kB] Get:411 http://localhost:3142/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:412 http://localhost:3142/debian unstable/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:413 http://localhost:3142/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:414 http://localhost:3142/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:415 http://localhost:3142/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:416 http://localhost:3142/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:417 http://localhost:3142/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:418 http://localhost:3142/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:419 http://localhost:3142/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:420 http://localhost:3142/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:421 http://localhost:3142/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:422 http://localhost:3142/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:423 http://localhost:3142/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:424 http://localhost:3142/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:425 http://localhost:3142/debian unstable/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:426 http://localhost:3142/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:427 http://localhost:3142/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get:428 http://localhost:3142/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b1 [651 kB] Get:429 http://localhost:3142/debian unstable/main amd64 minimap2 amd64 2.27+dfsg-1 [389 kB] Get:430 http://localhost:3142/debian unstable/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get:431 http://localhost:3142/debian unstable/main amd64 parallel all 20240222+ds-2 [2163 kB] Get:432 http://localhost:3142/debian unstable/main amd64 samclip all 0.4.0-4 [20.1 kB] Get:433 http://localhost:3142/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:434 http://localhost:3142/debian unstable/main amd64 seqtk amd64 1.4-2 [34.6 kB] Get:435 http://localhost:3142/debian unstable/main amd64 snp-sites amd64 2.5.1-2+b1 [14.5 kB] Get:436 http://localhost:3142/debian unstable/main amd64 snpeff all 5.2.b+dfsg-1 [7164 B] Get:437 http://localhost:3142/debian unstable/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 380 MB in 17s (21.9 MB/s) Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... 19683 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 19999 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. 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Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libsnappy1v5:amd64 (1.2.1-1) ... Setting up libcharts4j-java (1.3-4) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jun 5 19:06:01 UTC 2024. Universal Time is now: Wed Jun 5 19:06:01 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up unicode-data (15.1.0-1) ... 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 libasound2-data (1.2.11-1) ... Setting up libio-string-perl (1.08-4) ... Setting up zip (3.0-13) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.80.2-2) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... 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 (1.2.11-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libapiguardian-java (1.1.2-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.2.3-1) ... Setting up libsensors5:amd64 (1:3.6.0-10) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.1.0-2) ... Setting up libgfortran5:amd64 (14.1.0-1) ... Setting up libvulkan1:amd64 (1.3.283.0-1) ... Setting up autoconf (2.71-3) ... Setting up libapfloat-java (1.13.0-1) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up libtrove3-java (3.0.3-5) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libfreemarker-java (2.3.32-2) ... Setting up sensible-utils (0.0.22) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up at-spi2-common (2.52.0-1) ... Setting up libcommons-math-java (2.2-8) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-4) ... 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 libxbean-reflect-java (4.5-8) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up libjackson2-core-java (2.14.1-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libsnp-sites1:amd64 (2.5.1-2+b1) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.31) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up openssl (3.2.2-1) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libcdi-api-java (1.2-3) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up libssw0:amd64 (1.1-14+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up libargs4j-java (2.33-2) ... Setting up libinchi1 (1.03+dfsg-4+b2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:amd64 (1.17.0-2) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.100-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libciftools-java (6.0.0-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjackson2-databind-java (2.14.0-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.17.0-2) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-12) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:amd64 (1.17.0-2) ... Setting up shared-mime-info (2.4-5) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up librngom-java (2.3.0.1-10.1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libjni-inchi-jni (0.8+dfsg-7) ... Setting up libjgraphx-java (2.1.0.7-3) ... Setting up snp-sites (2.5.1-2+b1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:amd64 (1.17.0-2) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.16.0-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... 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 Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.42-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libcurl4t64:amd64 (8.8.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdistlib-java (1.0-5) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.1.0-2) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.8.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up python3 (3.11.8-1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up python3-freetype (2.4.0-2) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up python3-tz (2024.1-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-simplejson (3.19.2-1+b1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up python3-cycler (0.12.1-1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up parallel (20240222+ds-2) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhttpclient-java (4.5.14-1) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-argcomplete (3.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-7+b1) ... Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-sympy (1.12.1-1) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-argh (0.31.2-1) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-7+b1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:amd64 (24.1.0-2) ... Setting up python3-cairo (1.26.0-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libxcursor1:amd64 (1:1.2.2-1) ... Setting up debhelper (13.15.3) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-zipp (1.0.0-6) ... Setting up samtools (1.20-3) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up r-base-core (4.4.0-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up python3-numpy (1:1.26.4+ds-10) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-farver (2.1.1-2) ... Setting up python3-reportlab (4.2.0-2) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up python3-contourpy (1.0.7-3) ... Setting up libngs-java:amd64 (3.0.3+dfsg-7+b1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libhtsjdk-java (4.1.0+dfsg-2) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-rcpp (1.0.12-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up r-cran-rlang (1.1.3-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up python3-scipy (1.12.0-2) ... Setting up python3-importlib-metadata (7.1.0-1) ... Setting up littler (0.3.20-1) ... Setting up vt (0.57721+ds-3+b1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up r-cran-mass (7.3-60.2-1) ... Setting up python3-tk:amd64 (3.12.3-3.1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-cli (3.6.2-1) ... 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 (2.1-0+dfsg-1) ... Setting up libvcflib2:amd64 (1.0.9+dfsg1-3+b1) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... 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 (0.3.5+dfsg-1) ... Setting up r-cran-matrix (1.7-0-3) ... 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 r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... 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+b1) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up python3-matplotlib (3.6.3-2) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libmaven-shared-incremental-java (1.1-4) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-compiler-java (2.12.1-2) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (16.2.15+dfsg-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.11.0-1) ... 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 (2.38-12) ... 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: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:SecureTrust_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian: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: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_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 ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up ant-optional (1.10.14-1) ... Setting up junit5 (5.10.1-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libjaxb-java (2.3.0.1-10.1) ... Setting up libbiojava6-java (6.1.0+dfsg-4) ... Setting up libsnpeff-java (5.2.b+dfsg-1) ... Setting up snpeff (5.2.b+dfsg-1) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-3) ... Setting up python3-gffutils (0.13-1) ... Setting up bcftools (1.20-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 adwaita-icon-theme_46.0-1 ant_1.10.14-1 ant-optional_1.10.14-1 any2fasta_0.4.2-2 apt_2.9.4 at-spi2-common_2.52.0-1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 bcftools_1.20-1 bedtools_2.31.1+dfsg-2 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 blt_2.5.3+dfsg-7 bsdextrautils_2.40.1-8 bsdutils_1:2.40.1-8 build-essential_12.10 bwa_0.7.17-7+b3 bzip2_1.0.8-5.1 ca-certificates_20240203 ca-certificates-java_20240118 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 default-jre_2:1.17-75 default-jre-headless_2:1.17-75 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 fontconfig_2.15.0-1.1 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lyx_2.4.0-1 fonts-urw-base35_20200910-8 freebayes_1.3.7-1 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gtk-update-icon-cache_3.24.42-1 gzip_1.12-1.1 hicolor-icon-theme_0.18-1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 java-common_0.75 junit4_4.13.2-4 junit5_5.10.1-1 libacl1_2.3.2-2 libactivation-java_1.2.0-2 libantlr4-runtime-java_4.9.2-2 libaopalliance-java_20070526-7 libapache-pom-java_29-2 libapfloat-java_1.13.0-1 libapiguardian-java_1.1.2-1 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libargs4j-java_2.33-2 libasan8_14.1.0-1 libasm-java_9.7-1 libasound2-data_1.2.11-1 libasound2t64_1.2.11-1+b1 libassuan0_2.5.6-1+b1 libatinject-jsr330-api-java_1.0+ds1-5 libatk1.0-0t64_2.52.0-1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libavahi-client3_0.8-13+b2 libavahi-common-data_0.8-13+b2 libavahi-common3_0.8-13+b2 libbinutils_2.42-4 libbio-perl-perl_1.7.8-1 libbiojava6-java_6.1.0+dfsg-4 libblas3_3.12.0-3 libblkid1_2.40.1-8 libbrotli1_1.1.0-2+b3 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcairo2_1.18.0-3+b1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcdi-api-java_1.2-3 libcharts4j-java_1.3-4 libciftools-java_6.0.0-1 libcodemodel-java_2.6+jaxb2.3.0.1-10.1 libcom-err2_1.47.1-1 libcommons-cli-java_1.6.0-1 libcommons-codec-java_1.16.0-1 libcommons-compress-java_1.25.0-1 libcommons-exec-java_1.3-2 libcommons-io-java_2.16.1-1 libcommons-jexl2-java_2.1.1-6 libcommons-lang-java_2.6-10 libcommons-lang3-java_3.14.0-1 libcommons-logging-java_1.3.0-1 libcommons-math-java_2.2-8 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libx11-xcb1_2:1.8.7-1+b1 libxau6_1:1.0.9-1+b1 libxbean-reflect-java_4.5-8 libxcb-dri2-0_1.17.0-2 libxcb-dri3-0_1.17.0-2 libxcb-glx0_1.17.0-2 libxcb-present0_1.17.0-2 libxcb-randr0_1.17.0-2 libxcb-render0_1.17.0-2 libxcb-shm0_1.17.0-2 libxcb-sync1_1.17.0-2 libxcb-xfixes0_1.17.0-2 libxcb1_1.17.0-2 libxcomposite1_1:0.4.5-1+b1 libxcursor1_1:1.2.2-1 libxdamage1_1:1.1.6-1+b1 libxdmcp6_1:1.1.2-3+b1 libxerces2-java_2.12.2-1 libxext6_2:1.3.4-1+b1 libxfixes3_1:6.0.0-2+b1 libxft2_2.3.6-1+b1 libxi6_2:1.8.1-1 libxinerama1_2:1.1.4-3+b1 libxml-commons-external-java_1.4.01-6 libxml-commons-resolver1.1-java_1.2-11 libxml2_2.12.7+dfsg-3 libxrandr2_2:1.5.4-1 libxrender1_1:0.9.10-1.1+b1 libxshmfence1_1.3-1+b1 libxslt1.1_1.1.35-1+b1 libxsom-java_2.3.0.1-10.1 libxss1_1:1.2.3-1+b1 libxt6t64_1:1.2.1-1.2 libxtst6_2:1.2.3-1.1+b1 libxxf86vm1_1:1.1.4-1+b2 libxxhash0_0.8.2-2+b1 libxz-java_1.9-1 libz3-4_4.8.12-3.1+b2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.12-1 littler_0.3.20-1 locales-all_2.38-12 login_1:4.13+dfsg1-5 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 media-types_10.1.0 minimap2_2.27+dfsg-1 ncbi-vdb-data_3.0.2+dfsg-2 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openjdk-17-jre_17.0.11+9-1 openjdk-17-jre-headless_17.0.11+9-1 openssl_3.2.2-1 parallel_20240222+ds-2 passwd_1:4.13+dfsg1-5 patch_2.7.6-7 perl_5.38.2-5 perl-base_5.38.2-5 perl-modules-5.38_5.38.2-5 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 procps_2:4.0.4-4 python-matplotlib-data_3.6.3-2 python3_3.11.8-1 python3-appdirs_1.4.4-4 python3-argcomplete_3.3.0-1 python3-argh_0.31.2-1 python3-attr_23.2.0-2 python3-biopython_1.83+dfsg1-3 python3-brotli_1.1.0-2+b3 python3-cairo_1.26.0-1 python3-chardet_5.2.0+dfsg-1 python3-contourpy_1.0.7-3 python3-cycler_0.12.1-1 python3-dateutil_2.9.0-2 python3-decorator_5.1.1-5 python3-fonttools_4.46.0-1 python3-freetype_2.4.0-2 python3-fs_2.4.16-4 python3-gffutils_0.13-1 python3-importlib-metadata_7.1.0-1 python3-kiwisolver_1.4.5-1 python3-lxml_5.2.1-1 python3-lz4_4.0.2+dfsg-1+b3 python3-matplotlib_3.6.3-2 python3-minimal_3.11.8-1 python3-more-itertools_10.2.0-1 python3-mpmath_1.3.0-1 python3-numpy_1:1.26.4+ds-10 python3-packaging_24.0-1 python3-pil_10.3.0-2 python3-pil.imagetk_10.3.0-2 python3-pkg-resources_68.1.2-2 python3-pyfaidx_0.8.1.1-2 python3-pyparsing_3.1.2-1 python3-reportlab_4.2.0-2 python3-rlpycairo_0.3.0-3 python3-scipy_1.12.0-2 python3-simplejson_3.19.2-1+b1 python3-six_1.16.0-6 python3-sympy_1.12.1-1 python3-tk_3.12.3-3.1 python3-tz_2024.1-2 python3-ufolib2_0.16.0+dfsg1-1 python3-unicodedata2_15.1.0+ds-1+b1 python3-zipp_1.0.0-6 python3.11_3.11.9-1 python3.11-minimal_3.11.9-1 r-base-core_4.4.0-2 r-cran-cli_3.6.2-1 r-cran-colorspace_2.1-0+dfsg-1 r-cran-fansi_1.0.5-1 r-cran-farver_2.1.1-2 r-cran-ggplot2_3.5.1+dfsg-1 r-cran-glue_1.7.0-1 r-cran-gridbase_0.4-7-5 r-cran-gtable_0.3.5+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_0.3.20-1 r-cran-magrittr_2.0.3-1 r-cran-mass_7.3-60.2-1 r-cran-matrix_1.7-0-3 r-cran-mgcv_1.9-1-1 r-cran-munsell_0.5.1-1 r-cran-nlme_3.1.164-1 r-cran-pillar_1.9.0+dfsg-1 r-cran-pkgconfig_2.0.3-2 r-cran-pkgkitten_0.2.3-1 r-cran-plyr_1.8.9-1 r-cran-r6_2.5.1-1 r-cran-rcolorbrewer_1.1-3-1 r-cran-rcpp_1.0.12-1 r-cran-rlang_1.1.3-1 r-cran-scales_1.3.0-1 r-cran-tibble_3.2.1+dfsg-2 r-cran-utf8_1.2.4-1 r-cran-vctrs_0.6.5-1 r-cran-viridislite_0.4.2-2 r-cran-withr_3.0.0+dfsg-1 readline-common_8.2-4 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_0.0.22 seqtk_1.4-2 sgml-base_1.31 shared-mime-info_2.4-5 snp-sites_2.5.1-2+b1 snpeff_5.2.b+dfsg-1 sysstat_12.7.5-2 sysvinit-utils_3.09-1 tar_1.35+dfsg-3 tk8.6-blt2.5_2.5.3+dfsg-7 tzdata_2024a-4 ucf_3.0043+nmu1 unicode-data_15.1.0-1 unzip_6.0-28 usr-is-merged_39 util-linux_2.40.1-8 vt_0.57721+ds-3+b1 w3c-sgml-lib_1.3-3 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+6 xml-core_0.19 xz-utils_5.6.1+really5.4.5-1 zip_3.0-13 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ 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-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/tseemann/snippy/ Standards-Version: 4.6.2 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 ed72d252dc2dfc9b61828bcaabd906645f2a1627 5012 snippy_4.6.0+dfsg-4.debian.tar.xz Checksums-Sha256: 96c9dea7aeab6f362100fb1774d3c4377f12c2209a1fdc63b2926de912997524 271400 snippy_4.6.0+dfsg.orig.tar.xz 5f205bb4db0bc0d24410f435d8797b35b51d75866c6cda6cfd13481882878172 5012 snippy_4.6.0+dfsg-4.debian.tar.xz Files: a4eea48e48f44589cb998e609fdd27ea 271400 snippy_4.6.0+dfsg.orig.tar.xz a8e9aacecccd6e1e616a3b896d60bee3 5012 snippy_4.6.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWBdvYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF/0g/+IsS4KUVSakhaf8DW59btJj0rpn+EW84T DUALBWhRA+1/CDS+pRt2YjM/x5Zu/z+DJLXLix7bXwakOpLNt1h1/uleJucyJPIr DyOp7O2622oawcTLuLoux0kkKGcq/2VGoIoH6KqbmeJAIThKR/+iY2v9RO0yOg5e SLD4tCuuZCLCEPNXByHQX8aSJ2CcVts0RQf6PgSsvB/x7nHiSHmzqTwCXQmyBz4R Q/jSoG9JhaqqBsI+KYCEDg7skaB9gIKN0s3eVUQZrDPeq3Urha04uB2JlR6/+B3m 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debian_packaged_libs.patch dpkg-source: info: applying snpeff.config.patch dpkg-source: info: applying snpeff_v5.1+.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network snippy_4.6.0+dfsg-4 sid amd64 ---------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network snippy_4.6.0+dfsg-4 sid 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=/<> SCHROOT_ALIAS_NAME=sid-amd64-debomatic SCHROOT_CHROOT_NAME=sid-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-amd64-debomatic-1d3f5b37-61a7-4672-a5ee-61b81b490064 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-4 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-4.debian.tar.xz dpkg-source: info: building snippy in snippy_4.6.0+dfsg-4.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd test && /usr/bin/make make[2]: Entering directory '/<>/test' mkdir -p S1 wgsim -S 1 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S1/R2.fq S1/R1.fq > S1/dwgsim.tab [wgsim] seed = 1 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S2/R2.fq S2/R1.fq > S2/dwgsim.tab [wgsim] seed = 2 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S3/R2.fq S3/R1.fq > S3/dwgsim.tab [wgsim] seed = 3 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S4/R2.fq S4/R1.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 S1 --R1 S1/R1.fq --R2 S1/R2.fq [19:07:41] This is snippy 4.6.0 [19:07:41] Written by Torsten Seemann [19:07:41] Obtained from https://github.com/tseemann/snippy [19:07:41] Detected operating system: linux [19:07:41] Enabling bundled linux tools. [19:07:41] Found bwa - /usr/bin/bwa [19:07:41] Found bcftools - /usr/bin/bcftools [19:07:41] Found samtools - /usr/bin/samtools [19:07:41] Found java - /usr/bin/java [19:07:41] Found snpEff - /usr/bin/snpEff [19:07:41] Found samclip - /usr/bin/samclip [19:07:41] Found seqtk - /usr/bin/seqtk [19:07:41] Found parallel - /usr/bin/parallel [19:07:41] Found freebayes - /usr/bin/freebayes [19:07:41] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [19:07:41] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [19:07:41] Found vcfstreamsort - /usr/bin/vcfstreamsort [19:07:41] Found vcfuniq - /usr/bin/vcfuniq [19:07:41] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [19:07:41] Found gzip - /usr/bin/gzip [19:07:41] Found vt - /usr/bin/vt [19:07:41] Found snippy-vcf_to_tab - /<>/bin/snippy-vcf_to_tab [19:07:41] Found snippy-vcf_report - /<>/bin/snippy-vcf_report [19:07:42] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [19:07:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [19:07:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [19:07:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [19:07:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:07:42] Using reference: /<>/test/example.fna [19:07:42] Treating reference as 'fasta' format. [19:07:42] Will use 2 CPU cores. [19:07:42] Using read file: /<>/test/S1/R1.fq [19:07:42] Using read file: /<>/test/S1/R2.fq [19:07:42] Used --force, will overwrite existing S1 [19:07:42] Changing working directory: S1 [19:07:42] Creating reference folder: reference [19:07:42] Extracting FASTA and GFF from reference. [19:07:42] Wrote 3 sequences to ref.fa [19:07:42] Wrote 0 features to ref.gff [19:07:42] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [19:07:42] Using BAM RG (Read Group) ID: S1 [19:07:42] Running: samtools faidx reference/ref.fa 2>> snps.log [19:07:42] Running: bwa index reference/ref.fa 2>> snps.log [19:07:42] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [19:07:42] Running: ln -sf reference/ref.fa . 2>> snps.log [19:07:42] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [19:07:42] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [19:07:42] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /<>/test/S1/R1.fq /<>/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 [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [M::process] read 24000 sequences (2400000 bp)... [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 1.159 CPU sec, 1.200 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /<>/test/S1/R1.fq /<>/test/S1/R2.fq [main] Real time: 1.316 sec; CPU: 1.191 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 5 lines [samclip] Done. [19:07:44] Running: samtools index snps.bam 2>> snps.log [19:07:44] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [19:07:44] 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 [19:07:46] 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 [19:07:46] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [19:07:46] Running: /<>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [19:07:46] Running: /<>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [19:07:46] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [19:07:46] Running: bcftools index -f snps.vcf.gz 2>> snps.log [19:07:46] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [19:07:46] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [19:07:46] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [19:07:46] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [19:07:46] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [19:07:46] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [19:07:46] Marked 749 heterozygous sites with 'n' [19:07:46] Creating extra output files: BED GFF CSV TXT HTML [19:07:46] Identified 261 variants. [19:07:46] Result folder: S1 [19:07:46] Result files: [19:07:46] * S1/snps.aligned.fa [19:07:46] * S1/snps.bam [19:07:46] * S1/snps.bam.bai [19:07:46] * S1/snps.bed [19:07:46] * S1/snps.consensus.fa [19:07:46] * S1/snps.consensus.subs.fa [19:07:46] * S1/snps.csv [19:07:46] * S1/snps.filt.vcf [19:07:46] * S1/snps.gff [19:07:46] * S1/snps.html [19:07:46] * S1/snps.log [19:07:46] * S1/snps.raw.vcf [19:07:46] * S1/snps.subs.vcf [19:07:46] * S1/snps.tab [19:07:46] * S1/snps.txt [19:07:46] * S1/snps.vcf [19:07:46] * S1/snps.vcf.gz [19:07:46] * S1/snps.vcf.gz.csi [19:07:46] Walltime used: 5 seconds [19:07:46] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md [19:07:46] Done. ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq [19:07:47] This is snippy 4.6.0 [19:07:47] Written by Torsten Seemann [19:07:47] Obtained from https://github.com/tseemann/snippy [19:07:47] Detected operating system: linux [19:07:47] Enabling bundled linux tools. [19:07:47] Found bwa - /usr/bin/bwa [19:07:47] Found bcftools - /usr/bin/bcftools [19:07:47] Found samtools - /usr/bin/samtools [19:07:47] Found java - /usr/bin/java [19:07:47] Found snpEff - /usr/bin/snpEff [19:07:47] Found samclip - /usr/bin/samclip [19:07:47] Found seqtk - /usr/bin/seqtk [19:07:47] Found parallel - /usr/bin/parallel [19:07:47] Found freebayes - /usr/bin/freebayes [19:07:47] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [19:07:47] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [19:07:47] Found vcfstreamsort - /usr/bin/vcfstreamsort [19:07:47] Found vcfuniq - /usr/bin/vcfuniq [19:07:47] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [19:07:47] Found gzip - /usr/bin/gzip [19:07:47] Found vt - /usr/bin/vt [19:07:47] Found snippy-vcf_to_tab - /<>/bin/snippy-vcf_to_tab [19:07:47] Found snippy-vcf_report - /<>/bin/snippy-vcf_report [19:07:47] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [19:07:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [19:07:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [19:07:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [19:07:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:07:47] Using reference: /<>/test/example.fna [19:07:47] Treating reference as 'fasta' format. [19:07:47] Will use 2 CPU cores. [19:07:47] Using read file: /<>/test/S2/R1.fq [19:07:47] Using read file: /<>/test/S2/R2.fq [19:07:47] Used --force, will overwrite existing S2 [19:07:47] Changing working directory: S2 [19:07:47] Creating reference folder: reference [19:07:47] Extracting FASTA and GFF from reference. [19:07:47] Wrote 3 sequences to ref.fa [19:07:47] Wrote 0 features to ref.gff [19:07:47] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [19:07:47] Using BAM RG (Read Group) ID: S2 [19:07:47] Running: samtools faidx reference/ref.fa 2>> snps.log [19:07:47] Running: bwa index reference/ref.fa 2>> snps.log [19:07:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [19:07:47] Running: ln -sf reference/ref.fa . 2>> snps.log [19:07:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [19:07:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [19:07:47] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /<>/test/S2/R1.fq /<>/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (165, 199, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 366) [M::mem_pestat] mean and std.dev: (199.27, 48.61) [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.133 CPU sec, 1.125 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /<>/test/S2/R1.fq /<>/test/S2/R2.fq [main] Real time: 1.280 sec; CPU: 1.161 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 5 lines [samclip] Done. [19:07:49] Running: samtools index snps.bam 2>> snps.log [19:07:49] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [19:07:49] 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 [19:07:51] 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 [19:07:51] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [19:07:51] Running: /<>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [19:07:51] Running: /<>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [19:07:51] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [19:07:51] Running: bcftools index -f snps.vcf.gz 2>> snps.log [19:07:51] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [19:07:51] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [19:07:51] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [19:07:51] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [19:07:51] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [19:07:52] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [19:07:52] Marked 841 heterozygous sites with 'n' [19:07:52] Creating extra output files: BED GFF CSV TXT HTML [19:07:52] Identified 246 variants. [19:07:52] Result folder: S2 [19:07:52] Result files: [19:07:52] * S2/snps.aligned.fa [19:07:52] * S2/snps.bam [19:07:52] * S2/snps.bam.bai [19:07:52] * S2/snps.bed [19:07:52] * S2/snps.consensus.fa [19:07:52] * S2/snps.consensus.subs.fa [19:07:52] * S2/snps.csv [19:07:52] * S2/snps.filt.vcf [19:07:52] * S2/snps.gff [19:07:52] * S2/snps.html [19:07:52] * S2/snps.log [19:07:52] * S2/snps.raw.vcf [19:07:52] * S2/snps.subs.vcf [19:07:52] * S2/snps.tab [19:07:52] * S2/snps.txt [19:07:52] * S2/snps.vcf [19:07:52] * S2/snps.vcf.gz [19:07:52] * S2/snps.vcf.gz.csi [19:07:52] Walltime used: 5 seconds [19:07:52] Did you know? Snippy is a combination of SNP, Skippy, and snappy. [19:07:52] Done. ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq [19:07:52] This is snippy 4.6.0 [19:07:52] Written by Torsten Seemann [19:07:52] Obtained from https://github.com/tseemann/snippy [19:07:52] Detected operating system: linux [19:07:52] Enabling bundled linux tools. [19:07:52] Found bwa - /usr/bin/bwa [19:07:52] Found bcftools - /usr/bin/bcftools [19:07:52] Found samtools - /usr/bin/samtools [19:07:52] Found java - /usr/bin/java [19:07:52] Found snpEff - /usr/bin/snpEff [19:07:52] Found samclip - /usr/bin/samclip [19:07:52] Found seqtk - /usr/bin/seqtk [19:07:52] Found parallel - /usr/bin/parallel [19:07:52] Found freebayes - /usr/bin/freebayes [19:07:52] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [19:07:52] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [19:07:52] Found vcfstreamsort - /usr/bin/vcfstreamsort [19:07:52] Found vcfuniq - /usr/bin/vcfuniq [19:07:52] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [19:07:52] Found gzip - /usr/bin/gzip [19:07:52] Found vt - /usr/bin/vt [19:07:52] Found snippy-vcf_to_tab - /<>/bin/snippy-vcf_to_tab [19:07:52] Found snippy-vcf_report - /<>/bin/snippy-vcf_report [19:07:52] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [19:07:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [19:07:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [19:07:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [19:07:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:07:53] Using reference: /<>/test/example.fna [19:07:53] Treating reference as 'fasta' format. [19:07:53] Will use 2 CPU cores. [19:07:53] Using read file: /<>/test/S3/R1.fq [19:07:53] Using read file: /<>/test/S3/R2.fq [19:07:53] Used --force, will overwrite existing S3 [19:07:53] Changing working directory: S3 [19:07:53] Creating reference folder: reference [19:07:53] Extracting FASTA and GFF from reference. [19:07:53] Wrote 3 sequences to ref.fa [19:07:53] Wrote 0 features to ref.gff [19:07:53] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [19:07:53] Using BAM RG (Read Group) ID: S3 [19:07:53] Running: samtools faidx reference/ref.fa 2>> snps.log [19:07:53] Running: bwa index reference/ref.fa 2>> snps.log [19:07:53] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [19:07:53] Running: ln -sf reference/ref.fa . 2>> snps.log [19:07:53] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [19:07:53] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [19:07:53] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /<>/test/S3/R1.fq /<>/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368) [M::mem_pestat] mean and std.dev: (198.46, 48.83) [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 24000 reads in 1.146 CPU sec, 1.166 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /<>/test/S3/R1.fq /<>/test/S3/R2.fq [main] Real time: 1.292 sec; CPU: 1.178 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 5 lines [samclip] Done. [19:07:55] Running: samtools index snps.bam 2>> snps.log [19:07:55] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [19:07:55] 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 [19:07:56] 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 [19:07:56] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [19:07:56] Running: /<>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [19:07:56] Running: /<>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [19:07:57] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [19:07:57] Running: bcftools index -f snps.vcf.gz 2>> snps.log [19:07:57] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [19:07:57] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [19:07:57] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [19:07:57] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [19:07:57] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [19:07:57] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [19:07:57] Marked 846 heterozygous sites with 'n' [19:07:57] Creating extra output files: BED GFF CSV TXT HTML [19:07:57] Identified 254 variants. [19:07:57] Result folder: S3 [19:07:57] Result files: [19:07:57] * S3/snps.aligned.fa [19:07:57] * S3/snps.bam [19:07:57] * S3/snps.bam.bai [19:07:57] * S3/snps.bed [19:07:57] * S3/snps.consensus.fa [19:07:57] * S3/snps.consensus.subs.fa [19:07:57] * S3/snps.csv [19:07:57] * S3/snps.filt.vcf [19:07:57] * S3/snps.gff [19:07:57] * S3/snps.html [19:07:57] * S3/snps.log [19:07:57] * S3/snps.raw.vcf [19:07:57] * S3/snps.subs.vcf [19:07:57] * S3/snps.tab [19:07:57] * S3/snps.txt [19:07:57] * S3/snps.vcf [19:07:57] * S3/snps.vcf.gz [19:07:57] * S3/snps.vcf.gz.csi [19:07:57] Walltime used: 5 seconds [19:07:57] Found a bug? Post it at https://github.com/tseemann/snippy/issues [19:07:57] Done. ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq [19:07:57] This is snippy 4.6.0 [19:07:57] Written by Torsten Seemann [19:07:57] Obtained from https://github.com/tseemann/snippy [19:07:57] Detected operating system: linux [19:07:57] Enabling bundled linux tools. [19:07:57] Found bwa - /usr/bin/bwa [19:07:57] Found bcftools - /usr/bin/bcftools [19:07:57] Found samtools - /usr/bin/samtools [19:07:57] Found java - /usr/bin/java [19:07:57] Found snpEff - /usr/bin/snpEff [19:07:57] Found samclip - /usr/bin/samclip [19:07:57] Found seqtk - /usr/bin/seqtk [19:07:57] Found parallel - /usr/bin/parallel [19:07:57] Found freebayes - /usr/bin/freebayes [19:07:57] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [19:07:57] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [19:07:57] Found vcfstreamsort - /usr/bin/vcfstreamsort [19:07:57] Found vcfuniq - /usr/bin/vcfuniq [19:07:57] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [19:07:57] Found gzip - /usr/bin/gzip [19:07:57] Found vt - /usr/bin/vt [19:07:57] Found snippy-vcf_to_tab - /<>/bin/snippy-vcf_to_tab [19:07:57] Found snippy-vcf_report - /<>/bin/snippy-vcf_report [19:07:57] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [19:07:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [19:07:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [19:07:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [19:07:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:07:57] Using reference: /<>/test/example.fna [19:07:57] Treating reference as 'fasta' format. [19:07:57] Will use 2 CPU cores. [19:07:57] Using read file: /<>/test/S4/R1.fq [19:07:57] Using read file: /<>/test/S4/R2.fq [19:07:57] Used --force, will overwrite existing S4 [19:07:57] Changing working directory: S4 [19:07:57] Creating reference folder: reference [19:07:57] Extracting FASTA and GFF from reference. [19:07:57] Wrote 3 sequences to ref.fa [19:07:57] Wrote 0 features to ref.gff [19:07:57] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. [19:07:57] Using BAM RG (Read Group) ID: S4 [19:07:57] Running: samtools faidx reference/ref.fa 2>> snps.log [19:07:57] Running: bwa index reference/ref.fa 2>> snps.log [19:07:57] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [19:07:57] Running: ln -sf reference/ref.fa . 2>> snps.log [19:07:57] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [19:07:57] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [19:07:57] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /<>/test/S4/R1.fq /<>/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 1.137 CPU sec, 1.161 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /<>/test/S4/R1.fq /<>/test/S4/R2.fq [main] Real time: 1.286 sec; CPU: 1.167 sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 5 lines [samclip] Done. [19:07:59] Running: samtools index snps.bam 2>> snps.log [19:07:59] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log [19:07:59] 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 [19:08:01] 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 [19:08:01] Running: cp snps.filt.vcf snps.vcf 2>> snps.log [19:08:01] Running: /<>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [19:08:02] Running: /<>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [19:08:02] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [19:08:02] Running: bcftools index -f snps.vcf.gz 2>> snps.log [19:08:02] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [19:08:02] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [19:08:02] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [19:08:02] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [19:08:02] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [19:08:02] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [19:08:02] Marked 799 heterozygous sites with 'n' [19:08:02] Creating extra output files: BED GFF CSV TXT HTML [19:08:02] Identified 257 variants. [19:08:02] Result folder: S4 [19:08:02] Result files: [19:08:02] * S4/snps.aligned.fa [19:08:02] * S4/snps.bam [19:08:02] * S4/snps.bam.bai [19:08:02] * S4/snps.bed [19:08:02] * S4/snps.consensus.fa [19:08:02] * S4/snps.consensus.subs.fa [19:08:02] * S4/snps.csv [19:08:02] * S4/snps.filt.vcf [19:08:02] * S4/snps.gff [19:08:02] * S4/snps.html [19:08:02] * S4/snps.log [19:08:02] * S4/snps.raw.vcf [19:08:02] * S4/snps.subs.vcf [19:08:02] * S4/snps.tab [19:08:02] * S4/snps.txt [19:08:02] * S4/snps.vcf [19:08:02] * S4/snps.vcf.gz [19:08:02] * S4/snps.vcf.gz.csi [19:08:02] Walltime used: 5 seconds [19:08:02] Found a bug? Post it at https://github.com/tseemann/snippy/issues [19:08:02] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Will mask 0 regions totalling 0 bp ~ 0.00% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core.tab Opening: core.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln Found a bug? Post it at http://github.com/tseemann/snippy/issues Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/bin/any2fasta Found samtools - /usr/bin/samtools Found minimap2 - /usr/bin/minimap2 Found bedtools - /usr/bin/bedtools Found snp-sites - /usr/bin/snp-sites Saving reference FASTA: core-mask.ref.fa This is any2fasta 0.4.2 Opening 'example.fna' Detected FASTA format Read 5294 lines from 'example.fna' Wrote 3 sequences from FASTA file. Processed 1 files. Done. Loaded 3 sequences totalling 317336 bp. Loading mask bed file: example.bed Will mask 8 regions totalling 3101 bp ~ 0.98% 0 S1 snp=239 del=23 ins=23 het=749 unaligned=9643 1 S2 snp=230 del=15 ins=11 het=841 unaligned=9428 2 S3 snp=226 del=28 ins=14 het=846 unaligned=9376 3 S4 snp=227 del=32 ins=14 het=799 unaligned=9707 Opening: core-mask.tab Opening: core-mask.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Masking alignment at 8 regions Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues Done. wc -l S?/snps.tab 262 S1/snps.tab 247 S2/snps.tab 255 S3/snps.tab 258 S4/snps.tab 1022 total make[2]: Leaving directory '/<>/test' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile make[1]: Leaving directory '/<>' 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-4_all.deb'. dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-4_all.deb'. dpkg-genbuildinfo -O../snippy_4.6.0+dfsg-4_amd64.buildinfo dpkg-genchanges -O../snippy_4.6.0+dfsg-4_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 2024-06-05T19:08:06Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ snippy_4.6.0+dfsg-4_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 19 Dec 2023 10:44:31 +0100 Source: snippy Binary: snippy snippy-examples Architecture: source all Version: 4.6.0+dfsg-4 Distribution: sid 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: 1029202 Changes: snippy (4.6.0+dfsg-4) unstable; urgency=medium . * Work with snpeff >= 5.1 Closes: #1029202 In the second part of the patch the first line which invalidates the resulting vcf file is removed via sed. This needs further discussion with SnpEff upstream (issue #510) * Add another test - for the moment just for users local machine in examples since its quite some effort for autopkgtest * Set upstream metadata fields: Repository. 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optional snippy_4.6.0+dfsg-4.dsc a8e9aacecccd6e1e616a3b896d60bee3 5012 science optional snippy_4.6.0+dfsg-4.debian.tar.xz 7822c0241d9f5ef5e41b25a6c4dda068 310448 science optional snippy-examples_4.6.0+dfsg-4_all.deb 935f121e2e0860252fec355bd79559d5 26836 science optional snippy_4.6.0+dfsg-4_all.deb 12cf538c53b470ac82a13a5f051bf03a 18325 science optional snippy_4.6.0+dfsg-4_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: snippy Binary: snippy snippy-examples Architecture: all source Version: 4.6.0+dfsg-4 Checksums-Md5: 1886d71e12c5155bf5d6e4ed0d21a549 1445 snippy_4.6.0+dfsg-4.dsc 7822c0241d9f5ef5e41b25a6c4dda068 310448 snippy-examples_4.6.0+dfsg-4_all.deb 935f121e2e0860252fec355bd79559d5 26836 snippy_4.6.0+dfsg-4_all.deb Checksums-Sha1: 36e9f139149f14b9061ca23e9260f95be3d69d42 1445 snippy_4.6.0+dfsg-4.dsc b2e17940a5f9cbae3028a134ea10d6f568177e40 310448 snippy-examples_4.6.0+dfsg-4_all.deb f83e64821e25c65ce7274fe3fc438adc68109c52 26836 snippy_4.6.0+dfsg-4_all.deb Checksums-Sha256: 19ef251b6e9c23080fd7daf51bf449ca02fd96f2a70a37d36f0709f493023d8b 1445 snippy_4.6.0+dfsg-4.dsc 3e5b3a0428aba3b9e3ea68c6758ad51ed3fab42f028ad7a17be26f48ce0793ab 310448 snippy-examples_4.6.0+dfsg-4_all.deb fc59e9199a4c60fedb85bd028a5ba399278da9e8be0247d0e367c4d92f6f8129 26836 snippy_4.6.0+dfsg-4_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 05 Jun 2024 19:08:06 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adwaita-icon-theme (= 46.0-1), ant (= 1.10.14-1), ant-optional (= 1.10.14-1), any2fasta (= 0.4.2-2), at-spi2-common (= 2.52.0-1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), bcftools (= 1.20-1), bedtools (= 2.31.1+dfsg-2), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), blt (= 2.5.3+dfsg-7), bsdextrautils (= 2.40.1-8), bsdutils (= 1:2.40.1-8), build-essential (= 12.10), bwa (= 0.7.17-7+b3), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), ca-certificates-java (= 20240118), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), default-jre (= 2:1.17-75), default-jre-headless (= 2:1.17-75), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), fontconfig (= 2.15.0-1.1), fontconfig-config (= 2.15.0-1.1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lyx (= 2.4.0-1), fonts-urw-base35 (= 20200910-8), freebayes (= 1.3.7-1), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gtk-update-icon-cache (= 3.24.42-1), gzip (= 1.12-1.1), hicolor-icon-theme (= 0.18-1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), java-common (= 0.75), junit4 (= 4.13.2-4), junit5 (= 5.10.1-1), libacl1 (= 2.3.2-2), libactivation-java (= 1.2.0-2), libantlr4-runtime-java (= 4.9.2-2), libaopalliance-java (= 20070526-7), libapache-pom-java (= 29-2), libapfloat-java (= 1.13.0-1), libapiguardian-java (= 1.1.2-1), libarchive-zip-perl (= 1.68-1), libargs4j-java (= 2.33-2), libasan8 (= 14.1.0-1), libasm-java (= 9.7-1), libasound2-data (= 1.2.11-1), libasound2t64 (= 1.2.11-1+b1), libatinject-jsr330-api-java (= 1.0+ds1-5), libatk1.0-0t64 (= 2.52.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libavahi-client3 (= 0.8-13+b2), libavahi-common-data (= 0.8-13+b2), libavahi-common3 (= 0.8-13+b2), libbinutils (= 2.42-4), libbio-perl-perl (= 1.7.8-1), libbiojava6-java (= 6.1.0+dfsg-4), libblas3 (= 3.12.0-3), libblkid1 (= 2.40.1-8), libbrotli1 (= 1.1.0-2+b3), libbsd0 (= 0.12.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcairo2 (= 1.18.0-3+b1), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.1.0-1), libcdi-api-java (= 1.2-3), libcharts4j-java (= 1.3-4), libciftools-java (= 6.0.0-1), libcodemodel-java (= 2.6+jaxb2.3.0.1-10.1), libcom-err2 (= 1.47.1-1), libcommons-cli-java (= 1.6.0-1), libcommons-codec-java (= 1.16.0-1), libcommons-compress-java (= 1.25.0-1), libcommons-exec-java (= 1.3-2), libcommons-io-java (= 2.16.1-1), libcommons-jexl2-java (= 2.1.1-6), libcommons-lang-java (= 2.6-10), libcommons-lang3-java (= 3.14.0-1), libcommons-logging-java (= 1.3.0-1), libcommons-math-java (= 2.2-8), libcommons-math3-java (= 3.6.1-3), libcommons-parent-java (= 56-1), libcommons-text-java (= 1.11.0-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libcups2t64 (= 2.4.7-1.2+b1), libcurl3t64-gnutls (= 8.8.0-1), libcurl4t64 (= 8.8.0-1), libdata-stag-perl (= 0.14-3), libdatrie1 (= 0.2.13-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdbus-1-3 (= 1.14.10-4+b1), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdeflate0 (= 1.20-1), libdisorder0 (= 0.0.2+git20130809.8062ee1-4+b1), libdistlib-java (= 1.0-5), libdom4j-java (= 2.1.4-1), libdpkg-perl (= 1.22.6), libdrm-amdgpu1 (= 2.4.120-2), libdrm-common (= 2.4.120-2), libdrm-intel1 (= 2.4.120-2), libdrm-radeon1 (= 2.4.120-2), libdrm2 (= 2.4.120-2), libdtd-parser-java (= 1.2-1), libedit2 (= 3.1-20240517-1), libelf1t64 (= 0.191-1+b1), liberror-prone-java (= 2.18.0-1), libexec-maven-plugin-java (= 3.1.0-2), libexpat1 (= 2.6.2-1), libfastahack0 (= 1.0.0+dfsg-11+b1), libfastinfoset-java (= 1.2.12-3), libfastutil-java (= 8.5.12+dfsg-2), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libfml0 (= 0.1+git20190320.b499514-1+b1), libfontconfig1 (= 2.15.0-1.1), libfontenc1 (= 1:1.1.8-1), libfreemarker-java (= 2.3.32-2), libfreetype6 (= 2.13.2+dfsg-1+b4), libfribidi0 (= 1.0.13-3+b1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgcrypt20 (= 1.10.3-3), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgdk-pixbuf-2.0-0 (= 2.42.12+dfsg-1), 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 (= 14.1.0-1), libgif7 (= 5.2.2-1), libgl1 (= 1.7.0-1+b1), libgl1-mesa-dri (= 24.1.0-2), libglapi-mesa (= 24.1.0-2), libglib2.0-0t64 (= 2.80.2-2), libglvnd0 (= 1.7.0-1+b1), libglx-mesa0 (= 24.1.0-2), libglx0 (= 1.7.0-1+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.5-4), libgomp1 (= 14.1.0-1), libgoogle-gson-java (= 2.10.1-1), libgpg-error0 (= 1.49-2), libgprofng0 (= 2.42-4), libgraphite2-3 (= 1.3.14-2), libgssapi-krb5-2 (= 1.20.1-6+b1), libgtk2.0-0t64 (= 2.24.33-4), libgtk2.0-common (= 2.24.33-4), libguava-java (= 32.0.1-1), libguice-java (= 4.2.3-2), libhamcrest-java (= 2.2-2), libharfbuzz0b (= 8.3.0-2+b1), libhogweed6t64 (= 3.9.1-2.2), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.0-1+b1), libhtsjdk-java (= 4.1.0+dfsg-2), libhttpclient-java (= 4.5.14-1), libhttpcore-java (= 4.4.16-1), libhwasan0 (= 14.1.0-1), libice6 (= 2:1.0.10-1+b1), libicu72 (= 72.1-4+b1), libidn2-0 (= 2.3.7-2), libimagequant0 (= 2.18.0-1+b1), libinchi1 (= 1.03+dfsg-4+b2), libio-string-perl (= 1.08-4), libisl23 (= 0.26-3+b2), libistack-commons-java (= 3.0.6-5), libitext5-java (= 5.5.13.3-4), libitm1 (= 14.1.0-1), 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+b2), libjaxb-api-java (= 2.3.1-1), libjaxb-java (= 2.3.0.1-10.1), libjaxen-java (= 1.1.6-4), libjbig0 (= 2.1-6.1+b1), libjgrapht-java (= 1.5.2-1), libjgraphx-java (= 2.1.0.7-3), libjheaps-java (= 0.14-2), libjmol-java (= 16.2.15+dfsg-1), libjni-inchi-java (= 0.8+dfsg-7), libjni-inchi-jni (= 0.8+dfsg-7), libjpeg62-turbo (= 1:2.1.5-3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjson-simple-java (= 2.3.0-1), libjsoncpp25 (= 1.9.5-6+b2), libjsoup-java (= 1.15.3-1), libjsr305-java (= 0.1~+svn49-11), libk5crypto3 (= 1.20.1-6+b1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6+b1), libkrb5support0 (= 1.20.1-6+b1), liblapack3 (= 3.12.0-3), liblbfgsb0 (= 3.0+dfsg.4-1+b1), liblcms2-2 (= 2.14-2+b1), libldap-2.5-0 (= 2.5.17+dfsg-1), liblerc4 (= 4.0.0+ds-4+b1), libllvm17t64 (= 1:17.0.6-12), liblog4j1.2-java (= 1.2.17-11), liblsan0 (= 14.1.0-1), liblz4-1 (= 1.9.4-2), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmaven-archiver-java (= 3.6.0-1), libmaven-compiler-plugin-java (= 3.10.1-2), libmaven-file-management-java (= 3.0.0-1), libmaven-jar-plugin-java (= 3.3.0-2), libmaven-parent-java (= 35-1), libmaven-resolver-java (= 1.6.3-1), libmaven-shared-incremental-java (= 1.1-4), libmaven-shared-io-java (= 3.0.0-4), libmaven-shared-utils-java (= 3.3.4-1), libmaven3-core-java (= 3.8.7-2), libmbedcrypto7t64 (= 2.28.8-1), libmbedtls14t64 (= 2.28.8-1), libmbedx509-1t64 (= 2.28.8-1), libmd0 (= 1.1.0-2), libmjson-java (= 1.4.0-3), libmmtf-java (= 1.0.11-1), libmount1 (= 2.40.1-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libmsgpack-java (= 0.9.6-1), libnaga-java (= 3.0+svn80-5), libncbi-ngs3 (= 3.0.3+dfsg-7+b1), libncbi-vdb3 (= 3.0.2+dfsg-2+b1), libncurses6 (= 6.5-2), libncursesw6 (= 6.5-2), libnettle8t64 (= 3.9.1-2.2), libnghttp2-14 (= 1.61.0-1+b1), libngs-java (= 3.0.3+dfsg-7+b1), libngs-jni (= 3.0.3+dfsg-7+b1), libnspr4 (= 2:4.35-1.1+b1), libnss3 (= 2:3.100-1), libopenjp2-7 (= 2.5.0-2+b3), libopentest4j-java (= 1.2.0-4), libopentest4j-reporting-java (= 0.1.0-M1-2), libp11-kit0 (= 0.25.3-5), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpango-1.0-0 (= 1.52.2+ds-1), libpangocairo-1.0-0 (= 1.52.2+ds-1), libpangoft2-1.0-0 (= 1.52.2+ds-1), libpaper-utils (= 1.1.29+b1), libpaper1 (= 1.1.29+b1), libpciaccess0 (= 0.17-3+b1), libpcre2-8-0 (= 10.42-4+b1), libpcsclite1 (= 2.2.3-1), libperl5.38t64 (= 5.38.2-5), libpicocli-java (= 4.6.2-2), libpipeline1 (= 1.5.7-2), libpixman-1-0 (= 0.42.2-1+b1), libplexus-archiver-java (= 4.6.1-1), libplexus-cipher-java (= 2.0-1), libplexus-classworlds-java (= 2.7.0-1), libplexus-compiler-java (= 2.12.1-2), libplexus-component-annotations-java (= 2.1.1-1), libplexus-container-default-java (= 2.1.1-1), libplexus-interpolation-java (= 1.26-1), 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 (= 1.6.43-5), libproc2-0 (= 2:4.0.4-4), libpsl5t64 (= 0.21.2-1.1), libpython3-stdlib (= 3.11.8-1), libpython3.11-minimal (= 3.11.9-1), libpython3.11-stdlib (= 3.11.9-1), libqdox2-java (= 2.0.3-1), libqhull-r8.0 (= 2020.2-6+b1), libquadmath0 (= 14.1.0-1), libraqm0 (= 0.10.1-1+b1), libreadline8t64 (= 8.2-4), librelaxng-datatype-java (= 1.0+ds1-3.1), librhino-java (= 1.7.14-2.1), librngom-java (= 2.3.0.1-10.1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-6), libsasl2-modules-db (= 2.1.28+dfsg1-6), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsensors-config (= 1:3.6.0-10), libsensors5 (= 1:3.6.0-10), libseqlib2 (= 1.2.0+dfsg-11+b1), libsframe1 (= 2.42-4), libsharpyuv0 (= 1.4.0-0.1), libsisu-inject-java (= 0.3.4-2), libsisu-plexus-java (= 0.3.4-3), libslf4j-java (= 1.7.32-1), libsm6 (= 2:1.2.3-1+b1), libsmartcols1 (= 2.40.1-8), libsmithwaterman0 (= 0.0+git20160702.2610e25-12+b1), libsnappy-java (= 1.1.10.5-2), libsnappy-jni (= 1.1.10.5-2), libsnappy1v5 (= 1.2.1-1), libsnp-sites1 (= 2.5.1-2+b1), libsnpeff-java (= 5.2.b+dfsg-1), libsqlite3-0 (= 3.46.0-1), libssh2-1t64 (= 1.11.0-5), libssl3t64 (= 3.2.2-1), libssw0 (= 1.1-14+b1), libstax-ex-java (= 1.7.8-3), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libstreambuffer-java (= 1.5.4-1.1), libsystemd0 (= 256~rc3-7), libtabixpp0t64 (= 1.1.2-2.1), libtasn1-6 (= 4.19.0-3+b2), libtcl8.6 (= 8.6.14+dfsg-1), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2), libtiff6 (= 4.5.1+git230720-4), libtinfo6 (= 6.5-2), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3), libtk8.6 (= 8.6.14-1), libtool (= 2.4.7-7), libtrove3-java (= 3.0.3-5), libtsan2 (= 14.1.0-1), libtxw2-java (= 2.3.0.1-10.1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), libunivocity-parsers-java (= 2.9.1-1), libuuid1 (= 2.40.1-8), libvcflib-tools (= 1.0.9+dfsg1-3+b1), libvcflib2 (= 1.0.9+dfsg1-3+b1), libvecmath-java (= 1.5.2-7), libvulkan1 (= 1.3.283.0-1), libwagon-http-java (= 3.5.3-1), libwagon-provider-api-java (= 3.5.3-1), libwebp7 (= 1.4.0-0.1), libwebpdemux2 (= 1.4.0-0.1), libwebpmux3 (= 1.4.0-0.1), libwfa2-0 (= 2.3.3-4), libx11-6 (= 2:1.8.7-1+b1), libx11-data (= 2:1.8.7-1), libx11-xcb1 (= 2:1.8.7-1+b1), libxau6 (= 1:1.0.9-1+b1), libxbean-reflect-java (= 4.5-8), libxcb-dri2-0 (= 1.17.0-2), libxcb-dri3-0 (= 1.17.0-2), libxcb-glx0 (= 1.17.0-2), libxcb-present0 (= 1.17.0-2), libxcb-randr0 (= 1.17.0-2), libxcb-render0 (= 1.17.0-2), libxcb-shm0 (= 1.17.0-2), libxcb-sync1 (= 1.17.0-2), libxcb-xfixes0 (= 1.17.0-2), libxcb1 (= 1.17.0-2), libxcomposite1 (= 1:0.4.5-1+b1), libxcursor1 (= 1:1.2.2-1), libxdamage1 (= 1:1.1.6-1+b1), libxdmcp6 (= 1:1.1.2-3+b1), libxerces2-java (= 2.12.2-1), libxext6 (= 2:1.3.4-1+b1), libxfixes3 (= 1:6.0.0-2+b1), libxft2 (= 2.3.6-1+b1), libxi6 (= 2:1.8.1-1), libxinerama1 (= 2:1.1.4-3+b1), libxml-commons-external-java (= 1.4.01-6), libxml-commons-resolver1.1-java (= 1.2-11), libxml2 (= 2.12.7+dfsg-3), libxrandr2 (= 2:1.5.4-1), libxrender1 (= 1:0.9.10-1.1+b1), libxshmfence1 (= 1.3-1+b1), libxslt1.1 (= 1.1.35-1+b1), libxsom-java (= 2.3.0.1-10.1), libxss1 (= 1:1.2.3-1+b1), libxt6t64 (= 1:1.2.1-1.2), libxtst6 (= 2:1.2.3-1.1+b1), libxxf86vm1 (= 1:1.1.4-1+b2), libxz-java (= 1.9-1), libz3-4 (= 4.8.12-3.1+b2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), littler (= 0.3.20-1), login (= 1:4.13+dfsg1-5), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), minimap2 (= 2.27+dfsg-1), ncbi-vdb-data (= 3.0.2+dfsg-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), openjdk-17-jre (= 17.0.11+9-1), openjdk-17-jre-headless (= 17.0.11+9-1), openssl (= 3.2.2-1), parallel (= 20240222+ds-2), patch (= 2.7.6-7), perl (= 5.38.2-5), perl-base (= 5.38.2-5), perl-modules-5.38 (= 5.38.2-5), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-4), python-matplotlib-data (= 3.6.3-2), python3 (= 3.11.8-1), python3-appdirs (= 1.4.4-4), python3-argcomplete (= 3.3.0-1), python3-argh (= 0.31.2-1), python3-attr (= 23.2.0-2), python3-biopython (= 1.83+dfsg1-3), python3-brotli (= 1.1.0-2+b3), python3-cairo (= 1.26.0-1), python3-chardet (= 5.2.0+dfsg-1), python3-contourpy (= 1.0.7-3), python3-cycler (= 0.12.1-1), python3-dateutil (= 2.9.0-2), python3-decorator (= 5.1.1-5), python3-fonttools (= 4.46.0-1), python3-freetype (= 2.4.0-2), python3-fs (= 2.4.16-4), python3-gffutils (= 0.13-1), python3-importlib-metadata (= 7.1.0-1), python3-kiwisolver (= 1.4.5-1), python3-lxml (= 5.2.1-1), python3-lz4 (= 4.0.2+dfsg-1+b3), python3-matplotlib (= 3.6.3-2), python3-minimal (= 3.11.8-1), python3-more-itertools (= 10.2.0-1), python3-mpmath (= 1.3.0-1), python3-numpy (= 1:1.26.4+ds-10), python3-packaging (= 24.0-1), python3-pil (= 10.3.0-2), python3-pil.imagetk (= 10.3.0-2), python3-pkg-resources (= 68.1.2-2), python3-pyfaidx (= 0.8.1.1-2), python3-pyparsing (= 3.1.2-1), python3-reportlab (= 4.2.0-2), python3-rlpycairo (= 0.3.0-3), python3-scipy (= 1.12.0-2), python3-simplejson (= 3.19.2-1+b1), python3-six (= 1.16.0-6), python3-sympy (= 1.12.1-1), python3-tk (= 3.12.3-3.1), python3-tz (= 2024.1-2), python3-ufolib2 (= 0.16.0+dfsg1-1), python3-unicodedata2 (= 15.1.0+ds-1+b1), python3-zipp (= 1.0.0-6), python3.11 (= 3.11.9-1), python3.11-minimal (= 3.11.9-1), r-base-core (= 4.4.0-2), r-cran-cli (= 3.6.2-1), r-cran-colorspace (= 2.1-0+dfsg-1), r-cran-fansi (= 1.0.5-1), r-cran-farver (= 2.1.1-2), r-cran-ggplot2 (= 3.5.1+dfsg-1), r-cran-glue (= 1.7.0-1), r-cran-gridbase (= 0.4-7-5), r-cran-gtable (= 0.3.5+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 (= 0.3.20-1), r-cran-magrittr (= 2.0.3-1), r-cran-mass (= 7.3-60.2-1), r-cran-matrix (= 1.7-0-3), r-cran-mgcv (= 1.9-1-1), r-cran-munsell (= 0.5.1-1), r-cran-nlme (= 3.1.164-1), r-cran-pillar (= 1.9.0+dfsg-1), r-cran-pkgconfig (= 2.0.3-2), r-cran-pkgkitten (= 0.2.3-1), r-cran-plyr (= 1.8.9-1), r-cran-r6 (= 2.5.1-1), r-cran-rcolorbrewer (= 1.1-3-1), r-cran-rcpp (= 1.0.12-1), r-cran-rlang (= 1.1.3-1), r-cran-scales (= 1.3.0-1), r-cran-tibble (= 3.2.1+dfsg-2), r-cran-utf8 (= 1.2.4-1), r-cran-vctrs (= 0.6.5-1), r-cran-viridislite (= 0.4.2-2), r-cran-withr (= 3.0.0+dfsg-1), readline-common (= 8.2-4), rpcsvc-proto (= 1.4.3-1), samclip (= 0.4.0-4), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.22), seqtk (= 1.4-2), sgml-base (= 1.31), shared-mime-info (= 2.4-5), snp-sites (= 2.5.1-2+b1), snpeff (= 5.2.b+dfsg-1), sysstat (= 12.7.5-2), sysvinit-utils (= 3.09-1), tar (= 1.35+dfsg-3), tk8.6-blt2.5 (= 2.5.3+dfsg-7), tzdata (= 2024a-4), ucf (= 3.0043+nmu1), unicode-data (= 15.1.0-1), unzip (= 6.0-28), usr-is-merged (= 39), util-linux (= 2.40.1-8), vt (= 0.57721+ds-3+b1), w3c-sgml-lib (= 1.3-3), x11-common (= 1:7.7+23), xdg-utils (= 1.1.3-4.1), xfonts-encodings (= 1:1.0.4-2.2), xfonts-utils (= 1:7.7+6), xml-core (= 0.19), xz-utils (= 5.6.1+really5.4.5-1), zip (= 3.0-13), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1702979071" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ snippy-examples_4.6.0+dfsg-4_all.deb ------------------------------------ new Debian package, version 2.0. size 310448 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-4 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 2023-12-19 09:44 ./ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/doc/snippy-examples/ -rw-r--r-- root/root 684 2023-12-19 09:44 ./usr/share/doc/snippy-examples/changelog.Debian.gz -rw-r--r-- root/root 890 2023-12-19 09:44 ./usr/share/doc/snippy-examples/copyright drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/doc/snippy/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/doc/snippy/examples/ -rw-r--r-- root/root 1593 2023-12-19 09:44 ./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 2023-12-19 09:44 ./usr/share/doc/snippy/examples/test_for_working_snpeff_v5.1+ snippy_4.6.0+dfsg-4_all.deb --------------------------- new Debian package, version 2.0. size 26836 bytes: control archive=1288 bytes. 984 bytes, 18 lines control 841 bytes, 13 lines md5sums Package: snippy Version: 4.6.0+dfsg-4 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 2023-12-19 09:44 ./ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/bin/ -rwxr-xr-x root/root 28069 2023-12-19 09:44 ./usr/bin/snippy -rwxr-xr-x root/root 2518 2023-12-19 09:44 ./usr/bin/snippy-clean_full_aln -rwxr-xr-x root/root 15844 2023-12-19 09:44 ./usr/bin/snippy-core -rwxr-xr-x root/root 2311 2023-12-19 09:44 ./usr/bin/snippy-multi -rwxr-xr-x root/root 6632 2023-12-19 09:44 ./usr/bin/snippy-vcf_extract_subs -rwxr-xr-x root/root 3720 2023-12-19 09:44 ./usr/bin/snippy-vcf_report -rwxr-xr-x root/root 5872 2023-12-19 09:44 ./usr/bin/snippy-vcf_to_tab drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/doc/snippy/ -rw-r--r-- root/root 662 2023-12-19 09:44 ./usr/share/doc/snippy/README.Debian -rw-r--r-- root/root 684 2023-12-19 09:44 ./usr/share/doc/snippy/changelog.Debian.gz -rw-r--r-- root/root 890 2023-12-19 09:44 ./usr/share/doc/snippy/copyright drwxr-xr-x root/root 0 2023-12-19 09:44 ./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 2023-12-19 09:44 ./usr/share/snippy/ drwxr-xr-x root/root 0 2023-12-19 09:44 ./usr/share/snippy/etc/ -rw-r--r-- root/root 12107 2020-03-09 02:53 ./usr/share/snippy/etc/snpeff.config +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 46036 Build-Time: 27 Distribution: sid Host Architecture: amd64 Install-Time: 185 Job: /srv/debomatic/incoming/snippy_4.6.0+dfsg-4.dsc Machine Architecture: amd64 Package: snippy Package-Time: 229 Source-Version: 4.6.0+dfsg-4 Space: 46036 Status: successful Version: 4.6.0+dfsg-4 -------------------------------------------------------------------------------- Finished at 2024-06-05T19:08:06Z Build needed 00:03:49, 46036k disk space