sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk

+==============================================================================+
| snippy 4.6.0+dfsg-6 (amd64)                  Sun, 12 Jul 2026 01:18:25 +0000 |
+==============================================================================+

Package: snippy
Version: 4.6.0+dfsg-6
Source Version: 4.6.0+dfsg-6
Distribution: perl-5.44-throwaway
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: full

I: Setting up the chroot...
I: Creating chroot session...
I: Setting up log color...

+------------------------------------------------------------------------------+
| Chroot Setup Commands                        Sun, 12 Jul 2026 01:18:25 +0000 |
+------------------------------------------------------------------------------+


/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-6 perl-5.44-throwaway amd64
--------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup snippy_4.6.0+dfsg-6 perl-5.44-throwaway amd64'.

Finished processing commands.
--------------------------------------------------------------------------------
I: Setting up apt archive...

+------------------------------------------------------------------------------+
| Update chroot                                Sun, 12 Jul 2026 01:18:26 +0000 |
+------------------------------------------------------------------------------+

Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B]
Hit:2 http://deb.debian.org/debian unstable InRelease
Hit:3 http://deb.debian.org/debian sid InRelease
Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 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                           Sun, 12 Jul 2026 01:18:27 +0000 |
+------------------------------------------------------------------------------+


Local sources
-------------

/srv/debomatic/incoming/snippy_4.6.0+dfsg-6.dsc exists in /srv/debomatic/incoming; copying to chroot

+------------------------------------------------------------------------------+
| Install package build dependencies           Sun, 12 Jul 2026 01:18:28 +0000 |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt, build-essential
Filtered Build-Depends: debhelper-compat (= 13), any2fasta, bcftools, bedtools, bwa, freebayes, libbio-perl-perl, libvcflib-tools, minimap2, parallel, samtools, samclip, seqtk, snp-sites, snpeff, vt, build-essential
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/snippy-jObLQy/resolver-NmjON5/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/build/snippy-jObLQy/resolver-NmjON5/apt_archive ./ InRelease
Get:2 copy:/build/snippy-jObLQy/resolver-NmjON5/apt_archive ./ Release [609 B]
Ign:3 copy:/build/snippy-jObLQy/resolver-NmjON5/apt_archive ./ Release.gpg
Get:4 copy:/build/snippy-jObLQy/resolver-NmjON5/apt_archive ./ Sources [916 B]
Get:5 copy:/build/snippy-jObLQy/resolver-NmjON5/apt_archive ./ Packages [790 B]
Fetched 2315 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Solving dependencies...
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 bubblewrap
  bwa ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon
  dbus-session-bus-common dbus-system-bus-common dbus-user-session
  dconf-gsettings-backend dconf-service debhelper default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file
  fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono freebayes
  gettext gettext-base glycin-loaders glycin-thumbnailers 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
  libbeam-java libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libbsd0
  libcairo-gobject2 libcairo2 libcap2 libcdi-api-java libcharts4j-java
  libciftools-java libcloudproviders0 libcodemodel-java libcolord2 libcom-err2
  libcommons-beanutils-java libcommons-cli-java libcommons-codec-java
  libcommons-collections3-java libcommons-collections4-java
  libcommons-compress-java libcommons-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 libcurl4-gnutls
  libcurl4t64 libdata-stag-perl libdatrie1 libdav1d7 libdbus-1-3 libdconf1
  libde265-0 libdebhelper-perl libdeflate0 libdisorder0 libdistlib-java
  libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2
  libdtd-parser-java libedit2 libelf1t64 libepoxy0 liberror-prone-java
  libexpat1 libezmorph-java libfastahack0 libfastinfoset-java libfastutil-java
  libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfreemarker-java
  libfreetype6 libfribidi0 libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common
  libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java
  libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0
  libglx-mesa0 libglx0 libglycin-2-0 libgoogle-gson-java libgraphite2-3
  libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libguice-java
  libhamcrest-java libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265
  libheif1 libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java
  libhttpcore-java libhwy1t64 libice6 libicu78 libinchi-dev 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 libjna-inchi-java libjna-java
  libjna-jni libjoptsimple-java libjpeg62-turbo libjson-java
  libjson-simple-java libjsoncpp26 libjsoup-java libjsr305-java libjxl0.11
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2
  liblerc4 libllvm21 libmagic-mgc libmagic1t64 libmaven-archiver-java
  libmaven-compiler-plugin-java libmaven-file-management-java
  libmaven-jar-plugin-java libmaven-parent-java libmaven-resolver-java
  libmaven-shared-incremental-java libmaven-shared-io-java
  libmaven-shared-utils-java libmaven3-core-java libmbedcrypto16 libmbedtls21
  libmbedx509-7 libmmtf-java libmsgpack-java libnaga-java libncbi-ngs3
  libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni
  libngtcp2-16 libngtcp2-crypto-gnutls8 libngtcp2-crypto-ossl0 libnspr4
  libnss3 libopentest4j-java libopentest4j-reporting-java libpam-systemd
  libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
  libpaper2 libpciaccess0 libpcsclite1 libpicocli-java libpipeline1
  libpixman-1-0 libplexus-archiver-java libplexus-cipher-java
  libplexus-classworlds-java libplexus-compiler-java
  libplexus-component-annotations-java libplexus-container-default-java
  libplexus-interpolation-java libplexus-io-java libplexus-languages-java
  libplexus-sec-dispatcher-java libplexus-utils2-java libpng16-16t64
  libproc2-1 libpsl5t64 libpython3-stdlib libpython3.14-minimal
  libpython3.14-stdlib libqdox2-java librelaxng-datatype-java librhino-java
  librngom-java librsvg2-2 libsensors-config libsensors5 libseqlib2
  libsharpyuv0 libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6
  libsmithwaterman0 libsnappy-java libsnappy-jni libsnappy1v5 libsnp-sites1
  libsnpeff-java libssh2-1t64 libssw0 libstax-ex-java libstreambuffer-java
  libtabixpp0t64 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl
  libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtool
  libtrove3-java libtxw2-java libuchardet0 libunivocity-parsers-java
  libvcflib-tools libvcflib2 libvecmath-java libvulkan1 libwagon-http-java
  libwagon-provider-api-java libwayland-client0 libwayland-cursor0
  libwayland-egl1 libwebp7 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6
  libxbean-reflect-java libxcb-dri3-0 libxcb-glx0 libxcb-present0
  libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1
  libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6
  libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0
  libxml-commons-external-java libxml-commons-resolver1.1-java libxml2-16
  libxom-java libxrandr2 libxrender1 libxres1 libxshmfence1 libxsom-java
  libxss1 libxt6t64 libxtst6 libxxf86vm1 libxz-java libz3-4 m4 man-db
  media-types mesa-libgallium minimap2 ncbi-vdb-data netbase openjdk-25-jre
  openjdk-25-jre-headless openssl parallel pci.ids po-debconf procps python3
  python3-minimal python3.14 python3.14-minimal r-base-core r-cran-cli
  r-cran-cpp11 r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase
  r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle r-cran-littler
  r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
  r-cran-rlang r-cran-s7 r-cran-scales r-cran-vctrs r-cran-viridislite
  r-cran-withr samclip samtools sensible-utils seqtk shared-mime-info
  snp-sites snpeff sysstat systemd-sysv tzdata ucf unzip vt x11-common
  xdg-utils xkb-data zip
Suggested packages:
  adwaita-icon-theme-legacy ant-doc default-jdk | java-compiler | java-sdk
  antlr javacc junit jython libbcel-java libbsf-java libcommons-net-java
  libmail-java libjaxp1.3-java libjdepend-java libjsch-java liblog4j1.2-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 gnulib-l10n libheif-plugin-x265
  | libheif-plugin-kvazaar groff alsa-utils libasound2-plugins
  libatinject-jsr330-api-java-doc bioperl libxml-sax-expatxs-perl
  libbio-alignio-stockholm-perl libbiojava6-java-doc libel-api-java colord
  libcommons-collections3-java-doc libcommons-collections4-java-doc
  libcommons-lang-java-doc libavalon-framework-java libexcalibur-logkit-java
  cups-common libdistlib-java-doc libmsv-java libxpp2-java libxpp3-java
  libjdom1-java low-memory-monitor libgoogle-gson-java-doc krb5-doc krb5-user
  gvfs libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc
  libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar
  libheif-plugin-rav1e libheif-plugin-svtenc picard-tools libbcpkix-java
  libbcprov-java libxml-security-java libjackson2-annotations-java-doc
  libjmol-java-doc libjson-simple-doc libjsoup-java-doc libjsr305-java-doc
  liblcms2-utils libmaven-file-management-java-doc liblogback-java
  libmmtf-java-doc libngs-java-doc pcscd libeclipse-jdt-core-java
  libplexus-utils2-java-doc rhino librsvg2-bin lm-sensors testng
  libsnpeff-java-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler
  r-cran-pracma libxerces2-java-doc libxml-commons-resolver1.1-java-doc
  libxom-java-doc m4-doc apparmor less www-browser libnss-mdns
  fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
  fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic csh fish ksh tcsh zsh
  libmail-box-perl python3-doc python3-tk python3-venv python3.14-venv
  python3.14-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib
  r-base-html r-cran-getopt r-cran-inline cwltool vcfanno isag
Recommended packages:
  librsvg2-common python3-gffutils python3-matplotlib curl | wget | lynx
  libheif-plugin-aomenc | libheif-plugin-rav1e | libheif-plugin-svtenc
  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 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 libgd-perl libmldbm-perl
  libxml-libxslt-perl libxml-perl perl-tk libarchive-cpio-perl libglib2.0-data
  xdg-user-dirs ibus-gtk3 libgtk-3-bin libheif-plugin-x265
  libheif-plugin-aomenc krb5-locales libjansi-java libgpm2 publicsuffix
  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 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 bubblewrap
  bwa ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon
  dbus-session-bus-common dbus-system-bus-common dbus-user-session
  dconf-gsettings-backend dconf-service debhelper default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file
  fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono freebayes
  gettext gettext-base glycin-loaders glycin-thumbnailers 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
  libbeam-java libbio-perl-perl libbiojava6-java libblas3 libbrotli1 libbsd0
  libcairo-gobject2 libcairo2 libcap2 libcdi-api-java libcharts4j-java
  libciftools-java libcloudproviders0 libcodemodel-java libcolord2 libcom-err2
  libcommons-beanutils-java libcommons-cli-java libcommons-codec-java
  libcommons-collections3-java libcommons-collections4-java
  libcommons-compress-java libcommons-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 libcurl4-gnutls
  libcurl4t64 libdata-stag-perl libdatrie1 libdav1d7 libdbus-1-3 libdconf1
  libde265-0 libdebhelper-perl libdeflate0 libdisorder0 libdistlib-java
  libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2
  libdtd-parser-java libedit2 libelf1t64 libepoxy0 liberror-prone-java
  libexpat1 libezmorph-java libfastahack0 libfastinfoset-java libfastutil-java
  libfile-stripnondeterminism-perl libfml0 libfontconfig1 libfreemarker-java
  libfreetype6 libfribidi0 libgbm1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common
  libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java
  libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0
  libglx-mesa0 libglx0 libglycin-2-0 libgoogle-gson-java libgraphite2-3
  libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libguice-java
  libhamcrest-java libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265
  libheif1 libhts3t64 libhtscodecs2 libhtsjdk-java libhttpclient-java
  libhttpcore-java libhwy1t64 libice6 libicu78 libinchi-dev 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 libjna-inchi-java libjna-java
  libjna-jni libjoptsimple-java libjpeg62-turbo libjson-java
  libjson-simple-java libjsoncpp26 libjsoup-java libjsr305-java libjxl0.11
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2
  liblerc4 libllvm21 libmagic-mgc libmagic1t64 libmaven-archiver-java
  libmaven-compiler-plugin-java libmaven-file-management-java
  libmaven-jar-plugin-java libmaven-parent-java libmaven-resolver-java
  libmaven-shared-incremental-java libmaven-shared-io-java
  libmaven-shared-utils-java libmaven3-core-java libmbedcrypto16 libmbedtls21
  libmbedx509-7 libmmtf-java libmsgpack-java libnaga-java libncbi-ngs3
  libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni
  libngtcp2-16 libngtcp2-crypto-gnutls8 libngtcp2-crypto-ossl0 libnspr4
  libnss3 libopentest4j-java libopentest4j-reporting-java libpam-systemd
  libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
  libpaper2 libpciaccess0 libpcsclite1 libpicocli-java libpipeline1
  libpixman-1-0 libplexus-archiver-java libplexus-cipher-java
  libplexus-classworlds-java libplexus-compiler-java
  libplexus-component-annotations-java libplexus-container-default-java
  libplexus-interpolation-java libplexus-io-java libplexus-languages-java
  libplexus-sec-dispatcher-java libplexus-utils2-java libpng16-16t64
  libproc2-1 libpsl5t64 libpython3-stdlib libpython3.14-minimal
  libpython3.14-stdlib libqdox2-java librelaxng-datatype-java librhino-java
  librngom-java librsvg2-2 libsensors-config libsensors5 libseqlib2
  libsharpyuv0 libsisu-inject-java libsisu-plexus-java libslf4j-java libsm6
  libsmithwaterman0 libsnappy-java libsnappy-jni libsnappy1v5 libsnp-sites1
  libsnpeff-java libssh2-1t64 libssw0 libstax-ex-java libstreambuffer-java
  libtabixpp0t64 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl
  libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtool
  libtrove3-java libtxw2-java libuchardet0 libunivocity-parsers-java
  libvcflib-tools libvcflib2 libvecmath-java libvulkan1 libwagon-http-java
  libwagon-provider-api-java libwayland-client0 libwayland-cursor0
  libwayland-egl1 libwebp7 libwfa2-0 libx11-6 libx11-data libx11-xcb1 libxau6
  libxbean-reflect-java libxcb-dri3-0 libxcb-glx0 libxcb-present0
  libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1
  libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6
  libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0
  libxml-commons-external-java libxml-commons-resolver1.1-java libxml2-16
  libxom-java libxrandr2 libxrender1 libxres1 libxshmfence1 libxsom-java
  libxss1 libxt6t64 libxtst6 libxxf86vm1 libxz-java libz3-4 m4 man-db
  media-types mesa-libgallium minimap2 ncbi-vdb-data netbase openjdk-25-jre
  openjdk-25-jre-headless openssl parallel pci.ids po-debconf procps python3
  python3-minimal python3.14 python3.14-minimal r-base-core r-cran-cli
  r-cran-cpp11 r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase
  r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle r-cran-littler
  r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
  r-cran-rlang r-cran-s7 r-cran-scales 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-sysv tzdata ucf
  unzip vt x11-common xdg-utils xkb-data zip
0 upgraded, 409 newly installed, 0 to remove and 0 not upgraded.
Need to get 334 MB/334 MB of archives.
After this operation, 1043 MB of additional disk space will be used.
Get:1 copy:/build/snippy-jObLQy/resolver-NmjON5/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B]
Get:2 file:/srv/reprepro perl-5.44/main amd64 libtext-charwidth-perl amd64 0.04-12+b1 [9324 B]
Get:3 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 261.1-2 [40.4 kB]
Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB]
Get:5 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.6-1 [896 kB]
Get:6 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.6-1 [2416 kB]
Get:7 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.14.6-1 [25.1 kB]
Get:8 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB]
Get:9 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB]
Get:10 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026b-1 [260 kB]
Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.6-1 [2278 kB]
Get:12 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.6-1 [846 kB]
Get:13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.14.6-1 [8108 B]
Get:14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.14.6-1 [25.1 kB]
Get:15 http://deb.debian.org/debian unstable/main amd64 libproc2-1 amd64 2:4.0.6-2 [69.2 kB]
Get:16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.6-2 [983 kB]
Get:17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB]
Get:18 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.6.3-1 [1522 kB]
Get:19 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20260601 [134 kB]
Get:20 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-5+b1 [176 kB]
Get:21 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.16.2-5+b1 [76.7 kB]
Get:22 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.16.2-5 [48.7 kB]
Get:23 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 4.1.7-4 [36.2 kB]
Get:24 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.16.2-5+b1 [156 kB]
Get:25 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.16.2-5 [49.6 kB]
Get:26 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.16.2-5+b1 [68.2 kB]
Get:27 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB]
Get:28 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB]
Get:29 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB]
Get:30 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB]
Get:31 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB]
Get:32 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB]
Get:33 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 261.1-2 [316 kB]
Get:34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB]
Get:35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB]
Get:36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB]
Get:37 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-11 [7788 B]
Get:38 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0056 [47.1 kB]
Get:39 http://deb.debian.org/debian unstable/main amd64 libcap2 amd64 1:2.78-1 [26.9 kB]
Get:40 http://deb.debian.org/debian unstable/main amd64 bubblewrap amd64 0.11.2-2 [49.7 kB]
Get:41 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB]
Get:42 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.58-1 [289 kB]
Get:43 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.14.3+dfsg-1 [493 kB]
Get:44 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-9 [488 kB]
Get:45 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-9 [840 kB]
Get:46 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.17.1-5 [56.1 kB]
Get:47 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.17.1-5 [132 kB]
Get:48 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.46.4-1+b2 [259 kB]
Get:49 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB]
Get:50 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB]
Get:51 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB]
Get:52 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB]
Get:53 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB]
Get:54 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b2 [115 kB]
Get:55 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b2 [105 kB]
Get:56 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB]
Get:57 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1+b2 [27.7 kB]
Get:58 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-3+b1 [543 kB]
Get:59 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.88.2-1 [1536 kB]
Get:60 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1+b2 [115 kB]
Get:61 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.1.1-1 [201 kB]
Get:62 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.23.1-1 [17.3 kB]
Get:63 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.3-1+b2 [563 kB]
Get:64 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.23.1-1 [19.8 kB]
Get:65 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.23.1-1 [761 kB]
Get:66 http://deb.debian.org/debian unstable/main amd64 libhwy1t64 amd64 1.3.0-2+b1 [707 kB]
Get:67 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.19.1-1 [164 kB]
Get:68 http://deb.debian.org/debian unstable/main amd64 libjxl0.11 amd64 0.11.2-5 [1256 kB]
Get:69 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.4-3+b1 [129 kB]
Get:70 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.17.1-5 [191 kB]
Get:71 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-5+b1 [26.2 kB]
Get:72 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.15-2 [75.8 kB]
Get:73 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 12.3.2-2+b2 [513 kB]
Get:74 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.30-2 [172 kB]
Get:75 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.14-2 [39.1 kB]
Get:76 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.30-2 [51.8 kB]
Get:77 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.58.0-1 [225 kB]
Get:78 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.58.0-1 [53.1 kB]
Get:79 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.58.0-1 [34.2 kB]
Get:80 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB]
Get:81 http://deb.debian.org/debian unstable/main amd64 librsvg2-2 amd64 2.62.1+dfsg-1 [1828 kB]
Get:82 http://deb.debian.org/debian unstable/main amd64 glycin-loaders amd64 2.1.5+ds-2 [2733 kB]
Get:83 http://deb.debian.org/debian unstable/main amd64 libglycin-2-0 amd64 2.1.5+ds-2 [1393 kB]
Get:84 http://deb.debian.org/debian unstable/main amd64 glycin-thumbnailers amd64 2.1.5+ds-2 [215 kB]
Get:85 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.44.6+dfsg-2 [313 kB]
Get:86 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b3 [758 kB]
Get:87 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.44.6+dfsg-2 [96.1 kB]
Get:88 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.22.4+ds-1 [41.2 kB]
Get:89 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB]
Get:90 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 50.0-2 [506 kB]
Get:91 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20260311 [11.2 kB]
Get:92 http://deb.debian.org/debian unstable/main amd64 java-common all 0.77 [6620 B]
Get:93 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:3.1.3-4 [213 kB]
Get:94 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.38.2-1+b1 [110 kB]
Get:95 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.124-1 [1422 kB]
Get:96 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.5.1-1 [54.8 kB]
Get:97 http://deb.debian.org/debian unstable/main amd64 openjdk-25-jre-headless amd64 25.0.4~4ea-1 [53.7 MB]
Get:98 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.25-77 [3012 B]
Get:99 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.17-1 [2172 kB]
Get:100 http://deb.debian.org/debian unstable/main amd64 ant-optional all 1.10.17-1 [456 kB]
Get:101 http://deb.debian.org/debian unstable/main amd64 any2fasta all 0.8.1-1 [8272 B]
Get:102 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.61.0-1 [171 kB]
Get:103 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB]
Get:104 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB]
Get:105 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB]
Get:106 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB]
Get:107 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB]
Get:108 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB]
Get:109 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB]
Get:110 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB]
Get:111 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB]
Get:112 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB]
Get:113 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B]
Get:114 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB]
Get:115 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB]
Get:116 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB]
Get:117 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB]
Get:118 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB]
Get:119 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB]
Get:120 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-2 [416 kB]
Get:121 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.21.0-2 [17.0 kB]
Get:122 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB]
Get:123 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB]
Get:124 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB]
Get:125 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.22-1 [829 kB]
Get:126 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-3 [698 kB]
Get:127 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.19-1 [213 kB]
Get:128 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.16.2-5+b1 [48.8 kB]
Get:129 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.49.0-4+b1 [42.5 kB]
Get:130 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.49.0-4+b1 [32.6 kB]
Get:131 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.49.0-4+b1 [28.7 kB]
Get:132 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB]
Get:133 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB]
Get:134 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB]
Get:135 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:136 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB]
Get:137 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B]
Get:138 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB]
Get:139 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB]
Get:140 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB]
Get:141 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:142 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB]
Get:143 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB]
Get:144 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.61.0-1 [49.7 kB]
Get:145 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-2+b1 [79.9 kB]
Get:146 http://deb.debian.org/debian unstable/main amd64 libxres1 amd64 2:1.2.1-2 [17.9 kB]
Get:147 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.61.0-1 [82.2 kB]
Get:148 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.61.0-1 [67.0 kB]
Get:149 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.4.0-2+b1 [29.2 kB]
Get:150 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.8-3 [141 kB]
Get:151 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-18 [113 kB]
Get:152 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-18 [45.2 kB]
Get:153 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-18 [49.2 kB]
Get:154 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.18-1 [252 kB]
Get:155 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2+b2 [199 kB]
Get:156 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.25.0-2 [29.2 kB]
Get:157 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.25.0-2 [11.7 kB]
Get:158 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.25.0-2 [5604 B]
Get:159 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1+b2 [16.6 kB]
Get:160 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b5 [20.3 kB]
Get:161 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.3-1+b2 [40.3 kB]
Get:162 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.7-1+b1 [16.3 kB]
Get:163 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b5 [16.0 kB]
Get:164 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.47-1 [835 kB]
Get:165 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.13.1-1 [148 kB]
Get:166 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b4 [36.5 kB]
Get:167 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.52-1 [4929 kB]
Get:168 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.52-1 [2920 kB]
Get:169 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-3+b1 [54.3 kB]
Get:170 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-3 [7860 B]
Get:171 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-3 [38.5 kB]
Get:172 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-3 [23.3 kB]
Get:173 http://deb.debian.org/debian unstable/main amd64 pci.ids all 0.0~2026.07.06-1 [285 kB]
Get:174 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.19-2 [18.5 kB]
Get:175 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.134-3 [64.2 kB]
Get:176 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-3 [132 kB]
Get:177 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20260512-1 [93.6 kB]
Get:178 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1.1 [8644 kB]
Get:179 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b4 [28.2 MB]
Get:180 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB]
Get:181 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.2-2+b2 [37.2 kB]
Get:182 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.13-1 [250 kB]
Get:183 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b2 [107 kB]
Get:184 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b2 [106 kB]
Get:185 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b2 [117 kB]
Get:186 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b2 [109 kB]
Get:187 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b2 [109 kB]
Get:188 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3.3-1+b2 [11.2 kB]
Get:189 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 26.1.4-1 [11.2 MB]
Get:190 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 26.1.4-1 [54.8 kB]
Get:191 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.341.0-1 [141 kB]
Get:192 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 26.1.4-1 [44.5 kB]
Get:193 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b2 [122 kB]
Get:194 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-2+b1 [20.2 kB]
Get:195 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 26.1.4-1 [125 kB]
Get:196 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-3+b1 [34.9 kB]
Get:197 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-3+b1 [87.1 kB]
Get:198 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.16.1-1 [19.4 kB]
Get:199 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.16.1-1 [397 kB]
Get:200 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 6.1.3-1 [46.1 kB]
Get:201 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+26 [217 kB]
Get:202 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.5-1+b2 [26.2 kB]
Get:203 http://deb.debian.org/debian unstable/main amd64 openjdk-25-jre amd64 25.0.4~4ea-1 [204 kB]
Get:204 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.25-77 [1028 B]
Get:205 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1+b2 [70.8 kB]
Get:206 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.8-1 [87.3 kB]
Get:207 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-16 [22.9 kB]
Get:208 http://deb.debian.org/debian unstable/main amd64 libseqlib2 amd64 1.2.0+dfsg-11+b4 [174 kB]
Get:209 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b2 [10.2 kB]
Get:210 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b3 [4892 B]
Get:211 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-12 [24.2 kB]
Get:212 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b3 [37.6 kB]
Get:213 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.6-2 [92.5 kB]
Get:214 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.12+dfsg-2 [234 kB]
Get:215 http://deb.debian.org/debian unstable/main amd64 freebayes amd64 1.3.9-2 [1527 kB]
Get:216 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB]
Get:217 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-6 [350 kB]
Get:218 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B]
Get:219 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B]
Get:220 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB]
Get:221 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.2.5-1 [155 kB]
Get:222 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB]
Get:223 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get:224 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.3-1 [2459 kB]
Get:225 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get:226 http://deb.debian.org/debian unstable/main amd64 libantlr4-runtime-java all 4.9.2-3 [318 kB]
Get:227 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get:228 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B]
Get:229 http://deb.debian.org/debian unstable/main amd64 libapfloat-java all 1.16.0-1 [813 kB]
Get:230 http://deb.debian.org/debian unstable/main amd64 libargs4j-java all 2.33-2 [138 kB]
Get:231 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.9.1-1 [393 kB]
Get:232 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B]
Get:233 http://deb.debian.org/debian unstable/main amd64 libjoptsimple-java all 5.0.4-7 [73.7 kB]
Get:234 http://deb.debian.org/debian unstable/main amd64 libbeam-java all 1.3.9-1 [195 kB]
Get:235 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:236 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-4 [440 kB]
Get:237 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-4 [2498 kB]
Get:238 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get:239 http://deb.debian.org/debian unstable/main amd64 libciftools-java all 7.0.2-1 [2228 kB]
Get:240 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get:241 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.22.0-1 [344 kB]
Get:242 http://deb.debian.org/debian unstable/main amd64 libcommons-math-java all 2.2-9 [933 kB]
Get:243 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get:244 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB]
Get:245 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB]
Get:246 http://deb.debian.org/debian unstable/main amd64 libitext5-java all 5.5.13.4-2 [2666 kB]
Get:247 http://deb.debian.org/debian unstable/main amd64 libjackson2-annotations-java all 2.14.0-1 [68.8 kB]
Get:248 http://deb.debian.org/debian unstable/main amd64 libjackson2-core-java all 2.14.1-2 [454 kB]
Get:249 http://deb.debian.org/debian unstable/main amd64 libjackson2-databind-java all 2.14.0+ds-2 [1532 kB]
Get:250 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get:251 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.2.0-1 [214 kB]
Get:252 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB]
Get:253 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.22.0-1 [570 kB]
Get:254 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-2 [142 kB]
Get:255 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB]
Get:256 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get:257 http://deb.debian.org/debian unstable/main amd64 libguice-java all 5.1.0-1 [932 kB]
Get:258 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 43-2 [6252 B]
Get:259 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.20.0-1 [679 kB]
Get:260 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get:261 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-2 [48.3 kB]
Get:262 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.9.25-1 [737 kB]
Get:263 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get:264 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get:265 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get:266 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB]
Get:267 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get:268 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B]
Get:269 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-4 [55.3 kB]
Get:270 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB]
Get:271 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB]
Get:272 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.9.12-1 [1674 kB]
Get:273 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get:274 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB]
Get:275 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB]
Get:276 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get:277 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.2-2+b2 [29.0 kB]
Get:278 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.8-1 [6548 B]
Get:279 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.8-1 [87.8 kB]
Get:280 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.11+repack-1 [159 kB]
Get:281 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get:282 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get:283 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-2 [68.6 kB]
Get:284 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get:285 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get:286 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.5.3-2 [49.6 kB]
Get:287 http://deb.debian.org/debian unstable/main amd64 libistack-commons-java all 3.0.6-5 [145 kB]
Get:288 http://deb.debian.org/debian unstable/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-11 [164 kB]
Get:289 http://deb.debian.org/debian unstable/main amd64 librelaxng-datatype-java all 1.0+ds1-4 [11.8 kB]
Get:290 http://deb.debian.org/debian unstable/main amd64 librngom-java all 2.3.0.1-11 [292 kB]
Get:291 http://deb.debian.org/debian unstable/main amd64 libxsom-java all 2.3.0.1-11 [401 kB]
Get:292 http://deb.debian.org/debian unstable/main amd64 libtxw2-java all 2.3.0.1-11 [134 kB]
Get:293 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get:294 http://deb.debian.org/debian unstable/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB]
Get:295 http://deb.debian.org/debian unstable/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB]
Get:296 http://deb.debian.org/debian unstable/main amd64 libstreambuffer-java all 1.5.4-2 [74.9 kB]
Get:297 http://deb.debian.org/debian unstable/main amd64 libfastinfoset-java all 1.2.12-4 [347 kB]
Get:298 http://deb.debian.org/debian unstable/main amd64 libjaxb-java all 2.3.0.1-11 [1980 kB]
Get:299 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB]
Get:300 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get:301 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.15.0-1 [233 kB]
Get:302 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.16+dfsg-1 [20.2 MB]
Get:303 http://deb.debian.org/debian unstable/main amd64 libjheaps-java all 0.14-3 [146 kB]
Get:304 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get:305 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get:306 http://deb.debian.org/debian unstable/main amd64 libjgraphx-java all 2.1.0.7-6 [577 kB]
Get:307 http://deb.debian.org/debian unstable/main amd64 libjgrapht-java all 1.5.2-2 [1616 kB]
Get:308 http://deb.debian.org/debian unstable/main amd64 libinchi1.07 amd64 1.07.3+dfsg-2 [556 kB]
Get:309 http://deb.debian.org/debian unstable/main amd64 libinchi-dev amd64 1.07.3+dfsg-2 [19.6 kB]
Get:310 http://deb.debian.org/debian unstable/main amd64 libjna-jni amd64 5.18.1-1 [64.5 kB]
Get:311 http://deb.debian.org/debian unstable/main amd64 libjna-java all 5.18.1-1 [239 kB]
Get:312 http://deb.debian.org/debian unstable/main amd64 libjna-inchi-java all 1.3.1+dfsg-1 [77.3 kB]
Get:313 http://deb.debian.org/debian unstable/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB]
Get:314 http://deb.debian.org/debian unstable/main amd64 libjmol-java all 16.3.55+dfsg-1 [10.6 MB]
Get:315 http://deb.debian.org/debian unstable/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB]
Get:316 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B]
Get:317 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-12 [273 kB]
Get:318 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-9 [132 kB]
Get:319 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get:320 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB]
Get:321 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get:322 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-3 [47.8 kB]
Get:323 http://deb.debian.org/debian unstable/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB]
Get:324 http://deb.debian.org/debian unstable/main amd64 libmsgpack-java all 0.9.6-1 [161 kB]
Get:325 http://deb.debian.org/debian unstable/main amd64 libmmtf-java all 1.0.11-1 [187 kB]
Get:326 http://deb.debian.org/debian unstable/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB]
Get:327 http://deb.debian.org/debian unstable/main amd64 libbiojava6-java all 6.1.0+dfsg-6 [5359 kB]
Get:328 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-8 [206 kB]
Get:329 http://deb.debian.org/debian unstable/main amd64 libcharts4j-java all 1.3-4 [162 kB]
Get:330 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get:331 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.10.1-1.1 [231 kB]
Get:332 http://deb.debian.org/debian unstable/main amd64 libcommons-collections4-java all 4.4-2 [682 kB]
Get:333 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get:334 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB]
Get:335 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.22.1-1 [23.3 kB]
Get:336 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.21.0-2 [422 kB]
Get:337 http://deb.debian.org/debian unstable/main amd64 libdistlib-java all 1.0-6 [72.2 kB]
Get:338 http://deb.debian.org/debian unstable/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB]
Get:339 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.32-2.1 [1525 kB]
Get:340 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.1.0-2 [877 kB]
Get:341 http://deb.debian.org/debian unstable/main amd64 libxom-java all 1.4.4-1 [177 kB]
Get:342 http://deb.debian.org/debian unstable/main amd64 libjson-java all 3.2.0+dfsg-2 [142 kB]
Get:343 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.6-0.1 [365 kB]
Get:344 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.6-0.1 [154 kB]
Get:345 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.6-0.1 [248 kB]
Get:346 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB]
Get:347 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2+b1 [1180 kB]
Get:348 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.2.1+dfsg-6+b1 [154 kB]
Get:349 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.2.1+dfsg-6+b1 [23.2 kB]
Get:350 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.2.1+dfsg-6+b1 [110 kB]
Get:351 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.15.1-0.1 [1388 kB]
Get:352 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 5.0.0+dfsg-1 [1929 kB]
Get:353 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1+b2 [66.8 kB]
Get:354 http://deb.debian.org/debian unstable/main amd64 libicu78 amd64 78.3-2 [10.0 MB]
Get:355 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b3 [32.2 kB]
Get:356 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-8 [2548 kB]
Get:357 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.1.1+ds-1 [199 kB]
Get:358 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20260608-2 [107 kB]
Get:359 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.4 [16.6 kB]
Get:360 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.4 [15.8 kB]
Get:361 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1+b2 [37.9 kB]
Get:362 http://deb.debian.org/debian unstable/main amd64 libsnp-sites1 amd64 2.5.1-2+b3 [14.9 kB]
Get:363 http://deb.debian.org/debian unstable/main amd64 libtrove3-java all 3.0.3-6 [2204 kB]
Get:364 http://deb.debian.org/debian unstable/main amd64 libsnpeff-java all 5.4.b+dfsg-2 [2157 kB]
Get:365 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.18+dfsg-1 [1053 kB]
Get:366 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1+b2 [335 kB]
Get:367 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.2-1 [383 kB]
Get:368 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.7+ds-1 [10.0 kB]
Get:369 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.7+ds-1 [82.9 kB]
Get:370 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b5 [54.8 kB]
Get:371 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b4 [17.0 kB]
Get:372 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.18-1 [801 kB]
Get:373 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-15 [235 kB]
Get:374 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-29 [173 kB]
Get:375 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get:376 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3+b2 [191 kB]
Get:377 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.6.1-1 [28.4 MB]
Get:378 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.23-1 [96.5 kB]
Get:379 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB]
Get:380 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.1.2-1 [2168 kB]
Get:381 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-2 [792 kB]
Get:382 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.6-1 [1391 kB]
Get:383 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.8.1-2 [172 kB]
Get:384 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.3.0-1 [1742 kB]
Get:385 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
Get:386 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-2 [228 kB]
Get:387 http://deb.debian.org/debian unstable/main amd64 r-cran-cpp11 all 0.5.5-1 [236 kB]
Get:388 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.3.0-1 [1644 kB]
Get:389 http://deb.debian.org/debian unstable/main amd64 r-cran-s7 amd64 0.2.2-1 [331 kB]
Get:390 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-3 [1414 kB]
Get:391 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-2 [63.2 kB]
Get:392 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.6.1-2 [106 kB]
Get:393 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-2 [54.0 kB]
Get:394 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.3-1 [1299 kB]
Get:395 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.4.0-1 [800 kB]
Get:396 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.7.3-2 [1983 kB]
Get:397 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.3+dfsg-1 [229 kB]
Get:398 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 4.0.3+dfsg-1 [4923 kB]
Get:399 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-6 [163 kB]
Get:400 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.12+dfsg-2 [620 kB]
Get:401 http://deb.debian.org/debian unstable/main amd64 minimap2 amd64 2.27+dfsg-1+b4 [388 kB]
Get:402 http://deb.debian.org/debian unstable/main amd64 sysstat amd64 12.7.5-2 [623 kB]
Get:403 http://deb.debian.org/debian unstable/main amd64 parallel all 20240222+ds-4 [2119 kB]
Get:404 http://deb.debian.org/debian unstable/main amd64 samclip all 0.4.0-4 [20.1 kB]
Get:405 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB]
Get:406 http://deb.debian.org/debian unstable/main amd64 seqtk amd64 1.4-2 [34.6 kB]
Get:407 http://deb.debian.org/debian unstable/main amd64 snp-sites amd64 2.5.1-2+b3 [14.0 kB]
Get:408 http://deb.debian.org/debian unstable/main amd64 snpeff all 5.4.b+dfsg-2 [6680 B]
Get:409 http://deb.debian.org/debian unstable/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB]
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Setting up libdav1d7:amd64 (1.5.3-1+b2) ...
Setting up libfreemarker-java (2.3.32-2.1) ...
Setting up sensible-utils (0.0.26) ...
Setting up libxshmfence1:amd64 (1.3.3-1+b2) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.61.0-1) ...
Setting up libcommons-math-java (2.2-9) ...
Setting up libtiff6:amd64 (4.7.2-1) ...
Setting up libxcb-randr0:amd64 (1.17.0-2+b2) ...
Setting up dbus-session-bus-common (1.16.2-5) ...
Setting up libuchardet0:amd64 (0.0.8-2+b2) ...
Setting up libxml-commons-external-java (1.4.01-6) ...
Setting up procps (2:4.0.6-2) ...
Setting up libjna-java (5.18.1-1) ...
Setting up libxbean-reflect-java (4.5-9) ...
Setting up libopentest4j-java (1.2.0-4) ...
Setting up libjackson2-core-java (2.14.1-2) ...
Setting up libx11-6:amd64 (2:1.8.13-1) ...
Setting up ncbi-vdb-data (3.2.1+dfsg-2) ...
Setting up libthai-data (0.1.30-2) ...
Setting up netbase (6.5) ...
Setting up libsnp-sites1:amd64 (2.5.1-2+b3) ...
Setting up libngtcp2-16:amd64 (1.22.1-1) ...
Setting up libcommons-math3-java (3.6.1-4) ...
Setting up libkrb5-3:amd64 (1.22.1-3) ...
Setting up libwayland-egl1:amd64 (1.25.0-2) ...
Setting up libbio-perl-perl (1.7.8-4) ...
Setting up libmbedcrypto16:amd64 (3.6.6-0.1) ...
Setting up libpaper2:amd64 (2.2.5-0.4) ...
Setting up libssh2-1t64:amd64 (1.11.1-4) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libjoptsimple-java (5.0.4-7) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up dbus-system-bus-common (1.16.2-5) ...
Setting up libde265-0:amd64 (1.1.1-1) ...
Setting up librelaxng-datatype-java (1.0+ds1-4) ...
Setting up openssl (3.6.3-1) ...
Setting up libbsd0:amd64 (0.12.2-3) ...
Setting up libinchi1.07 (1.07.3+dfsg-2) ...
Setting up libdrm-common (2.4.134-3) ...
Setting up libcdi-api-java (1.2-4) ...
Setting up libsnappy-jni (1.1.10.8-1) ...
Setting up libezmorph-java (1.0.6-4) ...
Setting up libxcomposite1:amd64 (1:0.4.6-1+b2) ...
Setting up libjxl0.11:amd64 (0.11.2-5) ...
Setting up libssw0:amd64 (1.1-16) ...
Setting up xdg-utils (1.2.1-2) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up bedtools (2.31.1+dfsg-3) ...
Setting up dbus-bin (1.16.2-5+b1) ...
Setting up libargs4j-java (2.33-2) ...
Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ...
Setting up libxkbcommon0:amd64 (1.13.1-1) ...
Setting up libnaga-java (3.0+svn80-5) ...
Setting up libwayland-client0:amd64 (1.25.0-2) ...
Setting up automake (1:1.18.1-4) ...
update-alternatives: using /usr/bin/automake-1.18 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 (1.15.1-1) ...
Setting up bubblewrap (0.11.2-2) ...
Setting up libxcb-dri3-0:amd64 (1.17.0-2+b2) ...
Setting up libwagon-provider-api-java (3.5.3-2) ...
Setting up libx11-xcb1:amd64 (2:1.8.13-1) ...
Setting up libice6:amd64 (2:1.1.1-1+b2) ...
Setting up libpciaccess0:amd64 (0.19-2) ...
Setting up libinchi-dev (1.07.3+dfsg-2) ...
Setting up liblapack3:amd64 (3.12.1-8) ...
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 (1.0-3) ...
Setting up libopentest4j-reporting-java (0.2.5-1) ...
Setting up libxdamage1:amd64 (1:1.1.7-1+b1) ...
Setting up libatk1.0-0t64:amd64 (2.61.0-1) ...
Setting up libplexus-languages-java (1.1.1-3) ...
Setting up libxrender1:amd64 (1:0.9.12-1+b2) ...
Setting up libtool (2.5.4-11) ...
Setting up libpython3.14-stdlib:amd64 (3.14.6-1) ...
Setting up fontconfig-config (2.17.1-5) ...
Setting up libstax-ex-java (1.7.8-3) ...
Setting up libmaven-parent-java (43-2) ...
Setting up libedit2:amd64 (3.1-20260512-1) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:amd64 (0.8-18) ...
Setting up libcloudproviders0:amd64 (0.4.0-2+b1) ...
Setting up libcommons-logging-java (1.3.0-2) ...
Setting up libxext6:amd64 (2:1.3.4-1+b4) ...
Setting up libsisu-inject-java (0.3.5-1) ...
Setting up libnss3:amd64 (2:3.124-1) ...
Setting up libciftools-java (7.0.2-1) ...
Setting up dbus-daemon (1.16.2-5+b1) ...
Setting up libpaper-utils (2.2.5-0.4) ...
Setting up libxom-java (1.4.4-1) ...
Setting up libcommons-lang-java (2.6-12) ...
Setting up libcolord2:amd64 (1.4.8-3) ...
Setting up libjackson2-databind-java (2.14.0+ds-2) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-2+b1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libbeam-java (1.3.9-1) ...
Setting up libdconf1:amd64 (0.49.0-4+b1) ...
Setting up dh-autoreconf (22) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:amd64 (0.1.30-2) ...
Setting up ca-certificates (20260601) ...
Updating certificates in /etc/ssl/certs...
121 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.5-1) ...
Setting up libmbedx509-7:amd64 (3.6.6-0.1) ...
Setting up libfreetype6:amd64 (2.14.3+dfsg-1) ...
Setting up libxfixes3:amd64 (1:6.0.0-2+b5) ...
Setting up libllvm21:amd64 (1:21.1.8-7+b4) ...
Setting up dbus (1.16.2-5+b1) ...
invoke-rc.d: could not determine current runlevel
Setting up libxinerama1:amd64 (2:1.1.4-3+b5) ...
Setting up libstreambuffer-java (1.5.4-2) ...
Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ...
Setting up libxrandr2:amd64 (2:1.5.4-1+b4) ...
Setting up libcommons-collections4-java (4.4-2) ...
Setting up libjna-inchi-java (1.3.1+dfsg-1) ...
Setting up ucf (3.0056) ...
Setting up libngtcp2-crypto-ossl0:amd64 (1.22.1-1) ...
Setting up libcommons-lang3-java (3.20.0-1) ...
Setting up libmbedtls21:amd64 (3.6.6-0.1) ...
Setting up dh-strip-nondeterminism (1.15.1-1) ...
Setting up librngom-java (2.3.0.1-11) ...
Setting up libdrm2:amd64 (2.4.134-3) ...
Setting up libjgraphx-java (2.1.0.7-6) ...
Setting up snp-sites (2.5.1-2+b3) ...
Setting up groff-base (1.24.1-1) ...
Setting up libwayland-cursor0:amd64 (1.25.0-2) ...
Setting up libpam-systemd:amd64 (261.1-2) ...
Setting up libcommons-beanutils-java (1.10.1-1.1) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libharfbuzz0b:amd64 (12.3.2-2+b2) ...
Setting up libsnappy-java (1.1.10.8-1) ...
Setting up libxss1:amd64 (1:1.2.3-1+b4) ...
Setting up libfontconfig1:amd64 (2.17.1-5) ...
Setting up python3.14 (3.14.6-1) ...
Setting up libxsom-java (2.3.0.1-11) ...
Setting up ca-certificates-java (20260311) ...
No JRE found. Skipping Java certificates setup.
Setting up libcommons-codec-java (1.22.0-1) ...
Setting up libsm6:amd64 (2:1.2.6-1+b2) ...
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 (0.8-18) ...
Setting up libjmol-java (16.3.55+dfsg-1) ...
Setting up libpython3-stdlib:amd64 (3.14.6-1) ...
Setting up libxres1:amd64 (2:1.2.1-2) ...
Setting up libdrm-amdgpu1:amd64 (2.4.134-3) ...
Setting up libcurl4-gnutls:amd64 (8.21.0-2) ...
Setting up fontconfig (2.17.1-5) ...
Regenerating fonts cache... done.
Setting up libxft2:amd64 (2.3.6-1+b5) ...
Setting up libxi6:amd64 (2:1.8.2-2+b1) ...
Setting up libcurl4t64:amd64 (8.21.0-2) ...
Setting up libtirpc3t64:amd64 (1.3.7+ds-1) ...
Setting up libcommons-io-java (2.22.0-1) ...
Setting up libxtst6:amd64 (2:1.2.5-1+b2) ...
Setting up po-debconf (1.0.22) ...
Setting up libtk8.6:amd64 (8.6.18-1) ...
Setting up libdistlib-java (1.0-6) ...
Setting up libxcursor1:amd64 (1:1.2.3-1+b2) ...
Setting up openjdk-25-jre-headless:amd64 (25.0.4~4ea-1) ...
update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libpango-1.0-0:amd64 (1.58.0-1) ...
Setting up libdrm-intel1:amd64 (2.4.134-3) ...
Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2+b1) ...
Setting up libcurl3t64-gnutls:amd64 (8.21.0-2) ...
Setting up python3 (3.14.6-1) ...
Setting up man-db (2.13.1-1) ...
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 (1.18.4-3+b1) ...
Setting up dbus-user-session (1.16.2-5+b1) ...
Setting up libmaven-resolver-java (1.9.25-1) ...
Setting up libatspi2.0-0t64:amd64 (2.61.0-1) ...
Setting up libxt6t64:amd64 (1:1.2.1-1.3+b2) ...
Setting up parallel (20240222+ds-4) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ...
Setting up libwagon-http-java (3.5.3-2) ...
Setting up libcairo-gobject2:amd64 (1.18.4-3+b1) ...
Setting up libmaven-shared-utils-java (3.4.2-1) ...
Setting up libfastinfoset-java (1.2.12-4) ...
Setting up libpangoft2-1.0-0:amd64 (1.58.0-1) ...
Setting up libcups2t64:amd64 (2.4.18-1) ...
Setting up libseqlib2:amd64 (1.2.0+dfsg-11+b4) ...
Setting up libpangocairo-1.0-0:amd64 (1.58.0-1) ...
Setting up libncbi-ngs3:amd64 (3.2.1+dfsg-6+b1) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.61.0-1) ...
Setting up mesa-libgallium:amd64 (26.1.4-1) ...
Setting up libngs-jni:amd64 (3.2.1+dfsg-6+b1) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libcommons-compress-java (1.27.1-2) ...
Setting up libgbm1:amd64 (26.1.4-1) ...
Setting up libgl1-mesa-dri:amd64 (26.1.4-1) ...
Setting up bcftools (1.22-1) ...
Setting up debhelper (14.3) ...
Setting up dconf-service (0.49.0-4+b1) ...
Setting up samtools (1.22.1-1) ...
Setting up r-base-core (4.6.1-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-labeling (0.4.3-2) ...
Setting up r-cran-farver (2.1.2-3) ...
Setting up r-cran-viridislite (0.4.3-1) ...
Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b2) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libngs-java:amd64 (3.2.1+dfsg-6+b1) ...
Setting up r-cran-r6 (2.6.1-2) ...
Setting up r-cran-pkgkitten (0.2.4-1) ...
Setting up r-cran-littler (0.3.23-1) ...
Setting up r-cran-rcpp (1.1.2-1) ...
Setting up r-cran-rlang (1.3.0-1) ...
Setting up libglx-mesa0:amd64 (26.1.4-1) ...
Setting up r-cran-gridbase (0.4-7-6) ...
Setting up vt (0.57721+ds-3+b1) ...
Setting up libglx0:amd64 (1.7.0-3+b1) ...
Setting up dconf-gsettings-backend:amd64 (0.49.0-4+b1) ...
Setting up r-cran-withr (3.0.3+dfsg-1) ...
Setting up libmaven-archiver-java (3.6.2-1) ...
Setting up r-cran-glue (1.8.1-2) ...
Setting up r-cran-cli (3.6.6-1) ...
Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
Setting up libgl1:amd64 (1.7.0-3+b1) ...
Setting up libvcflib2:amd64 (1.0.12+dfsg-2) ...
Setting up r-cran-s7 (0.2.2-1) ...
Setting up r-cran-cpp11 (0.5.5-1) ...
Setting up r-cran-plyr (1.8.9-2) ...
Setting up r-cran-rcolorbrewer (1.1-3-2) ...
Setting up r-cran-isoband (0.3.0-1) ...
Setting up r-cran-scales (1.4.0-1) ...
Setting up r-cran-gtable (0.3.6+dfsg-2) ...
Setting up freebayes (1.3.9-2) ...
Setting up r-cran-vctrs (0.7.3-2) ...
Setting up libgtk-3-common (3.24.52-1) ...
Setting up r-cran-ggplot2 (4.0.3+dfsg-1) ...
Setting up libvcflib-tools (1.0.12+dfsg-2) ...
Setting up libheif-plugin-dav1d:amd64 (1.23.1-1) ...
Setting up libheif-plugin-libde265:amd64 (1.23.1-1) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libheif1:amd64 (1.23.1-1) ...
Setting up librsvg2-2:amd64 (2.62.1+dfsg-1) ...
Setting up libguava-java (32.0.1-1) ...
Setting up glycin-loaders (2.1.5+ds-2) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up libglycin-2-0:amd64 (2.1.5+ds-2) ...
Setting up libguice-java (5.1.0-1) ...
Setting up glycin-thumbnailers (2.1.5+ds-2) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.44.6+dfsg-2) ...
Setting up gtk-update-icon-cache (4.22.4+ds-1) ...
Setting up libmaven3-core-java (3.9.12-1) ...
Setting up libmaven-shared-incremental-java (1.1-6) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up adwaita-icon-theme (50.0-2) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libplexus-compiler-java (2.13.0-1) ...
Setting up libmaven-compiler-plugin-java (3.13.0-1) ...
Setting up libgtk-3-0t64:amd64 (3.24.52-1) ...
Setting up libmaven-file-management-java (3.0.0-2) ...
Setting up libmaven-jar-plugin-java (3.3.0-2) ...
Setting up libcommons-text-java (1.15.0-1) ...
Setting up libmsgpack-java (0.9.6-1) ...
Setting up libmmtf-java (1.0.11-1) ...
Setting up libjgrapht-java (1.5.2-2) ...
Processing triggers for libc-bin (2.42-17) ...
Processing triggers for systemd (261.1-2) ...
Processing triggers for ca-certificates-java (20260311) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_BR_Root_CA_2_2023.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_2_2023.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_Server_Root_ECC_G1.pem
Adding debian:OISTE_Server_Root_RSA_G1.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_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_Root_CA12.pem
Adding debian:SecureSign_Root_CA14.pem
Adding debian:SecureSign_Root_CA15.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_RSA_TLS_Root_CA_2022_-_1.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_CYBER_Root_CA.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:TrustAsia_TLS_ECC_Root_CA.pem
Adding debian:TrustAsia_TLS_RSA_Root_CA.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:e-Szigno_TLS_Root_CA_2023.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up openjdk-25-jre:amd64 (25.0.4~4ea-1) ...
Setting up default-jre-headless (2:1.25-77) ...
Setting up default-jre (2:1.25-77) ...
Setting up ant (1.10.17-1) ...
Setting up junit4 (4.13.2-6) ...
Setting up ant-optional (1.10.17-1) ...
Setting up junit5 (5.10.3-1) ...
Setting up libjson-java (3.2.0+dfsg-2) ...
Setting up libhtsjdk-java (5.0.0+dfsg-1) ...
Setting up libistack-commons-java (3.0.6-5) ...
Setting up libcodemodel-java (2.6+jaxb2.3.0.1-11) ...
Setting up libtxw2-java (2.3.0.1-11) ...
Setting up libjaxb-java (2.3.0.1-11) ...
Setting up libbiojava6-java (6.1.0+dfsg-6) ...
Setting up libsnpeff-java (5.4.b+dfsg-2) ...
Setting up snpeff (5.4.b+dfsg-2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20260601) ...
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 (20260311) ...
done.

+------------------------------------------------------------------------------+
| Check architectures                          Sun, 12 Jul 2026 01:19:18 +0000 |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in all)

+------------------------------------------------------------------------------+
| Build environment                            Sun, 12 Jul 2026 01:19:18 +0000 |
+------------------------------------------------------------------------------+

Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64)
Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1
Package versions: adwaita-icon-theme_50.0-2 ant_1.10.17-1 ant-optional_1.10.17-1 any2fasta_0.8.1-1 apt_3.3.1 at-spi2-common_2.61.0-1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 bcftools_1.22-1 bedtools_2.31.1+dfsg-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 bubblewrap_0.11.2-2 build-essential_12.12 bwa_0.7.19-1 bzip2_1.0.8-6+b2 ca-certificates_20260601 ca-certificates-java_20260311 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 dbus_1.16.2-5+b1 dbus-bin_1.16.2-5+b1 dbus-daemon_1.16.2-5+b1 dbus-session-bus-common_1.16.2-5 dbus-system-bus-common_1.16.2-5 dbus-user-session_1.16.2-5+b1 dconf-gsettings-backend_0.49.0-4+b1 dconf-service_0.49.0-4+b1 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 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libpython3.14-minimal_3.14.6-1 libpython3.14-stdlib_3.14.6-1 libqdox2-java_2.0.3-1 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 librelaxng-datatype-java_1.0+ds1-4 librhino-java_1.7.15.1-0.1 librngom-java_2.3.0.1-11 librsvg2-2_2.62.1+dfsg-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1 libselinux1_3.11-2 libsensors-config_1:3.6.2-2 libsensors5_1:3.6.2-2+b2 libseqlib2_1.2.0+dfsg-11+b4 libsframe3_2.46.50.20260617-1 libsharpyuv0_1.5.0-0.1+b2 libsisu-inject-java_0.3.5-1 libsisu-plexus-java_0.3.5-1 libslf4j-java_1.7.32-2 libsm6_2:1.2.6-1+b2 libsmartcols1_2.42.2-1 libsmithwaterman0_0.0+git20160702.2610e25-12+b3 libsnappy-java_1.1.10.8-1 libsnappy-jni_1.1.10.8-1 libsnappy1v5_1.2.2-2+b2 libsnp-sites1_2.5.1-2+b3 libsnpeff-java_5.4.b+dfsg-2 libsqlite3-0_3.53.3-1 libssh2-1t64_1.11.1-4 libssl3t64_3.6.3-1 libssw0_1.1-16 libstax-ex-java_1.7.8-3 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libstreambuffer-java_1.5.4-2 libsystemd-shared_261.1-2 libsystemd0_261.1-2 libtabixpp0t64_1.1.2-2.1+b2 libtasn1-6_4.21.0-2+b1 libtcl8.6_8.6.18+dfsg-1 libtext-charwidth-perl_0.04-12+b1 libtext-wrapi18n-perl_0.06-11 libthai-data_0.1.30-2 libthai0_0.1.30-2 libtiff6_4.7.2-1 libtinfo6_6.6+20260608-2 libtirpc-common_1.3.7+ds-1 libtirpc3t64_1.3.7+ds-1 libtk8.6_8.6.18-1 libtool_2.5.4-11 libtrove3-java_3.0.3-6 libtsan2_16.1.0-2 libtss2-esys-3.0.2-0t64_4.1.3-6 libtss2-mu-4.0.1-0t64_4.1.3-6 libtss2-rc0t64_4.1.3-6 libtss2-sys1t64_4.1.3-6 libtss2-tcti-cmd0t64_4.1.3-6 libtss2-tcti-device0t64_4.1.3-6 libtss2-tcti-mssim0t64_4.1.3-6 libtss2-tcti-swtpm0t64_4.1.3-6 libtxw2-java_2.3.0.1-11 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunistring5_1.4.2-1 libunivocity-parsers-java_2.9.1-1 libuuid1_2.42.2-1 libvcflib-tools_1.0.12+dfsg-2 libvcflib2_1.0.12+dfsg-2 libvecmath-java_1.5.2-7 libvulkan1_1.4.341.0-1 libwagon-http-java_3.5.3-2 libwagon-provider-api-java_3.5.3-2 libwayland-client0_1.25.0-2 libwayland-cursor0_1.25.0-2 libwayland-egl1_1.25.0-2 libwebp7_1.5.0-0.1+b2 libwfa2-0_2.3.6-2 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libx11-xcb1_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxbean-reflect-java_4.5-9 libxcb-dri3-0_1.17.0-2+b2 libxcb-glx0_1.17.0-2+b2 libxcb-present0_1.17.0-2+b2 libxcb-randr0_1.17.0-2+b2 libxcb-render0_1.17.0-2+b2 libxcb-shm0_1.17.0-2+b2 libxcb-sync1_1.17.0-2+b2 libxcb-xfixes0_1.17.0-2+b2 libxcb1_1.17.0-2+b2 libxcomposite1_1:0.4.6-1+b2 libxcursor1_1:1.2.3-1+b2 libxdamage1_1:1.1.7-1+b1 libxdmcp6_1:1.1.5-2+b1 libxerces2-java_2.12.2-1 libxext6_2:1.3.4-1+b4 libxfixes3_1:6.0.0-2+b5 libxft2_2.3.6-1+b5 libxi6_2:1.8.2-2+b1 libxinerama1_2:1.1.4-3+b5 libxkbcommon0_1.13.1-1 libxml-commons-external-java_1.4.01-6 libxml-commons-resolver1.1-java_1.2-11 libxml2-16_2.15.3+dfsg-1 libxom-java_1.4.4-1 libxrandr2_2:1.5.4-1+b4 libxrender1_1:0.9.12-1+b2 libxres1_2:1.2.1-2 libxshmfence1_1.3.3-1+b2 libxsom-java_2.3.0.1-11 libxss1_1:1.2.3-1+b4 libxt6t64_1:1.2.1-1.3+b2 libxtst6_2:1.2.5-1+b2 libxxf86vm1_1:1.1.4-2+b1 libxxhash0_0.8.3-2+b2 libxz-java_1.11+repack-1 libz3-4_4.13.3-1.1 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 mesa-libgallium_26.1.4-1 minimap2_2.27+dfsg-1+b4 mount_2.42.2-1 ncbi-vdb-data_3.2.1+dfsg-2 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 netbase_6.5 openjdk-25-jre_25.0.4~4ea-1 openjdk-25-jre-headless_25.0.4~4ea-1 openssl_3.6.3-1 openssl-provider-legacy_3.6.3-1 parallel_20240222+ds-4 patch_2.8-2 pci.ids_0.0~2026.07.06-1 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.3-2 po-debconf_1.0.22 procps_2:4.0.6-2 python3_3.14.6-1 python3-minimal_3.14.6-1 python3.14_3.14.6-1 python3.14-minimal_3.14.6-1 r-base-core_4.6.1-1 r-cran-cli_3.6.6-1 r-cran-cpp11_0.5.5-1 r-cran-farver_2.1.2-3 r-cran-ggplot2_4.0.3+dfsg-1 r-cran-glue_1.8.1-2 r-cran-gridbase_0.4-7-6 r-cran-gtable_0.3.6+dfsg-2 r-cran-isoband_0.3.0-1 r-cran-labeling_0.4.3-2 r-cran-lifecycle_1.0.5+dfsg-1 r-cran-littler_0.3.23-1 r-cran-pkgkitten_0.2.4-1 r-cran-plyr_1.8.9-2 r-cran-r6_2.6.1-2 r-cran-rcolorbrewer_1.1-3-2 r-cran-rcpp_1.1.2-1 r-cran-rlang_1.3.0-1 r-cran-s7_0.2.2-1 r-cran-scales_1.4.0-1 r-cran-vctrs_0.7.3-2 r-cran-viridislite_0.4.3-1 r-cran-withr_3.0.3+dfsg-1 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 samclip_0.4.0-4 samtools_1.22.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 seqtk_1.4-2 shared-mime-info_2.4-5+b3 snp-sites_2.5.1-2+b3 snpeff_5.4.b+dfsg-2 sqv_1.4.0-1 sysstat_12.7.5-2 systemd_261.1-2 systemd-sysv_261.1-2 systemd-tpm_261.1-2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tpm-udev_4.1.3-6 tzdata_2026b-1 ucf_3.0056 unzip_6.0-29 util-linux_2.42.2-1 vt_0.57721+ds-3+b1 x11-common_1:7.7+26 xdg-utils_1.2.1-2 xkb-data_2.47-1 xz-utils_5.8.3-1 zip_3.0-15 zlib1g_1:1.3.dfsg+really1.3.2-3

+------------------------------------------------------------------------------+
| Build                                        Sun, 12 Jul 2026 01:19:18 +0000 |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: snippy
Binary: snippy, snippy-examples
Architecture: all
Version: 4.6.0+dfsg-6
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: 4.7.3
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
 510406b1e87f0efdd16e27598918f716a0cbb028 5488 snippy_4.6.0+dfsg-6.debian.tar.xz
Checksums-Sha256:
 96c9dea7aeab6f362100fb1774d3c4377f12c2209a1fdc63b2926de912997524 271400 snippy_4.6.0+dfsg.orig.tar.xz
 6919d9fbb2799099a297e8a06ccaba8c6f25bdd60dbf77475ee349e66f1138ee 5488 snippy_4.6.0+dfsg-6.debian.tar.xz
Files:
 a4eea48e48f44589cb998e609fdd27ea 271400 snippy_4.6.0+dfsg.orig.tar.xz
 d9aa80ae4e16d060e26fd07f172c3baf 5488 snippy_4.6.0+dfsg-6.debian.tar.xz

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dpkg-source: warning: cannot verify inline signature for ./snippy_4.6.0+dfsg-6.dsc: missing OpenPGP keyrings
dpkg-source: info: verifying ./snippy_4.6.0+dfsg-6.dsc
dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp
dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp
dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp
dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp
dpkg-source: info: extracting snippy in /build/snippy-jObLQy/snippy-4.6.0+dfsg
dpkg-source: info: unpacking snippy_4.6.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking snippy_4.6.0+dfsg-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying debian_packaged_libs.patch
dpkg-source: info: applying snpeff.config.patch
dpkg-source: info: applying snpeff_v5.1+.patch
dpkg-source: info: applying make-4.4.1.patch

clean up apt cache
------------------


Check disk space
----------------

Sufficient free space for build

+------------------------------------------------------------------------------+
| Starting Time Build Commands                 Sun, 12 Jul 2026 01:19:18 +0000 |
+------------------------------------------------------------------------------+


/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network snippy_4.6.0+dfsg-6 perl-5.44-throwaway amd64
--------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network snippy_4.6.0+dfsg-6 perl-5.44-throwaway amd64'.

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

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

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANGUAGE=en_GB:en
LC_ALL=C.UTF-8
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
LOGNAME=debomatic
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/build/snippy-jObLQy/snippy-4.6.0+dfsg
SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic
SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic
SCHROOT_COMMAND=env
SCHROOT_GID=110
SCHROOT_GROUP=sbuild
SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-819c5d5d-9e32-42fb-aa68-78a931c89b8d
SCHROOT_UID=1002
SCHROOT_USER=debomatic
SHELL=/bin/sh
USER=debomatic

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz
dpkg-buildpackage: info: source package snippy
dpkg-buildpackage: info: source version 4.6.0+dfsg-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Santiago Vila <sanvila@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-6.debian.tar.xz
dpkg-source: info: building snippy in ../snippy_4.6.0+dfsg-6.dsc
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/snippy-jObLQy/snippy-4.6.0+dfsg'
cd test && /usr/bin/make
make[2]: Entering directory '/build/snippy-jObLQy/snippy-4.6.0+dfsg/test'
mkdir -p S1
wgsim -S 1 \
         -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
         example.fna S1/R1.fq S1/R2.fq > S1/dwgsim.tab
[wgsim] seed = 1
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 3 sequences, total length: 317336
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq
[01:19:20] This is snippy 4.6.0
[01:19:20] Written by Torsten Seemann
[01:19:20] Obtained from https://github.com/tseemann/snippy
[01:19:20] Detected operating system: linux
[01:19:20] Enabling bundled linux tools.
[01:19:20] Found bwa - /usr/bin/bwa
[01:19:20] Found bcftools - /usr/bin/bcftools
[01:19:20] Found samtools - /usr/bin/samtools
[01:19:20] Found java - /usr/bin/java
[01:19:20] Found snpEff - /usr/bin/snpEff
[01:19:20] Found samclip - /usr/bin/samclip
[01:19:20] Found seqtk - /usr/bin/seqtk
[01:19:20] Found parallel - /usr/bin/parallel
[01:19:20] Found freebayes - /usr/bin/freebayes
[01:19:20] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[01:19:20] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[01:19:20] Found vcfstreamsort - /usr/bin/vcfstreamsort
[01:19:20] Found vcfuniq - /usr/bin/vcfuniq
[01:19:20] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[01:19:20] Found gzip - /usr/bin/gzip
[01:19:20] Found vt - /usr/bin/vt
[01:19:20] Found snippy-vcf_to_tab - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[01:19:20] Found snippy-vcf_report - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[01:19:20] Checking version: samtools --version is >= 1.7 - ok, have 1.22
[01:19:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.22
[01:19:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[01:19:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.4
[01:19:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19
[01:19:20] Using reference: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/example.fna
[01:19:20] Treating reference as 'fasta' format.
[01:19:20] Will use 2 CPU cores.
[01:19:20] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S1/R1.fq
[01:19:20] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S1/R2.fq
[01:19:20] Used --force, will overwrite existing S1
[01:19:20] Changing working directory: S1
[01:19:20] Creating reference folder: reference
[01:19:20] Extracting FASTA and GFF from reference.
[01:19:20] Wrote 3 sequences to ref.fa
[01:19:20] Wrote 0 features to ref.gff
[01:19:20] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[01:19:20] Using BAM RG (Read Group) ID: S1
[01:19:20] Running: samtools faidx reference/ref.fa 2>> snps.log
[01:19:20] Running: bwa index reference/ref.fa 2>> snps.log
[01:19:20] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[01:19:20] Running: ln -sf reference/ref.fa . 2>> snps.log
[01:19:20] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[01:19:20] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[01:19:20] Running: bwa mem  -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S1/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11587, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 199, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 369)
[M::mem_pestat] mean and std.dev: (199.53, 48.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 437)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 1.372 CPU sec, 0.694 real sec
[main] Version: 0.7.19-r1273
[samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978
[samclip] Header contained 6 lines
[samclip] Done.
[main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S1/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S1/R2.fq
[main] Real time: 0.788 sec; CPU: 1.408 sec
[01:19:21] Running: samtools index snps.bam 2>> snps.log
[01:19:21] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[01:19:21] 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
[01:19:22] 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

[01:19:22] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[01:19:22] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[01:19:22] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[01:19:22] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[01:19:22] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[01:19:22] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[01:19:22] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[01:19:22] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[01:19:22] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[01:19:22] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[01:19:22] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[01:19:23] Marked 749 heterozygous sites with 'n'
[01:19:23] Creating extra output files: BED GFF CSV TXT HTML
[01:19:23] Identified 261 variants.
[01:19:23] Result folder: S1
[01:19:23] Result files:
[01:19:23] * S1/snps.aligned.fa
[01:19:23] * S1/snps.bam
[01:19:23] * S1/snps.bam.bai
[01:19:23] * S1/snps.bed
[01:19:23] * S1/snps.consensus.fa
[01:19:23] * S1/snps.consensus.subs.fa
[01:19:23] * S1/snps.csv
[01:19:23] * S1/snps.filt.vcf
[01:19:23] * S1/snps.gff
[01:19:23] * S1/snps.html
[01:19:23] * S1/snps.log
[01:19:23] * S1/snps.raw.vcf
[01:19:23] * S1/snps.subs.vcf
[01:19:23] * S1/snps.tab
[01:19:23] * S1/snps.txt
[01:19:23] * S1/snps.vcf
[01:19:23] * S1/snps.vcf.gz
[01:19:23] * S1/snps.vcf.gz.csi
[01:19:23] Walltime used: 3 seconds
[01:19:23] Questionable SNP? Try the --report option to see the alignments.
[01:19:23] Done.
mkdir -p S2
wgsim -S 2 \
         -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
         example.fna S2/R1.fq S2/R2.fq > S2/dwgsim.tab
[wgsim] seed = 2
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 3 sequences, total length: 317336
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq
[01:19:23] This is snippy 4.6.0
[01:19:23] Written by Torsten Seemann
[01:19:23] Obtained from https://github.com/tseemann/snippy
[01:19:23] Detected operating system: linux
[01:19:23] Enabling bundled linux tools.
[01:19:23] Found bwa - /usr/bin/bwa
[01:19:23] Found bcftools - /usr/bin/bcftools
[01:19:23] Found samtools - /usr/bin/samtools
[01:19:23] Found java - /usr/bin/java
[01:19:23] Found snpEff - /usr/bin/snpEff
[01:19:23] Found samclip - /usr/bin/samclip
[01:19:23] Found seqtk - /usr/bin/seqtk
[01:19:23] Found parallel - /usr/bin/parallel
[01:19:23] Found freebayes - /usr/bin/freebayes
[01:19:23] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[01:19:23] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[01:19:23] Found vcfstreamsort - /usr/bin/vcfstreamsort
[01:19:23] Found vcfuniq - /usr/bin/vcfuniq
[01:19:23] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[01:19:23] Found gzip - /usr/bin/gzip
[01:19:23] Found vt - /usr/bin/vt
[01:19:23] Found snippy-vcf_to_tab - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[01:19:23] Found snippy-vcf_report - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[01:19:23] Checking version: samtools --version is >= 1.7 - ok, have 1.22
[01:19:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.22
[01:19:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[01:19:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.4
[01:19:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19
[01:19:23] Using reference: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/example.fna
[01:19:23] Treating reference as 'fasta' format.
[01:19:23] Will use 2 CPU cores.
[01:19:23] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S2/R1.fq
[01:19:23] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S2/R2.fq
[01:19:23] Used --force, will overwrite existing S2
[01:19:23] Changing working directory: S2
[01:19:23] Creating reference folder: reference
[01:19:23] Extracting FASTA and GFF from reference.
[01:19:23] Wrote 3 sequences to ref.fa
[01:19:23] Wrote 0 features to ref.gff
[01:19:23] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[01:19:23] Using BAM RG (Read Group) ID: S2
[01:19:23] Running: samtools faidx reference/ref.fa 2>> snps.log
[01:19:23] Running: bwa index reference/ref.fa 2>> snps.log
[01:19:23] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[01:19:23] Running: ln -sf reference/ref.fa . 2>> snps.log
[01:19:23] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[01:19:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[01:19:23] Running: bwa mem  -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S2/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 199, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 366)
[M::mem_pestat] mean and std.dev: (199.27, 48.61)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 433)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 1.181 CPU sec, 0.727 real sec
[main] Version: 0.7.19-r1273
[main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S2/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S2/R2.fq
[main] Real time: 0.830 sec; CPU: 1.210 sec
[samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987
[samclip] Header contained 6 lines
[samclip] Done.
[01:19:24] Running: samtools index snps.bam 2>> snps.log
[01:19:24] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[01:19:24] 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
[01:19:26] 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

[01:19:26] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[01:19:26] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[01:19:26] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[01:19:26] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[01:19:26] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[01:19:26] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[01:19:26] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[01:19:26] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[01:19:26] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[01:19:26] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[01:19:26] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[01:19:26] Marked 841 heterozygous sites with 'n'
[01:19:26] Creating extra output files: BED GFF CSV TXT HTML
[01:19:26] Identified 246 variants.
[01:19:26] Result folder: S2
[01:19:26] Result files:
[01:19:26] * S2/snps.aligned.fa
[01:19:26] * S2/snps.bam
[01:19:26] * S2/snps.bam.bai
[01:19:26] * S2/snps.bed
[01:19:26] * S2/snps.consensus.fa
[01:19:26] * S2/snps.consensus.subs.fa
[01:19:26] * S2/snps.csv
[01:19:26] * S2/snps.filt.vcf
[01:19:26] * S2/snps.gff
[01:19:26] * S2/snps.html
[01:19:26] * S2/snps.log
[01:19:26] * S2/snps.raw.vcf
[01:19:26] * S2/snps.subs.vcf
[01:19:26] * S2/snps.tab
[01:19:26] * S2/snps.txt
[01:19:26] * S2/snps.vcf
[01:19:26] * S2/snps.vcf.gz
[01:19:26] * S2/snps.vcf.gz.csi
[01:19:26] Walltime used: 3 seconds
[01:19:26] Questionable SNP? Try the --report option to see the alignments.
[01:19:26] Done.
mkdir -p S3
wgsim -S 3 \
         -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
         example.fna S3/R1.fq S3/R2.fq > S3/dwgsim.tab
[wgsim] seed = 3
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 3 sequences, total length: 317336
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq
[01:19:26] This is snippy 4.6.0
[01:19:26] Written by Torsten Seemann
[01:19:26] Obtained from https://github.com/tseemann/snippy
[01:19:26] Detected operating system: linux
[01:19:26] Enabling bundled linux tools.
[01:19:26] Found bwa - /usr/bin/bwa
[01:19:26] Found bcftools - /usr/bin/bcftools
[01:19:26] Found samtools - /usr/bin/samtools
[01:19:26] Found java - /usr/bin/java
[01:19:26] Found snpEff - /usr/bin/snpEff
[01:19:26] Found samclip - /usr/bin/samclip
[01:19:26] Found seqtk - /usr/bin/seqtk
[01:19:26] Found parallel - /usr/bin/parallel
[01:19:26] Found freebayes - /usr/bin/freebayes
[01:19:26] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[01:19:26] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[01:19:26] Found vcfstreamsort - /usr/bin/vcfstreamsort
[01:19:26] Found vcfuniq - /usr/bin/vcfuniq
[01:19:26] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[01:19:27] Found gzip - /usr/bin/gzip
[01:19:27] Found vt - /usr/bin/vt
[01:19:27] Found snippy-vcf_to_tab - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[01:19:27] Found snippy-vcf_report - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[01:19:27] Checking version: samtools --version is >= 1.7 - ok, have 1.22
[01:19:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.22
[01:19:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[01:19:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.4
[01:19:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19
[01:19:27] Using reference: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/example.fna
[01:19:27] Treating reference as 'fasta' format.
[01:19:27] Will use 2 CPU cores.
[01:19:27] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S3/R1.fq
[01:19:27] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S3/R2.fq
[01:19:27] Used --force, will overwrite existing S3
[01:19:27] Changing working directory: S3
[01:19:27] Creating reference folder: reference
[01:19:27] Extracting FASTA and GFF from reference.
[01:19:27] Wrote 3 sequences to ref.fa
[01:19:27] Wrote 0 features to ref.gff
[01:19:27] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[01:19:27] Using BAM RG (Read Group) ID: S3
[01:19:27] Running: samtools faidx reference/ref.fa 2>> snps.log
[01:19:27] Running: bwa index reference/ref.fa 2>> snps.log
[01:19:27] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[01:19:27] Running: ln -sf reference/ref.fa . 2>> snps.log
[01:19:27] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[01:19:27] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[01:19:27] Running: bwa mem  -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S3/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (164, 198, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 368)
[M::mem_pestat] mean and std.dev: (198.46, 48.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 436)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 1.266 CPU sec, 0.640 real sec
[main] Version: 0.7.19-r1273
[main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S3/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S3/R2.fq
[main] Real time: 0.716 sec; CPU: 1.297 sec
[samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970
[samclip] Header contained 6 lines
[samclip] Done.
[01:19:28] Running: samtools index snps.bam 2>> snps.log
[01:19:28] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[01:19:28] 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
[01:19:29] 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

[01:19:29] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[01:19:29] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[01:19:29] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[01:19:29] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[01:19:29] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[01:19:29] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[01:19:29] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[01:19:29] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[01:19:29] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[01:19:29] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[01:19:29] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[01:19:29] Marked 846 heterozygous sites with 'n'
[01:19:29] Creating extra output files: BED GFF CSV TXT HTML
[01:19:29] Identified 254 variants.
[01:19:29] Result folder: S3
[01:19:29] Result files:
[01:19:29] * S3/snps.aligned.fa
[01:19:29] * S3/snps.bam
[01:19:29] * S3/snps.bam.bai
[01:19:29] * S3/snps.bed
[01:19:29] * S3/snps.consensus.fa
[01:19:29] * S3/snps.consensus.subs.fa
[01:19:29] * S3/snps.csv
[01:19:29] * S3/snps.filt.vcf
[01:19:29] * S3/snps.gff
[01:19:29] * S3/snps.html
[01:19:29] * S3/snps.log
[01:19:29] * S3/snps.raw.vcf
[01:19:29] * S3/snps.subs.vcf
[01:19:29] * S3/snps.tab
[01:19:29] * S3/snps.txt
[01:19:29] * S3/snps.vcf
[01:19:29] * S3/snps.vcf.gz
[01:19:29] * S3/snps.vcf.gz.csi
[01:19:29] Walltime used: 3 seconds
[01:19:29] Wishing you a life free of homopolymer errors.
[01:19:29] Done.
mkdir -p S4
wgsim -S 4 \
         -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
         example.fna S4/R1.fq S4/R2.fq > S4/dwgsim.tab
[wgsim] seed = 4
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 3 sequences, total length: 317336
../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq
[01:19:29] This is snippy 4.6.0
[01:19:29] Written by Torsten Seemann
[01:19:29] Obtained from https://github.com/tseemann/snippy
[01:19:29] Detected operating system: linux
[01:19:29] Enabling bundled linux tools.
[01:19:29] Found bwa - /usr/bin/bwa
[01:19:29] Found bcftools - /usr/bin/bcftools
[01:19:29] Found samtools - /usr/bin/samtools
[01:19:29] Found java - /usr/bin/java
[01:19:29] Found snpEff - /usr/bin/snpEff
[01:19:29] Found samclip - /usr/bin/samclip
[01:19:29] Found seqtk - /usr/bin/seqtk
[01:19:29] Found parallel - /usr/bin/parallel
[01:19:29] Found freebayes - /usr/bin/freebayes
[01:19:29] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
[01:19:29] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
[01:19:29] Found vcfstreamsort - /usr/bin/vcfstreamsort
[01:19:29] Found vcfuniq - /usr/bin/vcfuniq
[01:19:29] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
[01:19:29] Found gzip - /usr/bin/gzip
[01:19:29] Found vt - /usr/bin/vt
[01:19:29] Found snippy-vcf_to_tab - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
[01:19:29] Found snippy-vcf_report - /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_report
[01:19:30] Checking version: samtools --version is >= 1.7 - ok, have 1.22
[01:19:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.22
[01:19:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
[01:19:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.4
[01:19:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19
[01:19:30] Using reference: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/example.fna
[01:19:30] Treating reference as 'fasta' format.
[01:19:30] Will use 2 CPU cores.
[01:19:30] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S4/R1.fq
[01:19:30] Using read file: /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S4/R2.fq
[01:19:30] Used --force, will overwrite existing S4
[01:19:30] Changing working directory: S4
[01:19:30] Creating reference folder: reference
[01:19:30] Extracting FASTA and GFF from reference.
[01:19:30] Wrote 3 sequences to ref.fa
[01:19:30] Wrote 0 features to ref.gff
[01:19:30] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
[01:19:30] Using BAM RG (Read Group) ID: S4
[01:19:30] Running: samtools faidx reference/ref.fa 2>> snps.log
[01:19:30] Running: bwa index reference/ref.fa 2>> snps.log
[01:19:30] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[01:19:30] Running: ln -sf reference/ref.fa . 2>> snps.log
[01:19:30] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[01:19:30] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[01:19:30] Running: bwa mem  -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S4/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 24000 sequences (2400000 bp)...
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11573, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (165, 198, 230)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (35, 360)
[M::mem_pestat] mean and std.dev: (198.20, 48.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 425)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 24000 reads in 1.181 CPU sec, 0.597 real sec
[main] Version: 0.7.19-r1273
[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974
[samclip] Header contained 6 lines
[samclip] Done.
[main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S4/R1.fq /build/snippy-jObLQy/snippy-4.6.0+dfsg/test/S4/R2.fq
[main] Real time: 0.677 sec; CPU: 1.211 sec
[01:19:31] Running: samtools index snps.bam 2>> snps.log
[01:19:31] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
[01:19:31] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
[01:19:32] 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

[01:19:32] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
[01:19:32] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[01:19:32] Running: /build/snippy-jObLQy/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[01:19:32] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[01:19:32] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[01:19:32] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[01:19:32] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[01:19:32] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[01:19:32] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[01:19:32] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[01:19:32] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[01:19:32] Marked 799 heterozygous sites with 'n'
[01:19:32] Creating extra output files: BED GFF CSV TXT HTML
[01:19:32] Identified 257 variants.
[01:19:32] Result folder: S4
[01:19:32] Result files:
[01:19:32] * S4/snps.aligned.fa
[01:19:32] * S4/snps.bam
[01:19:32] * S4/snps.bam.bai
[01:19:32] * S4/snps.bed
[01:19:32] * S4/snps.consensus.fa
[01:19:32] * S4/snps.consensus.subs.fa
[01:19:32] * S4/snps.csv
[01:19:32] * S4/snps.filt.vcf
[01:19:32] * S4/snps.gff
[01:19:32] * S4/snps.html
[01:19:32] * S4/snps.log
[01:19:32] * S4/snps.raw.vcf
[01:19:32] * S4/snps.subs.vcf
[01:19:32] * S4/snps.tab
[01:19:32] * S4/snps.txt
[01:19:32] * S4/snps.vcf
[01:19:32] * S4/snps.vcf.gz
[01:19:32] * S4/snps.vcf.gz.csi
[01:19:32] Walltime used: 3 seconds
[01:19:32] Wishing you a life free of homopolymer errors.
[01:19:32] 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 0.8.1
Opening 'example.fna'
Detected FASTA format
Read 5294 lines from 'example.fna'
Wrote 3 sequences from FASTA file.
Processed 1 files.
Done.
Loaded 3 sequences totalling 317336 bp.
Will mask 0 regions totalling 0 bp ~ 0.00%
0	S1	snp=239	del=23	ins=23	het=749	unaligned=9643
1	S2	snp=230	del=15	ins=11	het=841	unaligned=9428
2	S3	snp=226	del=28	ins=14	het=846	unaligned=9376
3	S4	snp=227	del=32	ins=14	het=799	unaligned=9707
Opening: core.tab
Opening: core.vcf
Processing contig: LBB_contig000001
Processing contig: LBB_contig000002
Processing contig: LBB_contig000003
Generating core.full.aln
Creating TSV file: core.txt
Running: snp-sites -c -o core.aln core.full.aln
Found a bug? Post it at http://github.com/tseemann/snippy/issues
Done.
This is snippy-core 4.6.0
Obtained from http://github.com/tseemann/snippy
Enabling bundled tools for linux
Found any2fasta - /usr/bin/any2fasta
Found samtools - /usr/bin/samtools
Found minimap2 - /usr/bin/minimap2
Found bedtools - /usr/bin/bedtools
Found snp-sites - /usr/bin/snp-sites
Saving reference FASTA: core-mask.ref.fa
This is any2fasta 0.8.1
Opening 'example.fna'
Detected FASTA format
Read 5294 lines from 'example.fna'
Wrote 3 sequences from FASTA file.
Processed 1 files.
Done.
Loaded 3 sequences totalling 317336 bp.
Loading mask bed file: example.bed
Will mask 8 regions totalling 3101 bp ~ 0.98%
0	S1	snp=239	del=23	ins=23	het=749	unaligned=9643
1	S2	snp=230	del=15	ins=11	het=841	unaligned=9428
2	S3	snp=226	del=28	ins=14	het=846	unaligned=9376
3	S4	snp=227	del=32	ins=14	het=799	unaligned=9707
Opening: core-mask.tab
Opening: core-mask.vcf
Processing contig: LBB_contig000001
Processing contig: LBB_contig000002
Processing contig: LBB_contig000003
Masking alignment at 8 regions
Generating core-mask.full.aln
Creating TSV file: core-mask.txt
Running: snp-sites -c -o core-mask.aln core-mask.full.aln
Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues
Done.
wc -l S?/snps.tab
  262 S1/snps.tab
  247 S2/snps.tab
  255 S3/snps.tab
  258 S4/snps.tab
 1022 total
make[2]: Leaving directory '/build/snippy-jObLQy/snippy-4.6.0+dfsg/test'
make[1]: Leaving directory '/build/snippy-jObLQy/snippy-4.6.0+dfsg'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_install
make[1]: Entering directory '/build/snippy-jObLQy/snippy-4.6.0+dfsg'
dh_install
sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile
make[1]: Leaving directory '/build/snippy-jObLQy/snippy-4.6.0+dfsg'
   dh_installdocs
   dh_installchangelogs
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'snippy' in '../snippy_4.6.0+dfsg-6_all.deb'.
dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-6_all.deb'.
 dpkg-genbuildinfo -O../snippy_4.6.0+dfsg-6_amd64.buildinfo
 dpkg-genchanges -O../snippy_4.6.0+dfsg-6_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 2026-07-12T01:19:35Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                      Sun, 12 Jul 2026 01:19:35 +0000 |
+------------------------------------------------------------------------------+


snippy_4.6.0+dfsg-6_amd64.changes:
----------------------------------

Format: 1.8
Date: Sun, 08 Feb 2026 11:40:00 +0100
Source: snippy
Binary: snippy snippy-examples
Architecture: source all
Version: 4.6.0+dfsg-6
Distribution: perl-5.44-throwaway
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Santiago Vila <sanvila@debian.org>
Description:
 snippy     - rapid haploid variant calling and core genome alignment
 snippy-examples - rapid haploid variant calling and core genome alignment (examples
Changes:
 snippy (4.6.0+dfsg-6) unstable; urgency=medium
 .
   * Team upload.
   * Fix clean target.
   * Drop "Rules-Requires-Root: no" (default).
   * Drop "Priority: optional" (default).
   * Update standards-version.
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Files:
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 2d8db77f335c9d9e00daae607a903ea7 5484 science optional snippy_4.6.0+dfsg-6.debian.tar.xz
 4e83e4081fa7f640aa2c8189df2d0c23 310476 science optional snippy-examples_4.6.0+dfsg-6_all.deb
 e8e07889189921868e27abaacfa3bec9 26880 science optional snippy_4.6.0+dfsg-6_all.deb
 c5c2715d19212c09f577e1a67226e155 17880 science optional snippy_4.6.0+dfsg-6_amd64.buildinfo

+------------------------------------------------------------------------------+
| Buildinfo                                    Sun, 12 Jul 2026 01:19:35 +0000 |
+------------------------------------------------------------------------------+

Format: 1.0
Source: snippy
Binary: snippy snippy-examples
Architecture: all source
Version: 4.6.0+dfsg-6
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Sun, 12 Jul 2026 01:19:35 +0000
Build-Path: /build/snippy-jObLQy/snippy-4.6.0+dfsg
Build-Tainted-By:
 usr-local-has-programs
Installed-Build-Depends:
 adwaita-icon-theme (= 50.0-2),
 ant (= 1.10.17-1),
 ant-optional (= 1.10.17-1),
 any2fasta (= 0.8.1-1),
 at-spi2-common (= 2.61.0-1),
 autoconf (= 2.73-2),
 automake (= 1:1.18.1-4),
 autopoint (= 1.0-3),
 autotools-dev (= 20240727.1+nmu1),
 base-files (= 14.2),
 base-passwd (= 3.6.8),
 bash (= 5.3-3),
 bcftools (= 1.22-1),
 bedtools (= 2.31.1+dfsg-3),
 binutils (= 2.46.50.20260617-1),
 binutils-common (= 2.46.50.20260617-1),
 binutils-x86-64-linux-gnu (= 2.46.50.20260617-1),
 bsdextrautils (= 2.42.2-1),
 bubblewrap (= 0.11.2-2),
 build-essential (= 12.12),
 bwa (= 0.7.19-1),
 bzip2 (= 1.0.8-6+b2),
 ca-certificates (= 20260601),
 ca-certificates-java (= 20260311),
 coreutils (= 9.10-1),
 cpp (= 4:15.2.0-5+b1),
 cpp-15 (= 15.3.0-1),
 cpp-15-x86-64-linux-gnu (= 15.3.0-1),
 cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1),
 dash (= 0.5.12-12),
 dbus (= 1.16.2-5+b1),
 dbus-bin (= 1.16.2-5+b1),
 dbus-daemon (= 1.16.2-5+b1),
 dbus-session-bus-common (= 1.16.2-5),
 dbus-system-bus-common (= 1.16.2-5),
 dbus-user-session (= 1.16.2-5+b1),
 dconf-gsettings-backend (= 0.49.0-4+b1),
 dconf-service (= 0.49.0-4+b1),
 debconf (= 1.5.92),
 debhelper (= 14.3),
 debianutils (= 5.23.2),
 default-jre (= 2:1.25-77),
 default-jre-headless (= 2:1.25-77),
 dh-autoreconf (= 22),
 dh-strip-nondeterminism (= 1.15.1-1),
 diffutils (= 1:3.12-1),
 dpkg (= 1.23.7),
 dpkg-dev (= 1.23.7),
 dwz (= 0.16-4),
 file (= 1:5.47-4),
 findutils (= 4.10.0-4),
 fontconfig (= 2.17.1-5),
 fontconfig-config (= 2.17.1-5),
 fonts-dejavu-core (= 2.37-9),
 fonts-dejavu-mono (= 2.37-9),
 freebayes (= 1.3.9-2),
 g++ (= 4:15.2.0-5+b1),
 g++-15 (= 15.3.0-1),
 g++-15-x86-64-linux-gnu (= 15.3.0-1),
 g++-x86-64-linux-gnu (= 4:15.2.0-5+b1),
 gcc (= 4:15.2.0-5+b1),
 gcc-15 (= 15.3.0-1),
 gcc-15-base (= 15.3.0-1),
 gcc-15-x86-64-linux-gnu (= 15.3.0-1),
 gcc-16-base (= 16.1.0-2),
 gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1),
 gettext (= 1.0-3),
 gettext-base (= 1.0-3),
 glycin-loaders (= 2.1.5+ds-2),
 glycin-thumbnailers (= 2.1.5+ds-2),
 grep (= 3.12-1),
 groff-base (= 1.24.1-1),
 gtk-update-icon-cache (= 4.22.4+ds-1),
 gzip (= 1.13-1),
 hicolor-icon-theme (= 0.18-2),
 hostname (= 3.25),
 init-system-helpers (= 1.69),
 intltool-debian (= 0.35.0+20060710.6),
 java-common (= 0.77),
 junit4 (= 4.13.2-6),
 junit5 (= 5.10.3-1),
 libacl1 (= 2.4.0-1),
 libactivation-java (= 1.2.0-2),
 libantlr4-runtime-java (= 4.9.2-3),
 libaopalliance-java (= 20070526-7),
 libapache-pom-java (= 33-2),
 libapfloat-java (= 1.16.0-1),
 libapiguardian-java (= 1.1.2-1),
 libapparmor1 (= 4.1.7-4),
 libarchive-zip-perl (= 1.68-1),
 libargs4j-java (= 2.33-2),
 libasan8 (= 16.1.0-2),
 libasm-java (= 9.9.1-1),
 libasound2-data (= 1.2.16.1-1),
 libasound2t64 (= 1.2.16.1-1),
 libatinject-jsr330-api-java (= 1.0+ds1-6),
 libatk-bridge2.0-0t64 (= 2.61.0-1),
 libatk1.0-0t64 (= 2.61.0-1),
 libatomic1 (= 16.1.0-2),
 libatspi2.0-0t64 (= 2.61.0-1),
 libattr1 (= 1:2.6.0-1),
 libaudit-common (= 1:4.1.2-1),
 libaudit1 (= 1:4.1.2-1+b1),
 libavahi-client3 (= 0.8-18),
 libavahi-common-data (= 0.8-18),
 libavahi-common3 (= 0.8-18),
 libbeam-java (= 1.3.9-1),
 libbinutils (= 2.46.50.20260617-1),
 libbio-perl-perl (= 1.7.8-4),
 libbiojava6-java (= 6.1.0+dfsg-6),
 libblas3 (= 3.12.1-8),
 libblkid1 (= 2.42.2-1),
 libbrotli1 (= 1.2.0-3),
 libbsd0 (= 0.12.2-3),
 libbz2-1.0 (= 1.0.8-6+b2),
 libc-bin (= 2.42-17),
 libc-dev-bin (= 2.42-17),
 libc-gconv-modules-extra (= 2.42-17),
 libc6 (= 2.42-17),
 libc6-dev (= 2.42-17),
 libcairo-gobject2 (= 1.18.4-3+b1),
 libcairo2 (= 1.18.4-3+b1),
 libcap-ng0 (= 0.9.3-1+b1),
 libcap2 (= 1:2.78-1),
 libcc1-0 (= 16.1.0-2),
 libcdi-api-java (= 1.2-4),
 libcharts4j-java (= 1.3-4),
 libciftools-java (= 7.0.2-1),
 libcloudproviders0 (= 0.4.0-2+b1),
 libcodemodel-java (= 2.6+jaxb2.3.0.1-11),
 libcolord2 (= 1.4.8-3),
 libcom-err2 (= 1.47.4-1),
 libcommons-beanutils-java (= 1.10.1-1.1),
 libcommons-cli-java (= 1.6.0-1),
 libcommons-codec-java (= 1.22.0-1),
 libcommons-collections3-java (= 3.2.2-3),
 libcommons-collections4-java (= 4.4-2),
 libcommons-compress-java (= 1.27.1-2),
 libcommons-io-java (= 2.22.0-1),
 libcommons-jexl2-java (= 2.1.1-6),
 libcommons-lang-java (= 2.6-12),
 libcommons-lang3-java (= 3.20.0-1),
 libcommons-logging-java (= 1.3.0-2),
 libcommons-math-java (= 2.2-9),
 libcommons-math3-java (= 3.6.1-4),
 libcommons-parent-java (= 56-1),
 libcommons-text-java (= 1.15.0-1),
 libcrypt1 (= 1:4.5.1-1+b1),
 libctf-nobfd0 (= 2.46.50.20260617-1),
 libctf0 (= 2.46.50.20260617-1),
 libcups2t64 (= 2.4.18-1),
 libcurl3t64-gnutls (= 8.21.0-2),
 libcurl4-gnutls (= 8.21.0-2),
 libcurl4t64 (= 8.21.0-2),
 libdata-stag-perl (= 0.14-4),
 libdatrie1 (= 0.2.14-2),
 libdav1d7 (= 1.5.3-1+b2),
 libdb5.3t64 (= 5.3.28+dfsg2-11+b1),
 libdbus-1-3 (= 1.16.2-5+b1),
 libdconf1 (= 0.49.0-4+b1),
 libde265-0 (= 1.1.1-1),
 libdebconfclient0 (= 0.283),
 libdebhelper-perl (= 14.3),
 libdeflate0 (= 1.25-1),
 libdisorder0 (= 0.0.2+git20130809.8062ee1-4+b3),
 libdistlib-java (= 1.0-6),
 libdom4j-java (= 2.1.4-1),
 libdpkg-perl (= 1.23.7),
 libdrm-amdgpu1 (= 2.4.134-3),
 libdrm-common (= 2.4.134-3),
 libdrm-intel1 (= 2.4.134-3),
 libdrm2 (= 2.4.134-3),
 libdtd-parser-java (= 1.2-1),
 libedit2 (= 3.1-20260512-1),
 libelf1t64 (= 0.195-1),
 libepoxy0 (= 1.5.10-2+b2),
 liberror-prone-java (= 2.18.0-1),
 libexpat1 (= 2.8.2-1),
 libezmorph-java (= 1.0.6-4),
 libfastahack0 (= 1.0.0+dfsg-12),
 libfastinfoset-java (= 1.2.12-4),
 libfastutil-java (= 8.5.16+dfsg-1),
 libffi8 (= 3.5.2-4),
 libfile-stripnondeterminism-perl (= 1.15.1-1),
 libfml0 (= 0.1+git20221215.85f159e-1+b2),
 libfontconfig1 (= 2.17.1-5),
 libfreemarker-java (= 2.3.32-2.1),
 libfreetype6 (= 2.14.3+dfsg-1),
 libfribidi0 (= 1.0.16-5+b1),
 libgbm1 (= 26.1.4-1),
 libgcc-15-dev (= 15.3.0-1),
 libgcc-s1 (= 16.1.0-2),
 libgdbm-compat4t64 (= 1.26-1+b2),
 libgdbm6t64 (= 1.26-1+b2),
 libgdk-pixbuf-2.0-0 (= 2.44.6+dfsg-2),
 libgdk-pixbuf2.0-common (= 2.44.6+dfsg-2),
 libgeronimo-annotation-1.3-spec-java (= 1.3-1),
 libgeronimo-interceptor-3.0-spec-java (= 1.0.1-5),
 libgfortran5 (= 16.1.0-2),
 libgif7 (= 6.1.3-1),
 libgl1 (= 1.7.0-3+b1),
 libgl1-mesa-dri (= 26.1.4-1),
 libglib2.0-0t64 (= 2.88.2-1),
 libglvnd0 (= 1.7.0-3+b1),
 libglx-mesa0 (= 26.1.4-1),
 libglx0 (= 1.7.0-3+b1),
 libglycin-2-0 (= 2.1.5+ds-2),
 libgmp10 (= 2:6.3.0+dfsg-5+b2),
 libgnutls30t64 (= 3.8.13-1),
 libgomp1 (= 16.1.0-2),
 libgoogle-gson-java (= 2.10.1-1),
 libgprofng0 (= 2.46.50.20260617-1),
 libgraphite2-3 (= 1.3.15-2),
 libgssapi-krb5-2 (= 1.22.1-3),
 libgtk-3-0t64 (= 3.24.52-1),
 libgtk-3-common (= 3.24.52-1),
 libguava-java (= 32.0.1-1),
 libguice-java (= 5.1.0-1),
 libhamcrest-java (= 2.2-2),
 libharfbuzz0b (= 12.3.2-2+b2),
 libheif-plugin-dav1d (= 1.23.1-1),
 libheif-plugin-libde265 (= 1.23.1-1),
 libheif1 (= 1.23.1-1),
 libhogweed6t64 (= 3.10.2-1+b1),
 libhts3t64 (= 1.22.1+ds2-1+b2),
 libhtscodecs2 (= 1.6.6-1),
 libhtsjdk-java (= 5.0.0+dfsg-1),
 libhttpclient-java (= 4.5.14-1),
 libhttpcore-java (= 4.4.16-1),
 libhwasan0 (= 16.1.0-2),
 libhwy1t64 (= 1.3.0-2+b1),
 libice6 (= 2:1.1.1-1+b2),
 libicu78 (= 78.3-2),
 libidn2-0 (= 2.3.8-5),
 libinchi-dev (= 1.07.3+dfsg-2),
 libinchi1.07 (= 1.07.3+dfsg-2),
 libio-string-perl (= 1.08-4),
 libisl23 (= 0.27-2),
 libistack-commons-java (= 3.0.6-5),
 libitext5-java (= 5.5.13.4-2),
 libitm1 (= 16.1.0-2),
 libjackson2-annotations-java (= 2.14.0-1),
 libjackson2-core-java (= 2.14.1-2),
 libjackson2-databind-java (= 2.14.0+ds-2),
 libjansson4 (= 2.15.1-1),
 libjaxb-api-java (= 2.3.1-1),
 libjaxb-java (= 2.3.0.1-11),
 libjaxen-java (= 1.2.0-1),
 libjbig0 (= 2.1-6.1+b3),
 libjgrapht-java (= 1.5.2-2),
 libjgraphx-java (= 2.1.0.7-6),
 libjheaps-java (= 0.14-3),
 libjmol-java (= 16.3.55+dfsg-1),
 libjna-inchi-java (= 1.3.1+dfsg-1),
 libjna-java (= 5.18.1-1),
 libjna-jni (= 5.18.1-1),
 libjoptsimple-java (= 5.0.4-7),
 libjpeg62-turbo (= 1:3.1.3-4),
 libjson-java (= 3.2.0+dfsg-2),
 libjson-simple-java (= 2.3.0-2),
 libjsoncpp26 (= 1.9.8-1),
 libjsoup-java (= 1.15.3-1),
 libjsr305-java (= 0.1~+svn49-12),
 libjxl0.11 (= 0.11.2-5),
 libk5crypto3 (= 1.22.1-3),
 libkeyutils1 (= 1.6.3-6+b2),
 libkrb5-3 (= 1.22.1-3),
 libkrb5support0 (= 1.22.1-3),
 liblapack3 (= 3.12.1-8),
 liblcms2-2 (= 2.19.1-1),
 libldap2 (= 2.6.13+dfsg-1+b1),
 liblerc4 (= 4.1.1+ds-1),
 libllvm21 (= 1:21.1.8-7+b4),
 liblsan0 (= 16.1.0-2),
 liblzma5 (= 5.8.3-1),
 libmagic-mgc (= 1:5.47-4),
 libmagic1t64 (= 1:5.47-4),
 libmaven-archiver-java (= 3.6.2-1),
 libmaven-compiler-plugin-java (= 3.13.0-1),
 libmaven-file-management-java (= 3.0.0-2),
 libmaven-jar-plugin-java (= 3.3.0-2),
 libmaven-parent-java (= 43-2),
 libmaven-resolver-java (= 1.9.25-1),
 libmaven-shared-incremental-java (= 1.1-6),
 libmaven-shared-io-java (= 3.0.0-4),
 libmaven-shared-utils-java (= 3.4.2-1),
 libmaven3-core-java (= 3.9.12-1),
 libmbedcrypto16 (= 3.6.6-0.1),
 libmbedtls21 (= 3.6.6-0.1),
 libmbedx509-7 (= 3.6.6-0.1),
 libmd0 (= 1.2.0-2),
 libmmtf-java (= 1.0.11-1),
 libmount1 (= 2.42.2-1),
 libmpc3 (= 1.3.1-3),
 libmpfr6 (= 4.2.2-3),
 libmsgpack-java (= 0.9.6-1),
 libnaga-java (= 3.0+svn80-5),
 libncbi-ngs3 (= 3.2.1+dfsg-6+b1),
 libncbi-vdb3 (= 3.2.1+dfsg-2+b1),
 libncurses6 (= 6.6+20260608-2),
 libncursesw6 (= 6.6+20260608-2),
 libnettle8t64 (= 3.10.2-1+b1),
 libnghttp2-14 (= 1.69.0-1),
 libnghttp3-9 (= 1.15.0-1),
 libngs-java (= 3.2.1+dfsg-6+b1),
 libngs-jni (= 3.2.1+dfsg-6+b1),
 libngtcp2-16 (= 1.22.1-1),
 libngtcp2-crypto-gnutls8 (= 1.22.1-1),
 libngtcp2-crypto-ossl0 (= 1.22.1-1),
 libnspr4 (= 2:4.38.2-1+b1),
 libnss3 (= 2:3.124-1),
 libopentest4j-java (= 1.2.0-4),
 libopentest4j-reporting-java (= 0.2.5-1),
 libp11-kit0 (= 0.26.4-1),
 libpam-modules (= 1.7.0-8),
 libpam-modules-bin (= 1.7.0-8),
 libpam-runtime (= 1.7.0-8),
 libpam-systemd (= 261.1-2),
 libpam0g (= 1.7.0-8),
 libpango-1.0-0 (= 1.58.0-1),
 libpangocairo-1.0-0 (= 1.58.0-1),
 libpangoft2-1.0-0 (= 1.58.0-1),
 libpaper-utils (= 2.2.5-0.4),
 libpaper2 (= 2.2.5-0.4),
 libpciaccess0 (= 0.19-2),
 libpcre2-8-0 (= 10.46-1+b2),
 libpcsclite1 (= 2.5.1-1),
 libperl5.44 (= 5.44.0~rc2-1),
 libpicocli-java (= 4.6.2-2),
 libpipeline1 (= 1.5.8-3),
 libpixman-1-0 (= 0.46.4-1+b2),
 libplexus-archiver-java (= 4.6.1-1),
 libplexus-cipher-java (= 2.0-1),
 libplexus-classworlds-java (= 2.7.0-1),
 libplexus-compiler-java (= 2.13.0-1),
 libplexus-component-annotations-java (= 2.1.1-1),
 libplexus-container-default-java (= 2.1.1-1),
 libplexus-interpolation-java (= 1.27-1),
 libplexus-io-java (= 3.3.1-2),
 libplexus-languages-java (= 1.1.1-3),
 libplexus-sec-dispatcher-java (= 2.0-3),
 libplexus-utils2-java (= 3.4.2-1),
 libpng16-16t64 (= 1.6.58-1),
 libproc2-1 (= 2:4.0.6-2),
 libpsl5t64 (= 0.22.0-1),
 libpython3-stdlib (= 3.14.6-1),
 libpython3.14-minimal (= 3.14.6-1),
 libpython3.14-stdlib (= 3.14.6-1),
 libqdox2-java (= 2.0.3-1),
 libquadmath0 (= 16.1.0-2),
 libreadline8t64 (= 8.3-4),
 librelaxng-datatype-java (= 1.0+ds1-4),
 librhino-java (= 1.7.15.1-0.1),
 librngom-java (= 2.3.0.1-11),
 librsvg2-2 (= 2.62.1+dfsg-1),
 libsasl2-2 (= 2.1.28+dfsg1-11),
 libsasl2-modules-db (= 2.1.28+dfsg1-11),
 libseccomp2 (= 2.6.1-1),
 libselinux1 (= 3.11-2),
 libsensors-config (= 1:3.6.2-2),
 libsensors5 (= 1:3.6.2-2+b2),
 libseqlib2 (= 1.2.0+dfsg-11+b4),
 libsframe3 (= 2.46.50.20260617-1),
 libsharpyuv0 (= 1.5.0-0.1+b2),
 libsisu-inject-java (= 0.3.5-1),
 libsisu-plexus-java (= 0.3.5-1),
 libslf4j-java (= 1.7.32-2),
 libsm6 (= 2:1.2.6-1+b2),
 libsmartcols1 (= 2.42.2-1),
 libsmithwaterman0 (= 0.0+git20160702.2610e25-12+b3),
 libsnappy-java (= 1.1.10.8-1),
 libsnappy-jni (= 1.1.10.8-1),
 libsnappy1v5 (= 1.2.2-2+b2),
 libsnp-sites1 (= 2.5.1-2+b3),
 libsnpeff-java (= 5.4.b+dfsg-2),
 libsqlite3-0 (= 3.53.3-1),
 libssh2-1t64 (= 1.11.1-4),
 libssl3t64 (= 3.6.3-1),
 libssw0 (= 1.1-16),
 libstax-ex-java (= 1.7.8-3),
 libstdc++-15-dev (= 15.3.0-1),
 libstdc++6 (= 16.1.0-2),
 libstreambuffer-java (= 1.5.4-2),
 libsystemd-shared (= 261.1-2),
 libsystemd0 (= 261.1-2),
 libtabixpp0t64 (= 1.1.2-2.1+b2),
 libtasn1-6 (= 4.21.0-2+b1),
 libtcl8.6 (= 8.6.18+dfsg-1),
 libtext-charwidth-perl (= 0.04-12+b1),
 libtext-wrapi18n-perl (= 0.06-11),
 libthai-data (= 0.1.30-2),
 libthai0 (= 0.1.30-2),
 libtiff6 (= 4.7.2-1),
 libtinfo6 (= 6.6+20260608-2),
 libtirpc-common (= 1.3.7+ds-1),
 libtirpc3t64 (= 1.3.7+ds-1),
 libtk8.6 (= 8.6.18-1),
 libtool (= 2.5.4-11),
 libtrove3-java (= 3.0.3-6),
 libtsan2 (= 16.1.0-2),
 libtss2-esys-3.0.2-0t64 (= 4.1.3-6),
 libtss2-mu-4.0.1-0t64 (= 4.1.3-6),
 libtss2-rc0t64 (= 4.1.3-6),
 libtss2-sys1t64 (= 4.1.3-6),
 libtss2-tcti-cmd0t64 (= 4.1.3-6),
 libtss2-tcti-device0t64 (= 4.1.3-6),
 libtss2-tcti-mssim0t64 (= 4.1.3-6),
 libtss2-tcti-swtpm0t64 (= 4.1.3-6),
 libtxw2-java (= 2.3.0.1-11),
 libubsan1 (= 16.1.0-2),
 libuchardet0 (= 0.0.8-2+b2),
 libudev1 (= 261.1-2),
 libunistring5 (= 1.4.2-1),
 libunivocity-parsers-java (= 2.9.1-1),
 libuuid1 (= 2.42.2-1),
 libvcflib-tools (= 1.0.12+dfsg-2),
 libvcflib2 (= 1.0.12+dfsg-2),
 libvecmath-java (= 1.5.2-7),
 libvulkan1 (= 1.4.341.0-1),
 libwagon-http-java (= 3.5.3-2),
 libwagon-provider-api-java (= 3.5.3-2),
 libwayland-client0 (= 1.25.0-2),
 libwayland-cursor0 (= 1.25.0-2),
 libwayland-egl1 (= 1.25.0-2),
 libwebp7 (= 1.5.0-0.1+b2),
 libwfa2-0 (= 2.3.6-2),
 libx11-6 (= 2:1.8.13-1),
 libx11-data (= 2:1.8.13-1),
 libx11-xcb1 (= 2:1.8.13-1),
 libxau6 (= 1:1.0.11-1+b2),
 libxbean-reflect-java (= 4.5-9),
 libxcb-dri3-0 (= 1.17.0-2+b2),
 libxcb-glx0 (= 1.17.0-2+b2),
 libxcb-present0 (= 1.17.0-2+b2),
 libxcb-randr0 (= 1.17.0-2+b2),
 libxcb-render0 (= 1.17.0-2+b2),
 libxcb-shm0 (= 1.17.0-2+b2),
 libxcb-sync1 (= 1.17.0-2+b2),
 libxcb-xfixes0 (= 1.17.0-2+b2),
 libxcb1 (= 1.17.0-2+b2),
 libxcomposite1 (= 1:0.4.6-1+b2),
 libxcursor1 (= 1:1.2.3-1+b2),
 libxdamage1 (= 1:1.1.7-1+b1),
 libxdmcp6 (= 1:1.1.5-2+b1),
 libxerces2-java (= 2.12.2-1),
 libxext6 (= 2:1.3.4-1+b4),
 libxfixes3 (= 1:6.0.0-2+b5),
 libxft2 (= 2.3.6-1+b5),
 libxi6 (= 2:1.8.2-2+b1),
 libxinerama1 (= 2:1.1.4-3+b5),
 libxkbcommon0 (= 1.13.1-1),
 libxml-commons-external-java (= 1.4.01-6),
 libxml-commons-resolver1.1-java (= 1.2-11),
 libxml2-16 (= 2.15.3+dfsg-1),
 libxom-java (= 1.4.4-1),
 libxrandr2 (= 2:1.5.4-1+b4),
 libxrender1 (= 1:0.9.12-1+b2),
 libxres1 (= 2:1.2.1-2),
 libxshmfence1 (= 1.3.3-1+b2),
 libxsom-java (= 2.3.0.1-11),
 libxss1 (= 1:1.2.3-1+b4),
 libxt6t64 (= 1:1.2.1-1.3+b2),
 libxtst6 (= 2:1.2.5-1+b2),
 libxxf86vm1 (= 1:1.1.4-2+b1),
 libxz-java (= 1.11+repack-1),
 libz3-4 (= 4.13.3-1.1),
 libzstd1 (= 1.5.7+dfsg-3+b2),
 linux-libc-dev (= 7.1.3-1),
 m4 (= 1.4.21-1),
 make (= 4.4.1-3),
 man-db (= 2.13.1-1),
 mawk (= 1.3.4.20260302-1),
 media-types (= 14.0.0),
 mesa-libgallium (= 26.1.4-1),
 minimap2 (= 2.27+dfsg-1+b4),
 mount (= 2.42.2-1),
 ncbi-vdb-data (= 3.2.1+dfsg-2),
 ncurses-base (= 6.6+20260608-2),
 ncurses-bin (= 6.6+20260608-2),
 netbase (= 6.5),
 openjdk-25-jre (= 25.0.4~4ea-1),
 openjdk-25-jre-headless (= 25.0.4~4ea-1),
 openssl (= 3.6.3-1),
 openssl-provider-legacy (= 3.6.3-1),
 parallel (= 20240222+ds-4),
 patch (= 2.8-2),
 pci.ids (= 0.0~2026.07.06-1),
 perl (= 5.44.0~rc2-1),
 perl-base (= 5.44.0~rc2-1),
 perl-modules-5.44 (= 5.44.0~rc2-1),
 po-debconf (= 1.0.22),
 procps (= 2:4.0.6-2),
 python3 (= 3.14.6-1),
 python3-minimal (= 3.14.6-1),
 python3.14 (= 3.14.6-1),
 python3.14-minimal (= 3.14.6-1),
 r-base-core (= 4.6.1-1),
 r-cran-cli (= 3.6.6-1),
 r-cran-cpp11 (= 0.5.5-1),
 r-cran-farver (= 2.1.2-3),
 r-cran-ggplot2 (= 4.0.3+dfsg-1),
 r-cran-glue (= 1.8.1-2),
 r-cran-gridbase (= 0.4-7-6),
 r-cran-gtable (= 0.3.6+dfsg-2),
 r-cran-isoband (= 0.3.0-1),
 r-cran-labeling (= 0.4.3-2),
 r-cran-lifecycle (= 1.0.5+dfsg-1),
 r-cran-littler (= 0.3.23-1),
 r-cran-pkgkitten (= 0.2.4-1),
 r-cran-plyr (= 1.8.9-2),
 r-cran-r6 (= 2.6.1-2),
 r-cran-rcolorbrewer (= 1.1-3-2),
 r-cran-rcpp (= 1.1.2-1),
 r-cran-rlang (= 1.3.0-1),
 r-cran-s7 (= 0.2.2-1),
 r-cran-scales (= 1.4.0-1),
 r-cran-vctrs (= 0.7.3-2),
 r-cran-viridislite (= 0.4.3-1),
 r-cran-withr (= 3.0.3+dfsg-1),
 readline-common (= 8.3-4),
 rpcsvc-proto (= 1.4.4-1),
 samclip (= 0.4.0-4),
 samtools (= 1.22.1-1),
 sed (= 4.9-3),
 sensible-utils (= 0.0.26),
 seqtk (= 1.4-2),
 shared-mime-info (= 2.4-5+b3),
 snp-sites (= 2.5.1-2+b3),
 snpeff (= 5.4.b+dfsg-2),
 sysstat (= 12.7.5-2),
 systemd (= 261.1-2),
 systemd-sysv (= 261.1-2),
 systemd-tpm (= 261.1-2),
 sysvinit-utils (= 3.18-1),
 tar (= 1.35+dfsg-4),
 tpm-udev (= 4.1.3-6),
 tzdata (= 2026b-1),
 ucf (= 3.0056),
 unzip (= 6.0-29),
 util-linux (= 2.42.2-1),
 vt (= 0.57721+ds-3+b1),
 x11-common (= 1:7.7+26),
 xdg-utils (= 1.2.1-2),
 xkb-data (= 2.47-1),
 xz-utils (= 5.8.3-1),
 zip (= 3.0-15),
 zlib1g (= 1:1.3.dfsg+really1.3.2-3)
Environment:
 DEB_BUILD_OPTIONS="parallel=2"
 LANG="C.UTF-8"
 LANGUAGE="en_GB:en"
 LC_COLLATE="C.UTF-8"
 LC_CTYPE="C.UTF-8"
 LD_LIBRARY_PATH="/usr/lib/libeatmydata"
 LD_PRELOAD="libeatmydata.so"
 SOURCE_DATE_EPOCH="1770547200"


+------------------------------------------------------------------------------+
| Package contents                             Sun, 12 Jul 2026 01:19:35 +0000 |
+------------------------------------------------------------------------------+


snippy-examples_4.6.0+dfsg-6_all.deb
------------------------------------

 new Debian package, version 2.0.
 size 310476 bytes: control archive=1064 bytes.
     931 bytes,    22 lines      control
     559 bytes,     7 lines      md5sums
 Package: snippy-examples
 Source: snippy
 Version: 4.6.0+dfsg-6
 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 2026-02-08 10:40 ./
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/doc/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/doc/snippy-examples/
-rw-r--r-- root/root       721 2026-02-08 10:40 ./usr/share/doc/snippy-examples/changelog.Debian.gz
-rw-r--r-- root/root       890 2026-02-08 09:00 ./usr/share/doc/snippy-examples/copyright
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/doc/snippy/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/doc/snippy/examples/
-rw-r--r-- root/root      1610 2026-02-08 10:40 ./usr/share/doc/snippy/examples/Makefile
-rw-r--r-- root/root       220 2020-03-09 02:53 ./usr/share/doc/snippy/examples/example.bed
-rw-r--r-- root/root     95810 2020-03-09 02:53 ./usr/share/doc/snippy/examples/example.fna.gz
-rw-r--r-- root/root    208951 2020-03-09 02:53 ./usr/share/doc/snippy/examples/example.gbk.gz
-rwxr-xr-x root/root       836 2026-02-08 09:00 ./usr/share/doc/snippy/examples/test_for_working_snpeff_v5.1+


snippy_4.6.0+dfsg-6_all.deb
---------------------------

 new Debian package, version 2.0.
 size 26880 bytes: control archive=1288 bytes.
     984 bytes,    18 lines      control
     841 bytes,    13 lines      md5sums
 Package: snippy
 Version: 4.6.0+dfsg-6
 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 2026-02-08 10:40 ./
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/bin/
-rwxr-xr-x root/root     28069 2026-02-08 10:40 ./usr/bin/snippy
-rwxr-xr-x root/root      2518 2026-02-08 10:40 ./usr/bin/snippy-clean_full_aln
-rwxr-xr-x root/root     15844 2026-02-08 10:40 ./usr/bin/snippy-core
-rwxr-xr-x root/root      2311 2026-02-08 10:40 ./usr/bin/snippy-multi
-rwxr-xr-x root/root      6632 2026-02-08 10:40 ./usr/bin/snippy-vcf_extract_subs
-rwxr-xr-x root/root      3720 2026-02-08 10:40 ./usr/bin/snippy-vcf_report
-rwxr-xr-x root/root      5872 2026-02-08 10:40 ./usr/bin/snippy-vcf_to_tab
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/doc/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/doc/snippy/
-rw-r--r-- root/root       662 2026-02-08 09:00 ./usr/share/doc/snippy/README.Debian
-rw-r--r-- root/root       718 2026-02-08 10:40 ./usr/share/doc/snippy/changelog.Debian.gz
-rw-r--r-- root/root       890 2026-02-08 09:00 ./usr/share/doc/snippy/copyright
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/doc/snippy/etc/
-rw-r--r-- root/root      4825 2020-03-09 02:53 ./usr/share/doc/snippy/etc/Mtb_NC_000962.3_mask.bed.gz
drwxr-xr-x root/root         0 2020-03-09 02:53 ./usr/share/perl5/
drwxr-xr-x root/root         0 2020-03-09 02:53 ./usr/share/perl5/Snippy/
-rw-r--r-- root/root       342 2020-03-09 02:53 ./usr/share/perl5/Snippy/Version.pm
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/snippy/
drwxr-xr-x root/root         0 2026-02-08 10:40 ./usr/share/snippy/etc/
-rw-r--r-- root/root     12107 2020-03-09 02:53 ./usr/share/snippy/etc/snpeff.config


+------------------------------------------------------------------------------+
| Post Build                                   Sun, 12 Jul 2026 01:19:36 +0000 |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                      Sun, 12 Jul 2026 01:19:36 +0000 |
+------------------------------------------------------------------------------+

Purging /build/snippy-jObLQy
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                      Sun, 12 Jul 2026 01:19:37 +0000 |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: full
Build-Space: 46056
Build-Time: 17
Distribution: perl-5.44-throwaway
Host Architecture: amd64
Install-Time: 50
Job: /srv/debomatic/incoming/snippy_4.6.0+dfsg-6.dsc
Machine Architecture: amd64
Package: snippy
Package-Time: 70
Source-Version: 4.6.0+dfsg-6
Space: 46056
Status: successful
Version: 4.6.0+dfsg-6
--------------------------------------------------------------------------------
Finished at 2026-07-12T01:19:35Z
Build needed 00:01:10, 46056k disk space