sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk

+==============================================================================+
| snippy 4.6.0+dfsg-4 (amd64)                  Mon, 16 Sep 2024 18:32:54 +0000 |
+==============================================================================+

Package: snippy
Version: 4.6.0+dfsg-4
Source Version: 4.6.0+dfsg-4
Distribution: perl-5.40-throwaway
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: full

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-c32cd8da-e930-4314-99be-fc66f96e6634' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Chroot Setup Commands                                                        |
+------------------------------------------------------------------------------+


/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-4 perl-5.40-throwaway amd64
--------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-4 perl-5.40-throwaway amd64'.

Finished processing commands.
--------------------------------------------------------------------------------
I: NOTICE: Log filtering will replace 'build/snippy-PBTKJp/resolver-nBbaG0' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B]
Hit:2 http://deb.debian.org/debian unstable InRelease
Hit:3 http://localhost:3142/debian sid InRelease
Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B]
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| 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-PBTKJp/snippy-4.6.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/snippy-PBTKJp' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| 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 '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [933 B]
Get:5 copy:/<<RESOLVERDIR>>/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 bsdextrautils bwa
  ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon
  dbus-session-bus-common dbus-system-bus-common dbus-user-session
  dconf-gsettings-backend dconf-service debhelper default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fakeroot file
  fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono freebayes
  gettext gettext-base groff-base gtk-update-icon-cache hicolor-icon-theme
  intltool-debian java-common junit4 junit5 libactivation-java
  libantlr4-runtime-java libaopalliance-java libapache-pom-java
  libapfloat-java libapiguardian-java libapparmor1 libarchive-zip-perl
  libargs4j-java libasm-java libasound2-data libasound2t64
  libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64
  libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3
  libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libcairo-gobject2
  libcairo2 libcdi-api-java libcharts4j-java libciftools-java
  libcloudproviders0 libcodemodel-java libcolord2 libcom-err2
  libcommons-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 libdconf1 libdebhelper-perl
  libdeflate0 libdisorder0 libdistlib-java libdom4j-java libdrm-amdgpu1
  libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libdtd-parser-java
  libedit2 libelf1t64 libepoxy0 liberror-prone-java libexec-maven-plugin-java
  libexpat1 libfakeroot libfastahack0 libfastinfoset-java libfastutil-java
  libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfreemarker-java
  libfreetype6 libfribidi0 libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common
  libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java
  libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64
  libglvnd0 libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3
  libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libguice-java
  libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java
  libhttpclient-java libhttpcore-java libice6 libicu72 libinchi1.07
  libio-string-perl libistack-commons-java libitext5-java
  libjackson2-annotations-java libjackson2-core-java libjackson2-databind-java
  libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjgrapht-java
  libjgraphx-java libjheaps-java libjmol-java libjni-inchi-java
  libjni-inchi-jni libjpeg62-turbo libjson-simple-java libjsoncpp25
  libjsoup-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack3 liblcms2-2 liblerc4 libllvm18 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
  libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8
  libnsl2 libnspr4 libnss3 libopentest4j-java libopentest4j-reporting-java
  libpam-systemd 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 libpython3.12-minimal
  libpython3.12-stdlib libqdox2-java librelaxng-datatype-java librhino-java
  librngom-java librtmp1 libsensors-config libsensors5 libseqlib2 libsharpyuv0
  libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6
  libsmithwaterman0 libsnappy-java libsnappy-jni libsnappy1v5 libsnp-sites1
  libsnpeff-java libssh2-1t64 libssw0 libstax-ex-java libstreambuffer-java
  libsystemd-shared libtabixpp0t64 libtcl8.6 libthai-data libthai0 libtiff6
  libtirpc-common libtirpc3t64 libtk8.6 libtool libtrove3-java libtxw2-java
  libuchardet0 libunivocity-parsers-java libvcflib-tools libvcflib2
  libvecmath-java libvulkan1 libwagon-http-java libwagon-provider-api-java
  libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0
  libwebp7 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6
  libxbean-reflect-java libxcb-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
  libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java
  libxml2 libxrandr2 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6t64
  libxtst6 libxxf86vm1 libxz-java libz3-4 littler m4 man-db media-types
  mesa-libgallium minimap2 mount ncbi-vdb-data netbase openjdk-21-jre
  openjdk-21-jre-headless openssl parallel po-debconf procps python3
  python3-minimal python3.12 python3.12-minimal r-base-core r-cran-cli
  r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue
  r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice
  r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix
  r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig
  r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
  r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs
  r-cran-viridislite r-cran-withr samclip samtools sensible-utils seqtk
  shared-mime-info snp-sites snpeff sysstat systemd systemd-sysv tzdata ucf
  unzip vt x11-common xdg-utils xkb-data zip
Suggested packages:
  ant-doc default-jdk | java-compiler | java-sdk antlr javacc junit jython
  libbcel-java libbsf-java libcommons-net-java libmail-java libjaxp1.3-java
  libjdepend-java libjsch-java liboro-java libregexp-java libxalan2-java
  autoconf-archive gnu-standards autoconf-doc python3-numpy
  texlive-latex-recommended dh-make gettext-doc libasprintf-dev
  libgettextpo-dev groff alsa-utils libasound2-plugins
  libatinject-jsr330-api-java-doc bioperl libxml-sax-expatxs-perl
  libbiojava6-java-doc libel-api-java colord libcommons-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 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 libcryptsetup12
  libtss2-rc0t64 pciutils pcscd libeclipse-jdt-core-java
  libplexus-utils2-java-doc rhino lm-sensors testng libsnpeff-java-doc
  libarchive13t64 libbpf1 libdw1t64 libfido2-1 libip4tc2 libpwquality1
  libqrencode4 tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk
  r-cran-pracma libxerces2-java-doc libxml-commons-resolver1.1-java-doc m4-doc
  apparmor less www-browser nfs-common libnss-mdns fonts-dejavu-extra
  fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei
  | fonts-wqy-zenhei fonts-indic csh fish ksh tcsh zsh libmail-box-perl
  python3-doc python3-tk python3-venv python3.12-venv python3.12-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 vcfanno isag systemd-container systemd-homed
  systemd-userdbd systemd-boot systemd-resolved systemd-repart
  libtss2-tcti-device0 polkitd
Recommended packages:
  librsvg2-common python3-gffutils python3-matplotlib curl | wget | lynx
  alsa-ucm-conf alsa-topology-conf at-spi2-core bioperl-run
  | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl
  libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl
  libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl
  libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl
  libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl
  libset-scalar-perl libsoap-lite-perl libsort-naturally-perl
  libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl
  libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl
  libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl
  libxml-writer-perl libxml-libxml-perl libwww-perl perl-tk libgd-gd2-perl
  | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl
  libarchive-cpio-perl libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs
  libgtk-3-bin krb5-locales libjansi-java libgpm2 publicsuffix libkmod2
  libltdl-dev mesa-vulkan-drivers | vulkan-icd libatk-wrapper-java-jni
  fonts-dejavu-extra libmail-sendmail-perl psmisc linux-sysctl-defaults
  r-recommended r-base-dev r-doc-html r-cran-callr r-cran-covr r-cran-crayon
  r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr
  r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot
  r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-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-timesyncd | time-daemon
  systemd-cryptsetup libnss-systemd libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  adwaita-icon-theme ant ant-optional any2fasta at-spi2-common autoconf
  automake autopoint autotools-dev bcftools bedtools bsdextrautils bwa
  ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon
  dbus-session-bus-common dbus-system-bus-common dbus-user-session
  dconf-gsettings-backend dconf-service debhelper default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fakeroot file
  fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono freebayes
  gettext gettext-base groff-base gtk-update-icon-cache hicolor-icon-theme
  intltool-debian java-common junit4 junit5 libactivation-java
  libantlr4-runtime-java libaopalliance-java libapache-pom-java
  libapfloat-java libapiguardian-java libapparmor1 libarchive-zip-perl
  libargs4j-java libasm-java libasound2-data libasound2t64
  libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64
  libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3
  libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libcairo-gobject2
  libcairo2 libcdi-api-java libcharts4j-java libciftools-java
  libcloudproviders0 libcodemodel-java libcolord2 libcom-err2
  libcommons-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 libdconf1 libdebhelper-perl
  libdeflate0 libdisorder0 libdistlib-java libdom4j-java libdrm-amdgpu1
  libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libdtd-parser-java
  libedit2 libelf1t64 libepoxy0 liberror-prone-java libexec-maven-plugin-java
  libexpat1 libfakeroot libfastahack0 libfastinfoset-java libfastutil-java
  libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfreemarker-java
  libfreetype6 libfribidi0 libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common
  libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java
  libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64
  libglvnd0 libglx-mesa0 libglx0 libgoogle-gson-java libgraphite2-3
  libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libguice-java
  libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java
  libhttpclient-java libhttpcore-java libice6 libicu72 libinchi1.07
  libio-string-perl libistack-commons-java libitext5-java
  libjackson2-annotations-java libjackson2-core-java libjackson2-databind-java
  libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjgrapht-java
  libjgraphx-java libjheaps-java libjmol-java libjni-inchi-java
  libjni-inchi-jni libjpeg62-turbo libjson-simple-java libjsoncpp25
  libjsoup-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack3 liblcms2-2 liblerc4 libllvm18 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
  libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8
  libnsl2 libnspr4 libnss3 libopentest4j-java libopentest4j-reporting-java
  libpam-systemd 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 libpython3.12-minimal
  libpython3.12-stdlib libqdox2-java librelaxng-datatype-java librhino-java
  librngom-java librtmp1 libsensors-config libsensors5 libseqlib2 libsharpyuv0
  libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6
  libsmithwaterman0 libsnappy-java libsnappy-jni libsnappy1v5 libsnp-sites1
  libsnpeff-java libssh2-1t64 libssw0 libstax-ex-java libstreambuffer-java
  libsystemd-shared libtabixpp0t64 libtcl8.6 libthai-data libthai0 libtiff6
  libtirpc-common libtirpc3t64 libtk8.6 libtool libtrove3-java libtxw2-java
  libuchardet0 libunivocity-parsers-java libvcflib-tools libvcflib2
  libvecmath-java libvulkan1 libwagon-http-java libwagon-provider-api-java
  libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0
  libwebp7 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6
  libxbean-reflect-java libxcb-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
  libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java
  libxml2 libxrandr2 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6t64
  libxtst6 libxxf86vm1 libxz-java libz3-4 littler m4 man-db media-types
  mesa-libgallium minimap2 mount ncbi-vdb-data netbase openjdk-21-jre
  openjdk-21-jre-headless openssl parallel po-debconf procps python3
  python3-minimal python3.12 python3.12-minimal r-base-core r-cran-cli
  r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue
  r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice
  r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix
  r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig
  r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
  r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs
  r-cran-viridislite r-cran-withr samclip samtools
  sbuild-build-depends-main-dummy sensible-utils seqtk shared-mime-info
  snp-sites snpeff sysstat systemd systemd-sysv tzdata ucf unzip vt x11-common
  xdg-utils xkb-data zip
0 upgraded, 406 newly installed, 0 to remove and 0 not upgraded.
Need to get 316 MB of archives.
After this operation, 926 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B]
Get:2 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.40.2-8 [154 kB]
Get:3 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 3.1.7-1+b1 [42.0 kB]
Get:4 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 256.6-1 [2061 kB]
Get:5 http://deb.debian.org/debian unstable/main amd64 systemd amd64 256.6-1 [3488 kB]
Get:6 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 256.6-1 [58.2 kB]
Get:7 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB]
Get:8 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.14.10-4+b1 [106 kB]
Get:9 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.14.10-4 [79.0 kB]
Get:10 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB]
Get:11 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.14.10-4+b1 [185 kB]
Get:12 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.14.10-4 [80.1 kB]
Get:13 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.14.10-4+b1 [98.6 kB]
Get:14 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB]
Get:15 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB]
Get:16 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB]
Get:17 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB]
Get:18 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get:19 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB]
Get:20 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB]
Get:21 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB]
Get:22 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB]
Get:23 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B]
Get:24 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB]
Get:25 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB]
Get:26 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:27 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB]
Get:28 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB]
Get:29 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB]
Get:30 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB]
Get:31 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B]
Get:32 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB]
Get:33 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB]
Get:34 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-5 [878 kB]
Get:35 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get:36 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-1 [1381 kB]
Get:37 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB]
Get:38 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB]
Get:39 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB]
Get:40 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB]
Get:41 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB]
Get:42 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB]
Get:43 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB]
Get:44 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 256.6-1 [278 kB]
Get:45 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB]
Get:46 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get:47 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get:48 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get:49 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB]
Get:50 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.0-1 [1498 kB]
Get:51 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB]
Get:52 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB]
Get:53 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5 [758 kB]
Get:54 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB]
Get:55 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB]
Get:56 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB]
Get:57 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB]
Get:58 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB]
Get:59 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB]
Get:60 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB]
Get:61 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get:62 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [139 kB]
Get:63 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.16.1+ds-2 [48.7 kB]
Get:64 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB]
Get:65 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 47.0-1 [463 kB]
Get:66 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get:67 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B]
Get:68 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB]
Get:69 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB]
Get:70 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.103-1 [1352 kB]
Get:71 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.0-1 [55.4 kB]
Get:72 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.5~6ea-1 [41.8 MB]
Get:73 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B]
Get:74 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.14-1 [2162 kB]
Get:75 http://deb.debian.org/debian unstable/main amd64 ant-optional all 1.10.14-1 [455 kB]
Get:76 http://deb.debian.org/debian unstable/main amd64 any2fasta all 0.4.2-2 [6232 B]
Get:77 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.54.0-1 [170 kB]
Get:78 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get:79 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get:80 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:81 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:82 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB]
Get:83 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB]
Get:84 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB]
Get:85 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB]
Get:86 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB]
Get:87 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB]
Get:88 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB]
Get:89 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB]
Get:90 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB]
Get:91 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.10.0-2 [359 kB]
Get:92 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB]
Get:93 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB]
Get:94 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.20-2 [760 kB]
Get:95 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB]
Get:96 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB]
Get:97 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.14.10-4+b1 [79.1 kB]
Get:98 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-4+b2 [41.9 kB]
Get:99 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-4+b2 [32.4 kB]
Get:100 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b2 [28.7 kB]
Get:101 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB]
Get:102 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB]
Get:103 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:104 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:105 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:106 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:107 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB]
Get:108 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get:109 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB]
Get:110 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:111 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:112 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB]
Get:113 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [51.2 kB]
Get:114 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB]
Get:115 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB]
Get:116 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB]
Get:117 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB]
Get:118 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB]
Get:119 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get:120 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB]
Get:121 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [76.4 kB]
Get:122 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [67.6 kB]
Get:123 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get:124 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:125 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:126 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB]
Get:127 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB]
Get:128 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB]
Get:129 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB]
Get:130 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB]
Get:131 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB]
Get:132 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-1 [534 kB]
Get:133 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-1 [130 kB]
Get:134 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1 [28.9 kB]
Get:135 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-1+b1 [139 kB]
Get:136 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB]
Get:137 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB]
Get:138 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB]
Get:139 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-1 [249 kB]
Get:140 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-1+b2 [191 kB]
Get:141 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB]
Get:142 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB]
Get:143 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB]
Get:144 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB]
Get:145 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get:146 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB]
Get:147 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB]
Get:148 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [223 kB]
Get:149 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [54.4 kB]
Get:150 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [35.2 kB]
Get:151 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.0-1 [26.4 kB]
Get:152 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.0-1 [11.3 kB]
Get:153 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.0-1 [5392 B]
Get:154 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB]
Get:155 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB]
Get:156 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.2-1 [37.1 kB]
Get:157 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB]
Get:158 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB]
Get:159 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB]
Get:160 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB]
Get:161 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB]
Get:162 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.43-4 [4657 kB]
Get:163 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.43-4 [2754 kB]
Get:164 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB]
Get:165 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B]
Get:166 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB]
Get:167 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.2.2-1 [37.8 kB]
Get:168 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB]
Get:169 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB]
Get:170 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB]
Get:171 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB]
Get:172 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB]
Get:173 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB]
Get:174 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB]
Get:175 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB]
Get:176 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B]
Get:177 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get:178 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB]
Get:179 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB]
Get:180 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB]
Get:181 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB]
Get:182 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB]
Get:183 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB]
Get:184 http://deb.debian.org/debian unstable/main amd64 libllvm18 amd64 1:18.1.8-11 [25.0 MB]
Get:185 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get:186 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10 [34.7 kB]
Get:187 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 24.2.2-1 [9058 kB]
Get:188 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.290.0-1 [126 kB]
Get:189 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.0-1 [34.0 kB]
Get:190 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.2.2-1 [42.6 kB]
Get:191 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.2.2-1 [43.7 kB]
Get:192 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.2.2-1 [154 kB]
Get:193 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB]
Get:194 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB]
Get:195 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.12-1 [21.0 kB]
Get:196 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.12-1 [369 kB]
Get:197 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB]
Get:198 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB]
Get:199 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB]
Get:200 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.5~6ea-1 [205 kB]
Get:201 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B]
Get:202 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB]
Get:203 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB]
Get:204 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB]
Get:205 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB]
Get:206 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15 [20.9 kB]
Get:207 http://deb.debian.org/debian unstable/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b1 [172 kB]
Get:208 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1 [10.1 kB]
Get:209 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b1 [4884 B]
Get:210 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b1 [27.6 kB]
Get:211 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB]
Get:212 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4 [60.5 kB]
Get:213 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b1 [188 kB]
Get:214 http://deb.debian.org/debian unstable/main amd64 freebayes amd64 1.3.7-1 [1488 kB]
Get:215 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB]
Get:216 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-4 [349 kB]
Get:217 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B]
Get:218 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B]
Get:219 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get:220 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB]
Get:221 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get:222 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.3-1 [2459 kB]
Get:223 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get:224 http://deb.debian.org/debian unstable/main amd64 libantlr4-runtime-java all 4.9.2-2 [317 kB]
Get:225 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get:226 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B]
Get:227 http://deb.debian.org/debian unstable/main amd64 libapfloat-java all 1.13.0-1 [700 kB]
Get:228 http://deb.debian.org/debian unstable/main amd64 libargs4j-java all 2.33-2 [138 kB]
Get:229 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7-1 [394 kB]
Get:230 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get:231 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:232 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB]
Get:233 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get:234 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get:235 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get:236 http://deb.debian.org/debian unstable/main amd64 libciftools-java all 6.0.0-1 [2211 kB]
Get:237 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get:238 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB]
Get:239 http://deb.debian.org/debian unstable/main amd64 libcommons-math-java all 2.2-8 [926 kB]
Get:240 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get:241 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get:242 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB]
Get:243 http://deb.debian.org/debian unstable/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB]
Get:244 http://deb.debian.org/debian unstable/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB]
Get:245 http://deb.debian.org/debian unstable/main amd64 libjackson2-core-java all 2.14.1-1 [447 kB]
Get:246 http://deb.debian.org/debian unstable/main amd64 libjackson2-databind-java all 2.14.0-1 [1584 kB]
Get:247 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get:248 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-4 [214 kB]
Get:249 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB]
Get:250 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.16.1-1 [480 kB]
Get:251 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB]
Get:252 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get:253 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB]
Get:254 http://deb.debian.org/debian unstable/main amd64 libguice-java all 4.2.3-2 [1435 kB]
Get:255 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 35-1 [6140 B]
Get:256 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get:257 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get:258 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB]
Get:259 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get:260 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get:261 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get:262 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB]
Get:263 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get:264 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B]
Get:265 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-3 [54.3 kB]
Get:266 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB]
Get:267 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB]
Get:268 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB]
Get:269 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.8.8-1 [1579 kB]
Get:270 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get:271 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB]
Get:272 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB]
Get:273 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get:274 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1 [29.1 kB]
Get:275 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B]
Get:276 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB]
Get:277 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB]
Get:278 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get:279 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get:280 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get:281 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get:282 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get:283 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get:284 http://deb.debian.org/debian unstable/main amd64 libistack-commons-java all 3.0.6-5 [145 kB]
Get:285 http://deb.debian.org/debian unstable/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB]
Get:286 http://deb.debian.org/debian unstable/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB]
Get:287 http://deb.debian.org/debian unstable/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB]
Get:288 http://deb.debian.org/debian unstable/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB]
Get:289 http://deb.debian.org/debian unstable/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB]
Get:290 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get:291 http://deb.debian.org/debian unstable/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB]
Get:292 http://deb.debian.org/debian unstable/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB]
Get:293 http://deb.debian.org/debian unstable/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB]
Get:294 http://deb.debian.org/debian unstable/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB]
Get:295 http://deb.debian.org/debian unstable/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB]
Get:296 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB]
Get:297 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get:298 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.11.0-1 [217 kB]
Get:299 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.14+dfsg-1 [19.8 MB]
Get:300 http://deb.debian.org/debian unstable/main amd64 libjheaps-java all 0.14-2 [144 kB]
Get:301 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get:302 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get:303 http://deb.debian.org/debian unstable/main amd64 libjgraphx-java all 2.1.0.7-4 [807 kB]
Get:304 http://deb.debian.org/debian unstable/main amd64 libjgrapht-java all 1.5.2-1 [1610 kB]
Get:305 http://deb.debian.org/debian unstable/main amd64 libinchi1.07 amd64 1.07.1+dfsg-3 [556 kB]
Get:306 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-jni amd64 0.8+dfsg-8 [9188 B]
Get:307 http://deb.debian.org/debian unstable/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get:308 http://deb.debian.org/debian unstable/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB]
Get:309 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-4 [9924 B]
Get:310 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get:311 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-8 [133 kB]
Get:312 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get:313 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.12.1-2 [99.0 kB]
Get:314 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get:315 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
Get:316 http://deb.debian.org/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB]
Get:317 http://deb.debian.org/debian unstable/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB]
Get:318 http://deb.debian.org/debian unstable/main amd64 libjni-inchi-java all 0.8+dfsg-8 [33.6 kB]
Get:319 http://deb.debian.org/debian unstable/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB]
Get:320 http://deb.debian.org/debian unstable/main amd64 libjmol-java all 16.2.15+dfsg-1 [8956 kB]
Get:321 http://deb.debian.org/debian unstable/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB]
Get:322 http://deb.debian.org/debian unstable/main amd64 libmsgpack-java all 0.9.6-1 [161 kB]
Get:323 http://deb.debian.org/debian unstable/main amd64 libmmtf-java all 1.0.11-1 [187 kB]
Get:324 http://deb.debian.org/debian unstable/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB]
Get:325 http://deb.debian.org/debian unstable/main amd64 libbiojava6-java all 6.1.0+dfsg-4 [5367 kB]
Get:326 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB]
Get:327 http://deb.debian.org/debian unstable/main amd64 libcharts4j-java all 1.3-4 [162 kB]
Get:328 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get:329 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB]
Get:330 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.10.0-2 [352 kB]
Get:331 http://deb.debian.org/debian unstable/main amd64 libdistlib-java all 1.0-5 [72.5 kB]
Get:332 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.32-2 [1546 kB]
Get:333 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-5 [837 kB]
Get:334 http://deb.debian.org/debian unstable/main amd64 libmjson-java all 1.4.0-3 [60.4 kB]
Get:335 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB]
Get:336 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB]
Get:337 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB]
Get:338 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB]
Get:339 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB]
Get:340 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-9 [155 kB]
Get:341 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.0.3+dfsg-9 [23.8 kB]
Get:342 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.0.3+dfsg-9 [110 kB]
Get:343 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.14-2.1 [1357 kB]
Get:344 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1833 kB]
Get:345 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB]
Get:346 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB]
Get:347 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB]
Get:348 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB]
Get:349 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B]
Get:350 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB]
Get:351 http://deb.debian.org/debian unstable/main amd64 libsnp-sites1 amd64 2.5.1-2+b1 [15.4 kB]
Get:352 http://deb.debian.org/debian unstable/main amd64 libtrove3-java all 3.0.3-5 [2146 kB]
Get:353 http://deb.debian.org/debian unstable/main amd64 libsnpeff-java all 5.2.b+dfsg-1 [1656 kB]
Get:354 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB]
Get:355 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB]
Get:356 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB]
Get:357 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB]
Get:358 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB]
Get:359 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB]
Get:360 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:361 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB]
Get:362 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB]
Get:363 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB]
Get:364 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-1 [16.0 kB]
Get:365 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB]
Get:366 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.13-1 [2082 kB]
Get:367 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
Get:368 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB]
Get:369 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB]
Get:370 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB]
Get:371 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
Get:372 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.5+dfsg-1 [222 kB]
Get:373 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB]
Get:374 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB]
Get:375 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB]
Get:376 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB]
Get:377 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-0-3 [4127 kB]
Get:378 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB]
Get:379 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB]
Get:380 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB]
Get:381 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB]
Get:382 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB]
Get:383 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB]
Get:384 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get:385 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB]
Get:386 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB]
Get:387 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB]
Get:388 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB]
Get:389 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB]
Get:390 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB]
Get:391 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB]
Get:392 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get:393 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB]
Get:394 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB]
Get:395 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB]
Get:396 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB]
Get:397 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b1 [651 kB]
Get:398 http://deb.debian.org/debian unstable/main amd64 minimap2 amd64 2.27+dfsg-1+b1 [389 kB]
Get:399 http://deb.debian.org/debian unstable/main amd64 sysstat amd64 12.7.5-2 [623 kB]
Get:400 http://deb.debian.org/debian unstable/main amd64 parallel all 20240222+ds-2 [2163 kB]
Get:401 http://deb.debian.org/debian unstable/main amd64 samclip all 0.4.0-4 [20.1 kB]
Get:402 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB]
Get:403 http://deb.debian.org/debian unstable/main amd64 seqtk amd64 1.4-2 [34.6 kB]
Get:404 http://deb.debian.org/debian unstable/main amd64 snp-sites amd64 2.5.1-2+b1 [14.5 kB]
Get:405 http://deb.debian.org/debian unstable/main amd64 snpeff all 5.2.b+dfsg-1 [7164 B]
Get:406 http://deb.debian.org/debian unstable/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB]
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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 libfribidi0:amd64 (1.0.15-1) ...
Setting up libproc2-0:amd64 (2:4.0.4-5) ...
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 (0.22.5-2) ...
Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libpcsclite1:amd64 (2.3.0-1) ...
Setting up libsensors5:amd64 (1:3.6.0-10) ...
Setting up libk5crypto3:amd64 (1.21.3-3) ...
Setting up libactivation-java (1.2.0-2) ...
Setting up libhamcrest-java (2.2-2) ...
Setting up libglapi-mesa:amd64 (24.2.2-1) ...
Setting up libgfortran5:amd64 (14.2.0-5) ...
Setting up libvulkan1:amd64 (1.3.290.0-1) ...
Setting up autoconf (2.72-3) ...
Setting up libnghttp3-9:amd64 (1.4.0-1) ...
Setting up libapfloat-java (1.13.0-1) ...
Setting up libwebp7:amd64 (1.4.0-0.1) ...
Setting up libxcb-dri2-0:amd64 (1.17.0-2) ...
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 (0.0.24) ...
Setting up libxshmfence1:amd64 (1.3-1+b1) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.54.0-1) ...
Setting up libcommons-math-java (2.2-8) ...
Setting up libtiff6:amd64 (4.5.1+git230720-5) ...
Setting up libxcb-randr0:amd64 (1.17.0-2) ...
Setting up dbus-session-bus-common (1.14.10-4) ...
Setting up libuchardet0:amd64 (0.0.8-1+b1) ...
Setting up libxml-commons-external-java (1.4.01-6) ...
Setting up procps (2:4.0.4-5) ...
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 libx11-6:amd64 (2:1.8.7-1+b1) ...
Setting up ncbi-vdb-data (3.0.2+dfsg-2) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...

Configuration file '/etc/protocols'
 ==> File on system created by you or by a script.
 ==> File also in package provided by package maintainer.
 ==> Using current old file as you requested.

Configuration file '/etc/services'
 ==> File on system created by you or by a script.
 ==> File also in package provided by package maintainer.
 ==> Using current old file as you requested.
Setting up libsnp-sites1:amd64 (2.5.1-2+b1) ...
Setting up libngtcp2-16:amd64 (1.6.0-1) ...
Setting up libcommons-math3-java (3.6.1-3) ...
Setting up libkrb5-3:amd64 (1.21.3-3) ...
Setting up libwayland-egl1:amd64 (1.23.0-1) ...
Setting up libbio-perl-perl (1.7.8-1) ...
Setting up libssh2-1t64:amd64 (1.11.0-7) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up dbus-system-bus-common (1.14.10-4) ...
Setting up librelaxng-datatype-java (1.0+ds1-3.1) ...
Setting up openssl (3.3.2-1) ...
Setting up libinchi1.07 (1.07.1+dfsg-3) ...
Setting up libdrm-common (2.4.123-1) ...
Setting up libcdi-api-java (1.2-3) ...
Setting up libsnappy-jni (1.1.10.5-2) ...
Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ...
Setting up libssw0:amd64 (1.1-15) ...
Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ...
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 dbus-bin (1.14.10-4+b1) ...
Setting up libargs4j-java (2.33-2) ...
Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ...
Setting up libllvm18:amd64 (1:18.1.8-11) ...
Setting up libxkbcommon0:amd64 (1.6.0-1+b1) ...
Setting up libnaga-java (3.0+svn80-5) ...
Setting up libwayland-client0:amd64 (1.23.0-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libdom4j-java (2.1.4-1) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libxcb-dri3-0:amd64 (1.17.0-2) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ...
Setting up libice6:amd64 (2:1.0.10-1+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 gettext (0.22.5-2) ...
Setting up libmbedx509-1t64:amd64 (2.28.8-1) ...
Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ...
Setting up libatk1.0-0t64:amd64 (2.54.0-1) ...
Setting up libplexus-languages-java (1.1.1-2) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ...
Setting up libtool (2.4.7-7) ...
Setting up fontconfig-config (2.15.0-1.1) ...
Setting up libstax-ex-java (1.7.8-3) ...
Setting up libmaven-parent-java (35-1) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:amd64 (0.8-13+b2) ...
Setting up libcloudproviders0:amd64 (0.3.6-1) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b1) ...
Setting up libsisu-inject-java (0.3.4-2) ...
Setting up libnss3:amd64 (2:3.103-1) ...
Setting up libciftools-java (6.0.0-1) ...
Setting up dbus-daemon (1.14.10-4+b1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libcolord2:amd64 (1.4.7-1+b1) ...
Setting up libjackson2-databind-java (2.14.0-1) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libdconf1:amd64 (0.40.0-4+b2) ...
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 libfreetype6:amd64 (2.13.3+dfsg-1) ...
Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ...
Setting up dbus (1.14.10-4+b1) ...
Running in chroot, ignoring request.
Setting up shared-mime-info (2.4-5) ...
Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ...
Setting up libstreambuffer-java (1.5.4-1.1) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ...
Setting up libxrandr2:amd64 (2:1.5.4-1) ...
Setting up ucf (3.0043+nmu1) ...
Setting up libcommons-lang3-java (3.14.0-1) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up librngom-java (2.3.0.1-10.1) ...
Setting up libdrm2:amd64 (2.4.123-1) ...
Setting up libjni-inchi-jni (0.8+dfsg-8) ...
Setting up libjgraphx-java (2.1.0.7-4) ...
Setting up snp-sites (2.5.1-2+b1) ...
Setting up libmbedtls14t64:amd64 (2.28.8-1) ...
Setting up groff-base (1.23.0-5) ...
Setting up libwayland-cursor0:amd64 (1.23.0-1) ...
Setting up libpam-systemd:amd64 (256.6-1) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libharfbuzz0b:amd64 (9.0.0-1) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ...
Setting up libsnappy-java (1.1.10.5-2) ...
Setting up libxss1:amd64 (1:1.2.3-1+b1) ...
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 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
Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-collect.timer' → '/usr/lib/systemd/system/sysstat-collect.timer'.
Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-rotate.timer' → '/usr/lib/systemd/system/sysstat-rotate.timer'.
Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-summary.timer' → '/usr/lib/systemd/system/sysstat-summary.timer'.
Created symlink '/etc/systemd/system/multi-user.target.wants/sysstat.service' → '/usr/lib/systemd/system/sysstat.service'.
Setting up libavahi-client3:amd64 (0.8-13+b2) ...
Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ...
Setting up libpaper1:amd64 (1.1.29+b1) ...

Creating config file /etc/papersize with new version
Setting up gtk-update-icon-cache (4.16.1+ds-2) ...
Setting up fontconfig (2.15.0-1.1) ...
Regenerating fonts cache... done.
Setting up libxft2:amd64 (2.3.6-1+b1) ...
Setting up openjdk-21-jre-headless:amd64 (21.0.5~6ea-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxi6:amd64 (2:1.8.1-1) ...
Setting up libcommons-compress-java (1.25.0-1) ...
Setting up libcurl4t64:amd64 (8.10.0-2) ...
Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ...
Setting up libcommons-io-java (2.16.1-1) ...
Setting up libdrm-radeon1:amd64 (2.4.123-1) ...
Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libtk8.6:amd64 (8.6.14-1) ...
Setting up libdistlib-java (1.0-5) ...
Setting up libxcursor1:amd64 (1:1.2.2-1) ...
Setting up libpango-1.0-0:amd64 (1.54.0+ds-2) ...
Setting up libdrm-intel1:amd64 (2.4.123-1) ...
Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ...
Setting up libcurl3t64-gnutls:amd64 (8.10.0-2) ...
Setting up libpaper-utils (1.1.29+b1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'.
Setting up libcairo2:amd64 (1.18.2-1) ...
Setting up dbus-user-session (1.14.10-4+b1) ...
Setting up libmaven-resolver-java (1.6.3-1) ...
Setting up adwaita-icon-theme (47.0-1) ...
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 libatspi2.0-0t64:amd64 (2.54.0-1) ...
Setting up libxt6t64:amd64 (1:1.2.1-1.2) ...
Setting up parallel (20240222+ds-2) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libnsl2:amd64 (1.3.0-3+b2) ...
Setting up libhts3t64:amd64 (1.20+ds-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libcairo-gobject2:amd64 (1.18.2-1) ...
Setting up libmaven-shared-utils-java (3.3.4-1) ...
Setting up libfastinfoset-java (1.2.12-3) ...
Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ...
Setting up libcups2t64:amd64 (2.4.10-1) ...
Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b1) ...
Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ...
Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-9) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ...
Setting up mesa-libgallium:amd64 (24.2.2-1) ...
Setting up libngs-jni:amd64 (3.0.3+dfsg-9) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ...
Setting up libgbm1:amd64 (24.2.2-1) ...
Setting up python3.12 (3.12.6-1) ...
Setting up libgl1-mesa-dri:amd64 (24.2.2-1) ...
Setting up bcftools (1.20-2) ...
Setting up debhelper (13.20) ...
Setting up dconf-service (0.40.0-4+b2) ...
Setting up samtools (1.20-3) ...
Setting up r-base-core (4.4.1-3) ...

Creating config file /etc/R/Renviron with new version
Setting up r-cran-labeling (0.4.3-1) ...
Setting up r-cran-lattice (0.22-6-1) ...
Setting up r-cran-nlme (3.1.166-1) ...
Setting up r-cran-farver (2.1.2-1) ...
Setting up r-cran-viridislite (0.4.2-2) ...
Setting up libtabixpp0t64:amd64 (1.1.2-2.1) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libngs-java:amd64 (3.0.3+dfsg-9) ...
Setting up r-cran-r6 (2.5.1-1) ...
Setting up r-cran-pkgkitten (0.2.4-1) ...
Setting up r-cran-magrittr (2.0.3-1) ...
Setting up libhtsjdk-java (4.1.0+dfsg-2) ...
Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ...
Setting up r-cran-littler (0.3.20-1) ...
Setting up r-cran-rcpp (1.0.13-1) ...
Setting up r-cran-rlang (1.1.4-1) ...
Setting up libglx-mesa0:amd64 (24.2.2-1) ...
Setting up r-cran-gridbase (0.4-7-5) ...
Setting up littler (0.3.20-1) ...
Setting up vt (0.57721+ds-3+b1) ...
Setting up libglx0:amd64 (1.7.0-1+b1) ...
Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b2) ...
Setting up r-cran-withr (3.0.0+dfsg-1) ...
Setting up r-cran-fansi (1.0.5-1) ...
Setting up libmaven-archiver-java (3.6.0-1) ...
Setting up r-cran-mass (7.3-61-1) ...
Setting up python3 (3.12.5-1+b1) ...
Setting up r-cran-glue (1.7.0-1) ...
Setting up r-cran-cli (3.6.3-1) ...
Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
Setting up r-cran-pkgconfig (2.0.3-2) ...
Setting up r-cran-utf8 (1.2.4-1) ...
Setting up r-cran-colorspace (2.1-0+dfsg-1) ...
Setting up libgl1:amd64 (1.7.0-1+b1) ...
Setting up libvcflib2:amd64 (1.0.9+dfsg1-3+b1) ...
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 libgtk-3-common (3.24.43-4) ...
Setting up r-cran-pillar (1.9.0+dfsg-1) ...
Setting up r-cran-munsell (0.5.1-1) ...
Setting up r-cran-tibble (3.2.1+dfsg-2) ...
Setting up libgtk-3-0t64:amd64 (3.24.43-4) ...
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 liberror-prone-java (2.18.0-1) ...
Setting up libguava-java (32.0.1-1) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up libguice-java (4.2.3-2) ...
Setting up libmaven3-core-java (3.8.8-1) ...
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-8) ...
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 (2.40-2) ...
Processing triggers for systemd (256.6-1) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian: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 openjdk-21-jre:amd64 (21.0.5~6ea-1) ...
Setting up ant (1.10.14-1) ...
Setting up junit4 (4.13.2-4) ...
Setting up default-jre-headless (2:1.21-76) ...
Setting up default-jre (2:1.21-76) ...
Setting up ant-optional (1.10.14-1) ...
Setting up junit5 (5.10.3-1) ...
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) ...
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 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64)
Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-5 gcc-13_13.3.0-6 gcc-14_14.2.0-5 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-5 libstdc++6_14.2.0-5 linux-libc-dev_6.10.9-1
Package versions: adduser_3.137 adwaita-icon-theme_47.0-1 ant_1.10.14-1 ant-optional_1.10.14-1 any2fasta_0.4.2-2 apt_2.9.8 at-spi2-common_2.54.0-1 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 bcftools_1.20-2 bedtools_2.31.1+dfsg-2 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bwa_0.7.18-1 bzip2_1.0.8-6 ca-certificates_20240203 ca-certificates-java_20240118 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-5 cpp-14-x86-64-linux-gnu_14.2.0-5 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 dbus_1.14.10-4+b1 dbus-bin_1.14.10-4+b1 dbus-daemon_1.14.10-4+b1 dbus-session-bus-common_1.14.10-4 dbus-system-bus-common_1.14.10-4 dbus-user-session_1.14.10-4+b1 dconf-gsettings-backend_0.40.0-4+b2 dconf-service_0.40.0-4+b2 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 default-jre_2:1.21-76 default-jre-headless_2:1.21-76 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 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 freebayes_1.3.7-1 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-5 g++-14-x86-64-linux-gnu_14.2.0-5 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-5 gcc-14-base_14.2.0-5 gcc-14-x86-64-linux-gnu_14.2.0-5 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 grep_3.11-4 groff-base_1.23.0-5 gtk-update-icon-cache_4.16.1+ds-2 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_0.76 junit4_4.13.2-4 junit5_5.10.3-1 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 libapparmor1_3.1.7-1+b1 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libargs4j-java_2.33-2 libasan8_14.2.0-5 libasm-java_9.7-1 libasound2-data_1.2.12-1 libasound2t64_1.2.12-1 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatinject-jsr330-api-java_1.0+ds1-5 libatk-bridge2.0-0t64_2.54.0-1 libatk1.0-0t64_2.54.0-1 libatomic1_14.2.0-5 libatspi2.0-0t64_2.54.0-1 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libavahi-client3_0.8-13+b2 libavahi-common-data_0.8-13+b2 libavahi-common3_0.8-13+b2 libbinutils_2.43.1-4 libbio-perl-perl_1.7.8-1 libbiojava6-java_6.1.0+dfsg-4 libblas3_3.12.0-3 libblkid1_2.40.2-8 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcairo-gobject2_1.18.2-1 libcairo2_1.18.2-1 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-5 libcdi-api-java_1.2-3 libcharts4j-java_1.3-4 libciftools-java_6.0.0-1 libcloudproviders0_0.3.6-1 libcodemodel-java_2.6+jaxb2.3.0.1-10.1 libcolord2_1.4.7-1+b1 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_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libcups2t64_2.4.10-1 libcurl3t64-gnutls_8.10.0-2 libcurl4t64_8.10.0-2 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 libdconf1_0.40.0-4+b2 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdeflate0_1.21-1 libdisorder0_0.0.2+git20130809.8062ee1-4+b1 libdistlib-java_1.0-5 libdom4j-java_2.1.4-1 libdpkg-perl_1.22.11 libdrm-amdgpu1_2.4.123-1 libdrm-common_2.4.123-1 libdrm-intel1_2.4.123-1 libdrm-radeon1_2.4.123-1 libdrm2_2.4.123-1 libdtd-parser-java_1.2-1 libeatmydata1_131-2 libedit2_3.1-20240808-1 libelf1t64_0.191-2 libepoxy0_1.5.10-1+b2 liberror-prone-java_2.18.0-1 libexec-maven-plugin-java_3.1.0-2 libexpat1_2.6.3-1 libfakeroot_1.36-1 libfastahack0_1.0.0+dfsg-11+b1 libfastinfoset-java_1.2.12-3 libfastutil-java_8.5.14+dfsg-1 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 libfreemarker-java_2.3.32-2 libfreetype6_2.13.3+dfsg-1 libfribidi0_1.0.15-1 libgbm1_24.2.2-1 libgcc-13-dev_13.3.0-6 libgcc-14-dev_14.2.0-5 libgcc-s1_14.2.0-5 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 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_14.2.0-5 libgif7_5.2.2-1 libgl1_1.7.0-1+b1 libgl1-mesa-dri_24.2.2-1 libglapi-mesa_24.2.2-1 libglib2.0-0t64_2.82.0-1 libglvnd0_1.7.0-1+b1 libglx-mesa0_24.2.2-1 libglx0_1.7.0-1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-5 libgoogle-gson-java_2.10.1-1 libgpg-error0_1.50-3 libgprofng0_2.43.1-4 libgraphite2-3_1.3.14-2 libgssapi-krb5-2_1.21.3-3 libgtk-3-0t64_3.24.43-4 libgtk-3-common_3.24.43-4 libguava-java_32.0.1-1 libguice-java_4.2.3-2 libhamcrest-java_2.2-2 libharfbuzz0b_9.0.0-1 libhogweed6t64_3.10-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.1-1 libhtsjdk-java_4.1.0+dfsg-2 libhttpclient-java_4.5.14-1 libhttpcore-java_4.4.16-1 libhwasan0_14.2.0-5 libice6_2:1.0.10-1+b1 libicu72_72.1-5 libidn2-0_2.3.7-2 libinchi1.07_1.07.1+dfsg-3 libio-string-perl_1.08-4 libisl23_0.27-1 libistack-commons-java_3.0.6-5 libitext5-java_5.5.13.3-4 libitm1_14.2.0-5 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_2.1.0.7-4 libjheaps-java_0.14-2 libjmol-java_16.2.15+dfsg-1 libjni-inchi-java_0.8+dfsg-8 libjni-inchi-jni_0.8+dfsg-8 libjpeg62-turbo_1:2.1.5-3 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_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 liblapack3_3.12.0-3 liblcms2-2_2.14-2+b1 libldap-2.5-0_2.5.18+dfsg-3+b1 liblerc4_4.0.0+ds-4+b1 libllvm18_1:18.1.8-11 liblog4j1.2-java_1.2.17-11 liblsan0_14.2.0-5 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 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_3.8.8-1 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_2.40.2-8 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-9 libncbi-vdb3_3.0.2+dfsg-2+b1 libncurses6_6.5-2 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.63.0-1 libnghttp3-9_1.4.0-1 libngs-java_3.0.3+dfsg-9 libngs-jni_3.0.3+dfsg-9 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libnpth0t64_1.6-3.1 libnsl2_1.3.0-3+b2 libnspr4_2:4.35-1.1+b1 libnss3_2:3.103-1 libopentest4j-java_1.2.0-4 libopentest4j-reporting-java_0.1.0-M1-2 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam-systemd_256.6-1 libpam0g_1.5.3-7 libpango-1.0-0_1.54.0+ds-2 libpangocairo-1.0-0_1.54.0+ds-2 libpangoft2-1.0-0_1.54.0+ds-2 libpaper-utils_1.1.29+b1 libpaper1_1.1.29+b1 libpciaccess0_0.17-3+b1 libpcre2-8-0_10.42-4+b1 libpcsclite1_2.3.0-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-5 libpicocli-java_4.6.2-2 libpipeline1_1.5.8-1 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_2:4.0.4-5 libpsl5t64_0.21.2-1.1 libpython3-stdlib_3.12.5-1+b1 libpython3.12-minimal_3.12.6-1 libpython3.12-stdlib_3.12.6-1 libqdox2-java_2.0.3-1 libquadmath0_14.2.0-5 libreadline8t64_8.2-5 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+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsensors-config_1:3.6.0-10 libsensors5_1:3.6.0-10 libsepol2_3.7-1 libseqlib2_1.2.0+dfsg-11+b1 libsframe1_2.43.1-4 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_2.40.2-8 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_3.46.1-1 libssh2-1t64_1.11.0-7 libssl3t64_3.3.2-1 libssw0_1.1-15 libstax-ex-java_1.7.8-3 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-5 libstdc++6_14.2.0-5 libstreambuffer-java_1.5.4-1.1 libsystemd-shared_256.6-1 libsystemd0_256.6-1 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+git230720-5 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_14.2.0-5 libtxw2-java_2.3.0.1-10.1 libubsan1_14.2.0-5 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunistring5_1.2-1 libunivocity-parsers-java_2.9.1-1 libuuid1_2.40.2-8 libvcflib-tools_1.0.9+dfsg1-3+b1 libvcflib2_1.0.9+dfsg1-3+b1 libvecmath-java_1.5.2-7 libvulkan1_1.3.290.0-1 libwagon-http-java_3.5.3-1 libwagon-provider-api-java_3.5.3-1 libwayland-client0_1.23.0-1 libwayland-cursor0_1.23.0-1 libwayland-egl1_1.23.0-1 libwayland-server0_1.23.0-1 libwebp7_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 libxkbcommon0_1.6.0-1+b1 libxml-commons-external-java_1.4.01-6 libxml-commons-resolver1.1-java_1.2-11 libxml2_2.12.7+dfsg-3+b1 libxrandr2_2:1.5.4-1 libxrender1_1:0.9.10-1.1+b1 libxshmfence1_1.3-1+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_1.5.6+dfsg-1 linux-libc-dev_6.10.9-1 littler_0.3.20-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-8 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mesa-libgallium_24.2.2-1 minimap2_2.27+dfsg-1+b1 mount_2.40.2-8 ncbi-vdb-data_3.0.2+dfsg-2 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openjdk-21-jre_21.0.5~6ea-1 openjdk-21-jre-headless_21.0.5~6ea-1 openssl_3.3.2-1 openssl-provider-legacy_3.3.2-1 parallel_20240222+ds-2 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 po-debconf_1.0.21+nmu1 procps_2:4.0.4-5 python3_3.12.5-1+b1 python3-minimal_3.12.5-1+b1 python3.12_3.12.6-1 python3.12-minimal_3.12.6-1 r-base-core_4.4.1-3 r-cran-cli_3.6.3-1 r-cran-colorspace_2.1-0+dfsg-1 r-cran-fansi_1.0.5-1 r-cran-farver_2.1.2-1 r-cran-ggplot2_3.5.1+dfsg-1 r-cran-glue_1.7.0-1 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_7.3-61-1 r-cran-matrix_1.7-0-3 r-cran-mgcv_1.9-1-1 r-cran-munsell_0.5.1-1 r-cran-nlme_3.1.166-1 r-cran-pillar_1.9.0+dfsg-1 r-cran-pkgconfig_2.0.3-2 r-cran-pkgkitten_0.2.4-1 r-cran-plyr_1.8.9-1 r-cran-r6_2.5.1-1 r-cran-rcolorbrewer_1.1-3-1 r-cran-rcpp_1.0.13-1 r-cran-rlang_1.1.4-1 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_8.2-5 rpcsvc-proto_1.4.3-1 samclip_0.4.0-4 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 seqtk_1.4-2 shared-mime-info_2.4-5 snp-sites_2.5.1-2+b1 snpeff_5.2.b+dfsg-1 sysstat_12.7.5-2 systemd_256.6-1 systemd-sysv_256.6-1 sysvinit-utils_3.10-2 tar_1.35+dfsg-3 tzdata_2024a-4 ucf_3.0043+nmu1 unzip_6.0-28 usr-is-merged_39 util-linux_2.40.2-8 vt_0.57721+ds-3+b1 x11-common_1:7.7+23.1 xdg-utils_1.1.3-4.1 xkb-data_2.42-1 xz-utils_5.6.2-2 zip_3.0-14 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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
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 <!nocheck>, bcftools <!nocheck>, bedtools <!nocheck>, bwa <!nocheck>, freebayes <!nocheck>, libbio-perl-perl <!nocheck>, libvcflib-tools <!nocheck>, minimap2 <!nocheck>, parallel <!nocheck>, samtools <!nocheck>, samclip <!nocheck>, seqtk <!nocheck>, snp-sites <!nocheck>, snpeff <!nocheck>, vt <!nocheck>
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

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gpgv: Signature made Tue Dec 19 10:56:54 2023 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./snippy_4.6.0+dfsg-4.dsc: no acceptable signature found
dpkg-source: info: extracting snippy in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking snippy_4.6.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking snippy_4.6.0+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying debian_packaged_libs.patch
dpkg-source: info: applying snpeff.config.patch
dpkg-source: info: applying snpeff_v5.1+.patch

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 perl-5.40-throwaway amd64
--------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network snippy_4.6.0+dfsg-4 perl-5.40-throwaway amd64'.

Finished processing commands.
--------------------------------------------------------------------------------

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LANGUAGE=en_GB:en
LC_ALL=C.UTF-8
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
LOGNAME=debomatic
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic
SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic
SCHROOT_COMMAND=env
SCHROOT_GID=110
SCHROOT_GROUP=sbuild
SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-c32cd8da-e930-4314-99be-fc66f96e6634
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 <tille@debian.org>
 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 '/<<PKGBUILDDIR>>'
cd test && /usr/bin/make
make[2]: Entering directory '/<<PKGBUILDDIR>>/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
[18:33:38] This is snippy 4.6.0
[18:33:38] Written by Torsten Seemann
[18:33:38] Obtained from https://github.com/tseemann/snippy
[18:33:38] Detected operating system: linux
[18:33:38] Enabling bundled linux tools.
[18:33:38] Found bwa - /usr/bin/bwa
[18:33:38] Found bcftools - /usr/bin/bcftools
[18:33:38] Found samtools - /usr/bin/samtools
[18:33:38] Found java - /usr/bin/java
[18:33:38] Found snpEff - /usr/bin/snpEff
[18:33:38] Found samclip - /usr/bin/samclip
[18:33:38] Found seqtk - /usr/bin/seqtk
[18:33:38] Found parallel - /usr/bin/parallel
[18:33:38] Found freebayes - /usr/bin/freebayes
[18:33:38] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[18:33:38] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[18:33:38] Found vcfstreamsort - /usr/bin/vcfstreamsort
[18:33:38] Found vcfuniq - /usr/bin/vcfuniq
[18:33:38] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[18:33:38] Found gzip - /usr/bin/gzip
[18:33:38] Found vt - /usr/bin/vt
[18:33:38] Found snippy-vcf_to_tab - /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab
[18:33:38] Found snippy-vcf_report - /<<PKGBUILDDIR>>/bin/snippy-vcf_report
[18:33:38] Checking version: samtools --version is >= 1.7 - ok, have 1.20
[18:33:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.20
[18:33:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7
[18:33:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[18:33:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[18:33:38] Using reference: /<<PKGBUILDDIR>>/test/example.fna
[18:33:38] Treating reference as 'fasta' format.
[18:33:38] Will use 2 CPU cores.
[18:33:38] Using read file: /<<PKGBUILDDIR>>/test/S1/R1.fq
[18:33:38] Using read file: /<<PKGBUILDDIR>>/test/S1/R2.fq
[18:33:38] Used --force, will overwrite existing S1
[18:33:38] Changing working directory: S1
[18:33:38] Creating reference folder: reference
[18:33:38] Extracting FASTA and GFF from reference.
[18:33:39] Wrote 3 sequences to ref.fa
[18:33:39] Wrote 0 features to ref.gff
[18:33:39] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[18:33:39] Using BAM RG (Read Group) ID: S1
[18:33:39] Running: samtools faidx reference/ref.fa 2>> snps.log
[18:33:39] Running: bwa index reference/ref.fa 2>> snps.log
[18:33:39] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[18:33:39] Running: ln -sf reference/ref.fa . 2>> snps.log
[18:33:39] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[18:33:39] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[18:33:39] Running: bwa mem  -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S1/R1.fq /<<PKGBUILDDIR>>/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11587, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 199, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 369)
[M::mem_pestat] mean and std.dev: (199.53, 48.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 437)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 1.134 CPU sec, 0.576 real sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S1/R1.fq /<<PKGBUILDDIR>>/test/S1/R2.fq
[main] Real time: 0.676 sec; CPU: 1.165 sec
[samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978
[samclip] Header contained 6 lines
[samclip] Done.
[18:33:39] Running: samtools index snps.bam 2>> snps.log
[18:33:40] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[18:33:40] 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
[18:33:40] 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

[18:33:40] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[18:33:40] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[18:33:41] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[18:33:41] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[18:33:41] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[18:33:41] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[18:33:41] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[18:33:41] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[18:33:41] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[18:33:41] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[18:33:41] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[18:33:41] Marked 749 heterozygous sites with 'n'
[18:33:41] Creating extra output files: BED GFF CSV TXT HTML
[18:33:41] Identified 261 variants.
[18:33:41] Result folder: S1
[18:33:41] Result files:
[18:33:41] * S1/snps.aligned.fa
[18:33:41] * S1/snps.bam
[18:33:41] * S1/snps.bam.bai
[18:33:41] * S1/snps.bed
[18:33:41] * S1/snps.consensus.fa
[18:33:41] * S1/snps.consensus.subs.fa
[18:33:41] * S1/snps.csv
[18:33:41] * S1/snps.filt.vcf
[18:33:41] * S1/snps.gff
[18:33:41] * S1/snps.html
[18:33:41] * S1/snps.log
[18:33:41] * S1/snps.raw.vcf
[18:33:41] * S1/snps.subs.vcf
[18:33:41] * S1/snps.tab
[18:33:41] * S1/snps.txt
[18:33:41] * S1/snps.vcf
[18:33:41] * S1/snps.vcf.gz
[18:33:41] * S1/snps.vcf.gz.csi
[18:33:41] Walltime used: 3 seconds
[18:33:41] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues
[18:33:41] Done.
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq
[18:33:41] This is snippy 4.6.0
[18:33:41] Written by Torsten Seemann
[18:33:41] Obtained from https://github.com/tseemann/snippy
[18:33:41] Detected operating system: linux
[18:33:41] Enabling bundled linux tools.
[18:33:41] Found bwa - /usr/bin/bwa
[18:33:41] Found bcftools - /usr/bin/bcftools
[18:33:41] Found samtools - /usr/bin/samtools
[18:33:41] Found java - /usr/bin/java
[18:33:41] Found snpEff - /usr/bin/snpEff
[18:33:41] Found samclip - /usr/bin/samclip
[18:33:41] Found seqtk - /usr/bin/seqtk
[18:33:41] Found parallel - /usr/bin/parallel
[18:33:41] Found freebayes - /usr/bin/freebayes
[18:33:41] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[18:33:41] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[18:33:41] Found vcfstreamsort - /usr/bin/vcfstreamsort
[18:33:41] Found vcfuniq - /usr/bin/vcfuniq
[18:33:41] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[18:33:41] Found gzip - /usr/bin/gzip
[18:33:41] Found vt - /usr/bin/vt
[18:33:41] Found snippy-vcf_to_tab - /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab
[18:33:41] Found snippy-vcf_report - /<<PKGBUILDDIR>>/bin/snippy-vcf_report
[18:33:41] Checking version: samtools --version is >= 1.7 - ok, have 1.20
[18:33:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.20
[18:33:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7
[18:33:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[18:33:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[18:33:41] Using reference: /<<PKGBUILDDIR>>/test/example.fna
[18:33:41] Treating reference as 'fasta' format.
[18:33:41] Will use 2 CPU cores.
[18:33:41] Using read file: /<<PKGBUILDDIR>>/test/S2/R1.fq
[18:33:41] Using read file: /<<PKGBUILDDIR>>/test/S2/R2.fq
[18:33:41] Used --force, will overwrite existing S2
[18:33:41] Changing working directory: S2
[18:33:41] Creating reference folder: reference
[18:33:41] Extracting FASTA and GFF from reference.
[18:33:41] Wrote 3 sequences to ref.fa
[18:33:41] Wrote 0 features to ref.gff
[18:33:41] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[18:33:41] Using BAM RG (Read Group) ID: S2
[18:33:41] Running: samtools faidx reference/ref.fa 2>> snps.log
[18:33:41] Running: bwa index reference/ref.fa 2>> snps.log
[18:33:41] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[18:33:41] Running: ln -sf reference/ref.fa . 2>> snps.log
[18:33:41] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[18:33:41] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[18:33:41] Running: bwa mem  -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S2/R1.fq /<<PKGBUILDDIR>>/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 1.088 CPU sec, 0.548 real sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S2/R1.fq /<<PKGBUILDDIR>>/test/S2/R2.fq
[main] Real time: 0.613 sec; CPU: 1.116 sec
[samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987
[samclip] Header contained 6 lines
[samclip] Done.
[18:33:42] Running: samtools index snps.bam 2>> snps.log
[18:33:42] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[18:33:42] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
[18:33:43] 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

[18:33:43] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[18:33:43] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[18:33:43] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[18:33:43] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[18:33:43] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[18:33:43] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[18:33:43] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[18:33:43] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[18:33:43] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[18:33:43] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[18:33:43] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[18:33:43] Marked 841 heterozygous sites with 'n'
[18:33:43] Creating extra output files: BED GFF CSV TXT HTML
[18:33:43] Identified 246 variants.
[18:33:43] Result folder: S2
[18:33:43] Result files:
[18:33:43] * S2/snps.aligned.fa
[18:33:43] * S2/snps.bam
[18:33:43] * S2/snps.bam.bai
[18:33:43] * S2/snps.bed
[18:33:43] * S2/snps.consensus.fa
[18:33:43] * S2/snps.consensus.subs.fa
[18:33:43] * S2/snps.csv
[18:33:43] * S2/snps.filt.vcf
[18:33:43] * S2/snps.gff
[18:33:43] * S2/snps.html
[18:33:43] * S2/snps.log
[18:33:43] * S2/snps.raw.vcf
[18:33:43] * S2/snps.subs.vcf
[18:33:43] * S2/snps.tab
[18:33:43] * S2/snps.txt
[18:33:43] * S2/snps.vcf
[18:33:43] * S2/snps.vcf.gz
[18:33:43] * S2/snps.vcf.gz.csi
[18:33:43] Walltime used: 2 seconds
[18:33:43] Questionable SNP? Try the --report option to see the alignments.
[18:33:43] Done.
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq
[18:33:43] This is snippy 4.6.0
[18:33:43] Written by Torsten Seemann
[18:33:43] Obtained from https://github.com/tseemann/snippy
[18:33:43] Detected operating system: linux
[18:33:43] Enabling bundled linux tools.
[18:33:43] Found bwa - /usr/bin/bwa
[18:33:43] Found bcftools - /usr/bin/bcftools
[18:33:43] Found samtools - /usr/bin/samtools
[18:33:43] Found java - /usr/bin/java
[18:33:43] Found snpEff - /usr/bin/snpEff
[18:33:43] Found samclip - /usr/bin/samclip
[18:33:43] Found seqtk - /usr/bin/seqtk
[18:33:43] Found parallel - /usr/bin/parallel
[18:33:43] Found freebayes - /usr/bin/freebayes
[18:33:43] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[18:33:43] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[18:33:43] Found vcfstreamsort - /usr/bin/vcfstreamsort
[18:33:43] Found vcfuniq - /usr/bin/vcfuniq
[18:33:43] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[18:33:43] Found gzip - /usr/bin/gzip
[18:33:43] Found vt - /usr/bin/vt
[18:33:43] Found snippy-vcf_to_tab - /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab
[18:33:43] Found snippy-vcf_report - /<<PKGBUILDDIR>>/bin/snippy-vcf_report
[18:33:44] Checking version: samtools --version is >= 1.7 - ok, have 1.20
[18:33:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.20
[18:33:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7
[18:33:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[18:33:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[18:33:44] Using reference: /<<PKGBUILDDIR>>/test/example.fna
[18:33:44] Treating reference as 'fasta' format.
[18:33:44] Will use 2 CPU cores.
[18:33:44] Using read file: /<<PKGBUILDDIR>>/test/S3/R1.fq
[18:33:44] Using read file: /<<PKGBUILDDIR>>/test/S3/R2.fq
[18:33:44] Used --force, will overwrite existing S3
[18:33:44] Changing working directory: S3
[18:33:44] Creating reference folder: reference
[18:33:44] Extracting FASTA and GFF from reference.
[18:33:44] Wrote 3 sequences to ref.fa
[18:33:44] Wrote 0 features to ref.gff
[18:33:44] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[18:33:44] Using BAM RG (Read Group) ID: S3
[18:33:44] Running: samtools faidx reference/ref.fa 2>> snps.log
[18:33:44] Running: bwa index reference/ref.fa 2>> snps.log
[18:33:44] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[18:33:44] Running: ln -sf reference/ref.fa . 2>> snps.log
[18:33:44] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[18:33:44] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[18:33:44] Running: bwa mem  -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S3/R1.fq /<<PKGBUILDDIR>>/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 24000 sequences (2400000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368)
[M::mem_pestat] mean and std.dev: (198.46, 48.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 436)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 1.143 CPU sec, 0.578 real sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S3/R1.fq /<<PKGBUILDDIR>>/test/S3/R2.fq
[main] Real time: 0.659 sec; CPU: 1.170 sec
[samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970
[samclip] Header contained 6 lines
[samclip] Done.
[18:33:45] Running: samtools index snps.bam 2>> snps.log
[18:33:45] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[18:33:45] 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
[18:33:46] 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                      : 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

[18:33:46] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[18:33:46] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[18:33:46] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[18:33:46] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[18:33:46] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[18:33:46] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[18:33:46] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[18:33:46] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[18:33:46] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[18:33:46] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[18:33:46] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[18:33:46] Marked 846 heterozygous sites with 'n'
[18:33:46] Creating extra output files: BED GFF CSV TXT HTML
[18:33:46] Identified 254 variants.
[18:33:46] Result folder: S3
[18:33:46] Result files:
[18:33:46] * S3/snps.aligned.fa
[18:33:46] * S3/snps.bam
[18:33:46] * S3/snps.bam.bai
[18:33:46] * S3/snps.bed
[18:33:46] * S3/snps.consensus.fa
[18:33:46] * S3/snps.consensus.subs.fa
[18:33:46] * S3/snps.csv
[18:33:46] * S3/snps.filt.vcf
[18:33:46] * S3/snps.gff
[18:33:46] * S3/snps.html
[18:33:46] * S3/snps.log
[18:33:46] * S3/snps.raw.vcf
[18:33:46] * S3/snps.subs.vcf
[18:33:46] * S3/snps.tab
[18:33:46] * S3/snps.txt
[18:33:46] * S3/snps.vcf
[18:33:46] * S3/snps.vcf.gz
[18:33:46] * S3/snps.vcf.gz.csi
[18:33:46] Walltime used: 3 seconds
[18:33:46] May the SNPs be with you.
[18:33:46] Done.
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq
[18:33:46] This is snippy 4.6.0
[18:33:46] Written by Torsten Seemann
[18:33:46] Obtained from https://github.com/tseemann/snippy
[18:33:46] Detected operating system: linux
[18:33:46] Enabling bundled linux tools.
[18:33:46] Found bwa - /usr/bin/bwa
[18:33:46] Found bcftools - /usr/bin/bcftools
[18:33:46] Found samtools - /usr/bin/samtools
[18:33:46] Found java - /usr/bin/java
[18:33:46] Found snpEff - /usr/bin/snpEff
[18:33:46] Found samclip - /usr/bin/samclip
[18:33:46] Found seqtk - /usr/bin/seqtk
[18:33:46] Found parallel - /usr/bin/parallel
[18:33:46] Found freebayes - /usr/bin/freebayes
[18:33:46] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[18:33:46] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[18:33:46] Found vcfstreamsort - /usr/bin/vcfstreamsort
[18:33:46] Found vcfuniq - /usr/bin/vcfuniq
[18:33:46] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[18:33:46] Found gzip - /usr/bin/gzip
[18:33:46] Found vt - /usr/bin/vt
[18:33:46] Found snippy-vcf_to_tab - /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab
[18:33:46] Found snippy-vcf_report - /<<PKGBUILDDIR>>/bin/snippy-vcf_report
[18:33:46] Checking version: samtools --version is >= 1.7 - ok, have 1.20
[18:33:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.20
[18:33:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7
[18:33:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
[18:33:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[18:33:46] Using reference: /<<PKGBUILDDIR>>/test/example.fna
[18:33:46] Treating reference as 'fasta' format.
[18:33:46] Will use 2 CPU cores.
[18:33:46] Using read file: /<<PKGBUILDDIR>>/test/S4/R1.fq
[18:33:46] Using read file: /<<PKGBUILDDIR>>/test/S4/R2.fq
[18:33:46] Used --force, will overwrite existing S4
[18:33:46] Changing working directory: S4
[18:33:46] Creating reference folder: reference
[18:33:46] Extracting FASTA and GFF from reference.
[18:33:46] Wrote 3 sequences to ref.fa
[18:33:46] Wrote 0 features to ref.gff
[18:33:46] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[18:33:46] Using BAM RG (Read Group) ID: S4
[18:33:46] Running: samtools faidx reference/ref.fa 2>> snps.log
[18:33:46] Running: bwa index reference/ref.fa 2>> snps.log
[18:33:46] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[18:33:46] Running: ln -sf reference/ref.fa . 2>> snps.log
[18:33:46] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[18:33:46] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[18:33:46] Running: bwa mem  -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S4/R1.fq /<<PKGBUILDDIR>>/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 1.080 CPU sec, 0.549 real sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /<<PKGBUILDDIR>>/test/S4/R1.fq /<<PKGBUILDDIR>>/test/S4/R2.fq
[main] Real time: 0.625 sec; CPU: 1.110 sec
[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974
[samclip] Header contained 6 lines
[samclip] Done.
[18:33:47] Running: samtools index snps.bam 2>> snps.log
[18:33:47] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[18:33:47] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
[18:33:48] 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

[18:33:48] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[18:33:48] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[18:33:48] Running: /<<PKGBUILDDIR>>/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[18:33:48] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[18:33:48] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[18:33:48] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[18:33:48] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[18:33:48] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[18:33:48] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[18:33:48] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[18:33:48] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[18:33:49] Marked 799 heterozygous sites with 'n'
[18:33:49] Creating extra output files: BED GFF CSV TXT HTML
[18:33:49] Identified 257 variants.
[18:33:49] Result folder: S4
[18:33:49] Result files:
[18:33:49] * S4/snps.aligned.fa
[18:33:49] * S4/snps.bam
[18:33:49] * S4/snps.bam.bai
[18:33:49] * S4/snps.bed
[18:33:49] * S4/snps.consensus.fa
[18:33:49] * S4/snps.consensus.subs.fa
[18:33:49] * S4/snps.csv
[18:33:49] * S4/snps.filt.vcf
[18:33:49] * S4/snps.gff
[18:33:49] * S4/snps.html
[18:33:49] * S4/snps.log
[18:33:49] * S4/snps.raw.vcf
[18:33:49] * S4/snps.subs.vcf
[18:33:49] * S4/snps.tab
[18:33:49] * S4/snps.txt
[18:33:49] * S4/snps.vcf
[18:33:49] * S4/snps.vcf.gz
[18:33:49] * S4/snps.vcf.gz.csi
[18:33:49] Walltime used: 3 seconds
[18:33:49] Questionable SNP? Try the --report option to see the alignments.
[18:33:49] 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
This analysis is totally hard-core!
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
You can mask columns using '--mask BEDFILE --mask-char X'
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 '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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-examples' in '../snippy-examples_4.6.0+dfsg-4_all.deb'.
dpkg-deb: building package 'snippy' in '../snippy_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 2024-09-16T18:33:51Z

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: perl-5.40-throwaway
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
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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Files:
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 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
 76487d06568bab1ef0adbc91fa15828a 17513 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
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Mon, 16 Sep 2024 18:33:51 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
 usr-local-has-programs
Installed-Build-Depends:
 adduser (= 3.137),
 adwaita-icon-theme (= 47.0-1),
 ant (= 1.10.14-1),
 ant-optional (= 1.10.14-1),
 any2fasta (= 0.4.2-2),
 at-spi2-common (= 2.54.0-1),
 autoconf (= 2.72-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.22.5-2),
 autotools-dev (= 20220109.1),
 base-files (= 13.5),
 base-passwd (= 3.6.4),
 bash (= 5.2.32-1+b1),
 bcftools (= 1.20-2),
 bedtools (= 2.31.1+dfsg-2),
 binutils (= 2.43.1-4),
 binutils-common (= 2.43.1-4),
 binutils-x86-64-linux-gnu (= 2.43.1-4),
 bsdextrautils (= 2.40.2-8),
 bsdutils (= 1:2.40.2-8),
 build-essential (= 12.10),
 bwa (= 0.7.18-1),
 bzip2 (= 1.0.8-6),
 ca-certificates (= 20240203),
 ca-certificates-java (= 20240118),
 coreutils (= 9.4-3.1),
 cpp (= 4:14.1.0-2),
 cpp-13 (= 13.3.0-6),
 cpp-13-x86-64-linux-gnu (= 13.3.0-6),
 cpp-14 (= 14.2.0-5),
 cpp-14-x86-64-linux-gnu (= 14.2.0-5),
 cpp-x86-64-linux-gnu (= 4:14.1.0-2),
 dash (= 0.5.12-9),
 dbus (= 1.14.10-4+b1),
 dbus-bin (= 1.14.10-4+b1),
 dbus-daemon (= 1.14.10-4+b1),
 dbus-session-bus-common (= 1.14.10-4),
 dbus-system-bus-common (= 1.14.10-4),
 dbus-user-session (= 1.14.10-4+b1),
 dconf-gsettings-backend (= 0.40.0-4+b2),
 dconf-service (= 0.40.0-4+b2),
 debconf (= 1.5.87),
 debhelper (= 13.20),
 debianutils (= 5.20),
 default-jre (= 2:1.21-76),
 default-jre-headless (= 2:1.21-76),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.14.0-1),
 diffutils (= 1:3.10-1),
 dpkg (= 1.22.11),
 dpkg-dev (= 1.22.11),
 dwz (= 0.15-1+b1),
 file (= 1:5.45-3),
 findutils (= 4.10.0-3),
 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),
 freebayes (= 1.3.7-1),
 g++ (= 4:14.1.0-2),
 g++-14 (= 14.2.0-5),
 g++-14-x86-64-linux-gnu (= 14.2.0-5),
 g++-x86-64-linux-gnu (= 4:14.1.0-2),
 gcc (= 4:14.1.0-2),
 gcc-13 (= 13.3.0-6),
 gcc-13-base (= 13.3.0-6),
 gcc-13-x86-64-linux-gnu (= 13.3.0-6),
 gcc-14 (= 14.2.0-5),
 gcc-14-base (= 14.2.0-5),
 gcc-14-x86-64-linux-gnu (= 14.2.0-5),
 gcc-x86-64-linux-gnu (= 4:14.1.0-2),
 gettext (= 0.22.5-2),
 gettext-base (= 0.22.5-2),
 grep (= 3.11-4),
 groff-base (= 1.23.0-5),
 gtk-update-icon-cache (= 4.16.1+ds-2),
 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 (= 0.76),
 junit4 (= 4.13.2-4),
 junit5 (= 5.10.3-1),
 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),
 libapparmor1 (= 3.1.7-1+b1),
 libarchive-zip-perl (= 1.68-1),
 libargs4j-java (= 2.33-2),
 libasan8 (= 14.2.0-5),
 libasm-java (= 9.7-1),
 libasound2-data (= 1.2.12-1),
 libasound2t64 (= 1.2.12-1),
 libatinject-jsr330-api-java (= 1.0+ds1-5),
 libatk-bridge2.0-0t64 (= 2.54.0-1),
 libatk1.0-0t64 (= 2.54.0-1),
 libatomic1 (= 14.2.0-5),
 libatspi2.0-0t64 (= 2.54.0-1),
 libattr1 (= 1:2.5.2-1),
 libaudit-common (= 1:4.0.1-1),
 libaudit1 (= 1:4.0.1-1),
 libavahi-client3 (= 0.8-13+b2),
 libavahi-common-data (= 0.8-13+b2),
 libavahi-common3 (= 0.8-13+b2),
 libbinutils (= 2.43.1-4),
 libbio-perl-perl (= 1.7.8-1),
 libbiojava6-java (= 6.1.0+dfsg-4),
 libblas3 (= 3.12.0-3),
 libblkid1 (= 2.40.2-8),
 libbrotli1 (= 1.1.0-2+b4),
 libbsd0 (= 0.12.2-1),
 libbz2-1.0 (= 1.0.8-6),
 libc-bin (= 2.40-2),
 libc-dev-bin (= 2.40-2),
 libc6 (= 2.40-2),
 libc6-dev (= 2.40-2),
 libcairo-gobject2 (= 1.18.2-1),
 libcairo2 (= 1.18.2-1),
 libcap-ng0 (= 0.8.5-2),
 libcap2 (= 1:2.66-5),
 libcc1-0 (= 14.2.0-5),
 libcdi-api-java (= 1.2-3),
 libcharts4j-java (= 1.3-4),
 libciftools-java (= 6.0.0-1),
 libcloudproviders0 (= 0.3.6-1),
 libcodemodel-java (= 2.6+jaxb2.3.0.1-10.1),
 libcolord2 (= 1.4.7-1+b1),
 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 (= 1:4.4.36-5),
 libcrypt1 (= 1:4.4.36-5),
 libctf-nobfd0 (= 2.43.1-4),
 libctf0 (= 2.43.1-4),
 libcups2t64 (= 2.4.10-1),
 libcurl3t64-gnutls (= 8.10.0-2),
 libcurl4t64 (= 8.10.0-2),
 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),
 libdconf1 (= 0.40.0-4+b2),
 libdebconfclient0 (= 0.272),
 libdebhelper-perl (= 13.20),
 libdeflate0 (= 1.21-1),
 libdisorder0 (= 0.0.2+git20130809.8062ee1-4+b1),
 libdistlib-java (= 1.0-5),
 libdom4j-java (= 2.1.4-1),
 libdpkg-perl (= 1.22.11),
 libdrm-amdgpu1 (= 2.4.123-1),
 libdrm-common (= 2.4.123-1),
 libdrm-intel1 (= 2.4.123-1),
 libdrm-radeon1 (= 2.4.123-1),
 libdrm2 (= 2.4.123-1),
 libdtd-parser-java (= 1.2-1),
 libedit2 (= 3.1-20240808-1),
 libelf1t64 (= 0.191-2),
 libepoxy0 (= 1.5.10-1+b2),
 liberror-prone-java (= 2.18.0-1),
 libexec-maven-plugin-java (= 3.1.0-2),
 libexpat1 (= 2.6.3-1),
 libfastahack0 (= 1.0.0+dfsg-11+b1),
 libfastinfoset-java (= 1.2.12-3),
 libfastutil-java (= 8.5.14+dfsg-1),
 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),
 libfreemarker-java (= 2.3.32-2),
 libfreetype6 (= 2.13.3+dfsg-1),
 libfribidi0 (= 1.0.15-1),
 libgbm1 (= 24.2.2-1),
 libgcc-13-dev (= 13.3.0-6),
 libgcc-14-dev (= 14.2.0-5),
 libgcc-s1 (= 14.2.0-5),
 libgdbm-compat4t64 (= 1.24-2),
 libgdbm6t64 (= 1.24-2),
 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 (= 14.2.0-5),
 libgif7 (= 5.2.2-1),
 libgl1 (= 1.7.0-1+b1),
 libgl1-mesa-dri (= 24.2.2-1),
 libglapi-mesa (= 24.2.2-1),
 libglib2.0-0t64 (= 2.82.0-1),
 libglvnd0 (= 1.7.0-1+b1),
 libglx-mesa0 (= 24.2.2-1),
 libglx0 (= 1.7.0-1+b1),
 libgmp10 (= 2:6.3.0+dfsg-2+b1),
 libgnutls30t64 (= 3.8.6-2),
 libgomp1 (= 14.2.0-5),
 libgoogle-gson-java (= 2.10.1-1),
 libgprofng0 (= 2.43.1-4),
 libgraphite2-3 (= 1.3.14-2),
 libgssapi-krb5-2 (= 1.21.3-3),
 libgtk-3-0t64 (= 3.24.43-4),
 libgtk-3-common (= 3.24.43-4),
 libguava-java (= 32.0.1-1),
 libguice-java (= 4.2.3-2),
 libhamcrest-java (= 2.2-2),
 libharfbuzz0b (= 9.0.0-1),
 libhogweed6t64 (= 3.10-1),
 libhts3t64 (= 1.20+ds-1),
 libhtscodecs2 (= 1.6.1-1),
 libhtsjdk-java (= 4.1.0+dfsg-2),
 libhttpclient-java (= 4.5.14-1),
 libhttpcore-java (= 4.4.16-1),
 libhwasan0 (= 14.2.0-5),
 libice6 (= 2:1.0.10-1+b1),
 libicu72 (= 72.1-5),
 libidn2-0 (= 2.3.7-2),
 libinchi1.07 (= 1.07.1+dfsg-3),
 libio-string-perl (= 1.08-4),
 libisl23 (= 0.27-1),
 libistack-commons-java (= 3.0.6-5),
 libitext5-java (= 5.5.13.3-4),
 libitm1 (= 14.2.0-5),
 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 (= 2.1.0.7-4),
 libjheaps-java (= 0.14-2),
 libjmol-java (= 16.2.15+dfsg-1),
 libjni-inchi-java (= 0.8+dfsg-8),
 libjni-inchi-jni (= 0.8+dfsg-8),
 libjpeg62-turbo (= 1:2.1.5-3),
 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 (= 1.21.3-3),
 libkeyutils1 (= 1.6.3-3),
 libkrb5-3 (= 1.21.3-3),
 libkrb5support0 (= 1.21.3-3),
 liblapack3 (= 3.12.0-3),
 liblcms2-2 (= 2.14-2+b1),
 libldap-2.5-0 (= 2.5.18+dfsg-3+b1),
 liblerc4 (= 4.0.0+ds-4+b1),
 libllvm18 (= 1:18.1.8-11),
 liblog4j1.2-java (= 1.2.17-11),
 liblsan0 (= 14.2.0-5),
 liblzma5 (= 5.6.2-2),
 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 (= 3.8.8-1),
 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 (= 2.40.2-8),
 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-9),
 libncbi-vdb3 (= 3.0.2+dfsg-2+b1),
 libncurses6 (= 6.5-2),
 libncursesw6 (= 6.5-2),
 libnettle8t64 (= 3.10-1),
 libnghttp2-14 (= 1.63.0-1),
 libnghttp3-9 (= 1.4.0-1),
 libngs-java (= 3.0.3+dfsg-9),
 libngs-jni (= 3.0.3+dfsg-9),
 libngtcp2-16 (= 1.6.0-1),
 libngtcp2-crypto-gnutls8 (= 1.6.0-1),
 libnsl2 (= 1.3.0-3+b2),
 libnspr4 (= 2:4.35-1.1+b1),
 libnss3 (= 2:3.103-1),
 libopentest4j-java (= 1.2.0-4),
 libopentest4j-reporting-java (= 0.1.0-M1-2),
 libp11-kit0 (= 0.25.5-2),
 libpam-modules (= 1.5.3-7),
 libpam-modules-bin (= 1.5.3-7),
 libpam-runtime (= 1.5.3-7),
 libpam-systemd (= 256.6-1),
 libpam0g (= 1.5.3-7),
 libpango-1.0-0 (= 1.54.0+ds-2),
 libpangocairo-1.0-0 (= 1.54.0+ds-2),
 libpangoft2-1.0-0 (= 1.54.0+ds-2),
 libpaper-utils (= 1.1.29+b1),
 libpaper1 (= 1.1.29+b1),
 libpciaccess0 (= 0.17-3+b1),
 libpcre2-8-0 (= 10.42-4+b1),
 libpcsclite1 (= 2.3.0-1),
 libperl5.40 (= 5.40.0-5),
 libpicocli-java (= 4.6.2-2),
 libpipeline1 (= 1.5.8-1),
 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 (= 2:4.0.4-5),
 libpsl5t64 (= 0.21.2-1.1),
 libpython3-stdlib (= 3.12.5-1+b1),
 libpython3.12-minimal (= 3.12.6-1),
 libpython3.12-stdlib (= 3.12.6-1),
 libqdox2-java (= 2.0.3-1),
 libquadmath0 (= 14.2.0-5),
 libreadline8t64 (= 8.2-5),
 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+dfsg1-8),
 libsasl2-modules-db (= 2.1.28+dfsg1-8),
 libseccomp2 (= 2.5.5-1+b1),
 libselinux1 (= 3.7-3),
 libsemanage-common (= 3.7-2),
 libsemanage2 (= 3.7-2),
 libsensors-config (= 1:3.6.0-10),
 libsensors5 (= 1:3.6.0-10),
 libsepol2 (= 3.7-1),
 libseqlib2 (= 1.2.0+dfsg-11+b1),
 libsframe1 (= 2.43.1-4),
 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 (= 2.40.2-8),
 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 (= 3.46.1-1),
 libssh2-1t64 (= 1.11.0-7),
 libssl3t64 (= 3.3.2-1),
 libssw0 (= 1.1-15),
 libstax-ex-java (= 1.7.8-3),
 libstdc++-14-dev (= 14.2.0-5),
 libstdc++6 (= 14.2.0-5),
 libstreambuffer-java (= 1.5.4-1.1),
 libsystemd-shared (= 256.6-1),
 libsystemd0 (= 256.6-1),
 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+git230720-5),
 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 (= 14.2.0-5),
 libtxw2-java (= 2.3.0.1-10.1),
 libubsan1 (= 14.2.0-5),
 libuchardet0 (= 0.0.8-1+b1),
 libudev1 (= 256.6-1),
 libunistring5 (= 1.2-1),
 libunivocity-parsers-java (= 2.9.1-1),
 libuuid1 (= 2.40.2-8),
 libvcflib-tools (= 1.0.9+dfsg1-3+b1),
 libvcflib2 (= 1.0.9+dfsg1-3+b1),
 libvecmath-java (= 1.5.2-7),
 libvulkan1 (= 1.3.290.0-1),
 libwagon-http-java (= 3.5.3-1),
 libwagon-provider-api-java (= 3.5.3-1),
 libwayland-client0 (= 1.23.0-1),
 libwayland-cursor0 (= 1.23.0-1),
 libwayland-egl1 (= 1.23.0-1),
 libwayland-server0 (= 1.23.0-1),
 libwebp7 (= 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),
 libxkbcommon0 (= 1.6.0-1+b1),
 libxml-commons-external-java (= 1.4.01-6),
 libxml-commons-resolver1.1-java (= 1.2-11),
 libxml2 (= 2.12.7+dfsg-3+b1),
 libxrandr2 (= 2:1.5.4-1),
 libxrender1 (= 1:0.9.10-1.1+b1),
 libxshmfence1 (= 1.3-1+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 (= 1.5.6+dfsg-1),
 linux-libc-dev (= 6.10.9-1),
 littler (= 0.3.20-1),
 login.defs (= 1:4.16.0-4),
 m4 (= 1.4.19-4),
 make (= 4.3-4.1),
 man-db (= 2.13.0-1),
 mawk (= 1.3.4.20240905-1),
 media-types (= 10.1.0),
 mesa-libgallium (= 24.2.2-1),
 minimap2 (= 2.27+dfsg-1+b1),
 mount (= 2.40.2-8),
 ncbi-vdb-data (= 3.0.2+dfsg-2),
 ncurses-base (= 6.5-2),
 ncurses-bin (= 6.5-2),
 netbase (= 6.4),
 openjdk-21-jre (= 21.0.5~6ea-1),
 openjdk-21-jre-headless (= 21.0.5~6ea-1),
 openssl (= 3.3.2-1),
 openssl-provider-legacy (= 3.3.2-1),
 parallel (= 20240222+ds-2),
 passwd (= 1:4.16.0-4),
 patch (= 2.7.6-7),
 perl (= 5.40.0-5),
 perl-base (= 5.40.0-5),
 perl-modules-5.40 (= 5.40.0-5),
 po-debconf (= 1.0.21+nmu1),
 procps (= 2:4.0.4-5),
 python3 (= 3.12.5-1+b1),
 python3-minimal (= 3.12.5-1+b1),
 python3.12 (= 3.12.6-1),
 python3.12-minimal (= 3.12.6-1),
 r-base-core (= 4.4.1-3),
 r-cran-cli (= 3.6.3-1),
 r-cran-colorspace (= 2.1-0+dfsg-1),
 r-cran-fansi (= 1.0.5-1),
 r-cran-farver (= 2.1.2-1),
 r-cran-ggplot2 (= 3.5.1+dfsg-1),
 r-cran-glue (= 1.7.0-1),
 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 (= 7.3-61-1),
 r-cran-matrix (= 1.7-0-3),
 r-cran-mgcv (= 1.9-1-1),
 r-cran-munsell (= 0.5.1-1),
 r-cran-nlme (= 3.1.166-1),
 r-cran-pillar (= 1.9.0+dfsg-1),
 r-cran-pkgconfig (= 2.0.3-2),
 r-cran-pkgkitten (= 0.2.4-1),
 r-cran-plyr (= 1.8.9-1),
 r-cran-r6 (= 2.5.1-1),
 r-cran-rcolorbrewer (= 1.1-3-1),
 r-cran-rcpp (= 1.0.13-1),
 r-cran-rlang (= 1.1.4-1),
 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 (= 8.2-5),
 rpcsvc-proto (= 1.4.3-1),
 samclip (= 0.4.0-4),
 samtools (= 1.20-3),
 sed (= 4.9-2),
 sensible-utils (= 0.0.24),
 seqtk (= 1.4-2),
 shared-mime-info (= 2.4-5),
 snp-sites (= 2.5.1-2+b1),
 snpeff (= 5.2.b+dfsg-1),
 sysstat (= 12.7.5-2),
 systemd (= 256.6-1),
 systemd-sysv (= 256.6-1),
 sysvinit-utils (= 3.10-2),
 tar (= 1.35+dfsg-3),
 tzdata (= 2024a-4),
 ucf (= 3.0043+nmu1),
 unzip (= 6.0-28),
 usr-is-merged (= 39),
 util-linux (= 2.40.2-8),
 vt (= 0.57721+ds-3+b1),
 x11-common (= 1:7.7+23.1),
 xdg-utils (= 1.1.3-4.1),
 xkb-data (= 2.42-1),
 xz-utils (= 5.6.2-2),
 zip (= 3.0-14),
 zlib1g (= 1:1.3.dfsg+really1.3.1-1)
Environment:
 DEB_BUILD_OPTIONS="parallel=2"
 LANG="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 LC_CTYPE="C.UTF-8"
 LD_LIBRARY_PATH="/usr/lib/libeatmydata"
 SOURCE_DATE_EPOCH="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 <debian-med-packaging@lists.alioth.debian.org>
 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 <debian-med-packaging@lists.alioth.debian.org>
 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 /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: full
Build-Space: 46036
Build-Time: 14
Distribution: perl-5.40-throwaway
Host Architecture: amd64
Install-Time: 40
Job: /srv/debomatic/incoming/snippy_4.6.0+dfsg-4.dsc
Machine Architecture: amd64
Package: snippy
Package-Time: 57
Source-Version: 4.6.0+dfsg-4
Space: 46036
Status: successful
Version: 4.6.0+dfsg-4
--------------------------------------------------------------------------------
Finished at 2024-09-16T18:33:51Z
Build needed 00:00:57, 46036k disk space