I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 15 05:59:26 +14 2024 I: pbuilder-time-stamp: 1718380766 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [plasmidid_1.6.5+dfsg-2.dsc] I: copying [./plasmidid_1.6.5+dfsg.orig.tar.xz] I: copying [./plasmidid_1.6.5+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Nov 25 06:34:28 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./plasmidid_1.6.5+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting plasmidid in plasmidid-1.6.5+dfsg dpkg-source: info: unpacking plasmidid_1.6.5+dfsg.orig.tar.xz dpkg-source: info: unpacking plasmidid_1.6.5+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fixTests.patch dpkg-source: info: applying AdjustPythonPath.patch dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 15 05:59 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=4ff3dce4b7cd443a806bcf352b1b1ab0 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3149875 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CYC8ysxj/pbuilderrc_JoBE --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CYC8ysxj/b2 --logfile b2/build.log --extrapackages usrmerge plasmidid_1.6.5+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 Jun 15 05:59 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all, help2man, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on prokka; however: Package prokka is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on circos; however: Package circos is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: adwaita-icon-theme{a} aragorn{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bowtie2{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} cd-hit{a} circos{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-circos-symbols{a} fonts-cmu{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} help2man{a} hicolor-icon-theme{a} hmmer{a} infernal{a} intltool-debian{a} java-common{a} less{a} libabsl20220623{a} libaom3{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif15{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbio-searchio-hmmer-perl{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcapnp-0.9.2{a} libcarp-always-perl{a} libclone-perl{a} libconfig-general-perl{a} libcups2{a} libcurl3-gnutls{a} libdata-dumper-simple-perl{a} libdata-stag-perl{a} libdatrie1{a} libdav1d6{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1{a} libexpat1{a} libfile-basedir-perl{a} libfile-stripnondeterminism-perl{a} libfont-ttf-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd-perl{a} libgd3{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgetopt-simple-perl{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphics-colornames-perl{a} libgraphics-colorobject-perl{a} libgraphite2-3{a} libgsl27{a} libgslcblas0{a} libgtk2.0-0{a} libgtk2.0-common{a} libharfbuzz0b{a} libheif1{a} libhts3{a} libhtscodecs2{a} libicu72{a} libio-all-perl{a} libio-string-perl{a} libipc-system-simple-perl{a} libjbig0{a} libjpeg62-turbo{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblist-allutils-perl{a} liblist-someutils-perl{a} liblist-utilsby-perl{a} libllvm15{a} liblmdb0{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmath-bezier-perl{a} libmath-round-perl{a} libmath-vec-perl{a} libmath-vecstat-perl{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmodule-implementation-perl{a} libmodule-runtime-perl{a} libmurmurhash2{a} libncbi6{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libnuma1{a} libnumber-format-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libparams-validate-perl{a} libpciaccess0{a} libpcre3{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} libreadline8{a} libreadonly-perl{a} libregexp-common-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libset-intspan-perl{a} libspiffy-perl{a} libssh2-1{a} libstatistics-basic-perl{a} libsub-override-perl{a} libsvg-perl{a} libsvtav1enc1{a} libswiss-perl{a} libtext-format-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libx265-199{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml2{a} libxpm4{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libyuv0{a} libz3-4{a} m4{a} man-db{a} mash{a} media-types{a} ncbi-blast+{a} ncbi-data{a} ncbi-tools-bin{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} parallel{a} po-debconf{a} procps{a} prodigal{a} prokka{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} shared-mime-info{a} sysstat{a} ucf{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf bcron bioperl-run circos-tools cron curl dbus fonts-dejavu-extra libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libatk-wrapper-java-jni libbio-asn1-entrezgene-perl libbio-perl-run-perl libcgi-pm-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libgtk2.0-bin libhtml-parser-perl libhtml-tableextract-perl libldap-common liblist-moreutils-perl liblist-someutils-xs-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpod-coverage-perl libpostscript-perl librsvg2-common libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libtest-pod-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-expat-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl lynx perl-tk psmisc publicsuffix systemd systemd-cron wget xdg-user-dirs 0 packages upgraded, 252 newly installed, 0 to remove and 0 not upgraded. Need to get 218 MB of archives. After unpacking 990 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 12 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 less amd64 590-1.2 [131 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.37-2 [43.3 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 aragorn amd64 1.2.38-4 [86.7 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 bedtools amd64 2.30.0+dfsg-3 [665 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.5.0-3+b2 [1409 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 75 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 fonts-circos-symbols all 0.69.9+dfsg-2 [46.7 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 fonts-cmu all 0.7.0-5 [4892 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libregexp-common-perl all 2017060201-3 [175 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libcarp-always-perl all 0.16-1 [9620 B] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libconfig-general-perl all 2.65-2 [71.8 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libdata-dumper-simple-perl all 0.11-7 [12.5 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libaom3 amd64 3.6.0-1 [1851 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libdav1d6 amd64 1.0.0-2 [495 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libabsl20220623 amd64 20220623.1-1 [391 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libgav1-1 amd64 0.18.0-1+b1 [332 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 librav1e0 amd64 0.5.1-6 [763 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libsvtav1enc1 amd64 1.4.1+dfsg-1 [2121 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libyuv0 amd64 0.0~git20230123.b2528b0-1 [168 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libavif15 amd64 0.11.1-1 [93.8 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libde265-0 amd64 1.0.11-1 [185 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libx265-199 amd64 3.5-2+b1 [1150 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libheif1 amd64 1.15.1-1 [215 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libxpm4 amd64 1:3.5.12-1.1 [48.4 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libgd3 amd64 2.3.3-9 [124 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libgd-perl amd64 2.76-4+b1 [132 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libgetopt-simple-perl all 1.52-7 [15.5 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libmath-bezier-perl all 0.01-4 [7032 B] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libmath-round-perl all 0.07-3 [9312 B] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libparams-validate-perl amd64 1.31-1 [64.4 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libreadonly-perl all 2.050-3 [23.1 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libset-intspan-perl all 1.19-3 [25.3 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 liblist-allutils-perl all 0.19-1 [42.0 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libmath-vec-perl all 1.01-5 [17.1 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libmath-vecstat-perl all 0.08-3 [8408 B] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libgraphics-colornames-perl all 3.5.0-3 [32.1 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libgraphics-colorobject-perl all 0.5.0-10 [29.1 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libtext-format-perl all 0.62-1 [22.7 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libnumber-format-perl all 1.75-3 [28.9 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libstatistics-basic-perl all 1.6611-3 [61.5 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libsvg-perl all 2.87-1 [64.3 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 circos all 0.69.9+dfsg-2 [14.0 MB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.6+10-1 [168 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get: 206 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 infernal amd64 1.1.4-1 [5523 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libbio-searchio-hmmer-perl all 1.7.3-2 [95.9 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libcapnp-0.9.2 amd64 0.9.2-2 [1305 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-3+b1 [116 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-3+b1 [948 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libmurmurhash2 amd64 1.5-3 [5860 B] Get: 234 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libncbi6 amd64 6.1.20170106+dfsg1-10 [4082 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libswiss-perl all 1.80-1 [776 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 mash amd64 2.3+dfsg-3+b1 [188 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 ncbi-tools-bin amd64 6.1.20170106+dfsg1-10 [1941 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 sysstat amd64 12.6.1-1 [596 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 parallel all 20221122+ds-2 [1873 kB] Get: 249 http://deb.debian.org/debian bookworm/main amd64 prodigal amd64 1:2.6.3-6 [508 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 prokka amd64 1.14.6+dfsg-4 [9968 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 252 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Fetched 218 MB in 4s (56.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20360 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package less. Preparing to unpack .../001-less_590-1.2_amd64.deb ... Unpacking less (590-1.2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../008-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../014-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../017-hicolor-icon-theme_0.17-2_all.deb ... Unpacking hicolor-icon-theme (0.17-2) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../018-libgdk-pixbuf2.0-common_2.42.10+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../019-libglib2.0-0_2.74.6-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.6-2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../020-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../021-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../022-shared-mime-info_2.2-1_amd64.deb ... Unpacking shared-mime-info (2.2-1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../023-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../024-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../025-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../026-libjbig0_2.1-6.1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../027-liblerc4_4.0.0+ds-2_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-2) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../028-libwebp7_1.2.4-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.2.4-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../029-libtiff6_4.5.0-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.0-5) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../030-libgdk-pixbuf-2.0-0_2.42.10+dfsg-1+b1_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../031-gtk-update-icon-cache_3.24.37-2_amd64.deb ... Unpacking gtk-update-icon-cache (3.24.37-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../032-adwaita-icon-theme_43-1_all.deb ... Unpacking adwaita-icon-theme (43-1) ... Selecting previously unselected package aragorn. Preparing to unpack .../033-aragorn_1.2.38-4_amd64.deb ... Unpacking aragorn (1.2.38-4) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../034-at-spi2-common_2.46.0-5_all.deb ... Unpacking at-spi2-common (2.46.0-5) ... Selecting previously unselected package m4. Preparing to unpack .../035-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../036-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../037-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../038-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../039-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package bedtools. Preparing to unpack .../040-bedtools_2.30.0+dfsg-3_amd64.deb ... Unpacking bedtools (2.30.0+dfsg-3) ... Selecting previously unselected package bowtie2. Preparing to unpack .../041-bowtie2_2.5.0-3+b2_amd64.deb ... Unpacking bowtie2 (2.5.0-3+b2) ... Selecting previously unselected package java-common. Preparing to unpack .../042-java-common_0.74_all.deb ... Unpacking java-common (0.74) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../043-libavahi-common-data_0.8-10_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.8-10) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../044-libavahi-common3_0.8-10_amd64.deb ... Unpacking libavahi-common3:amd64 (0.8-10) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../045-libdbus-1-3_1.14.6-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.14.6-1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../046-libavahi-client3_0.8-10_amd64.deb ... Unpacking libavahi-client3:amd64 (0.8-10) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../047-libcups2_2.4.2-3_amd64.deb ... Unpacking libcups2:amd64 (2.4.2-3) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../048-liblcms2-2_2.14-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.14-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../049-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../050-libfreetype6_2.12.1+dfsg-5_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../051-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../052-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../053-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../054-libnspr4_2%3a4.35-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.35-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../055-libnss3_2%3a3.87.1-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.87.1-1) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../056-libasound2-data_1.2.8-1_all.deb ... Unpacking libasound2-data (1.2.8-1) ... Selecting previously unselected package libasound2:amd64. Preparing to unpack .../057-libasound2_1.2.8-1+b1_amd64.deb ... Unpacking libasound2:amd64 (1.2.8-1+b1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../058-libgraphite2-3_1.3.14-1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../059-libharfbuzz0b_6.0.0+dfsg-3_amd64.deb ... Unpacking libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../060-libpcsclite1_1.9.9-2_amd64.deb ... Unpacking libpcsclite1:amd64 (1.9.9-2) ... Selecting previously unselected package openjdk-17-jre-headless:amd64. Preparing to unpack .../061-openjdk-17-jre-headless_17.0.6+10-1_amd64.deb ... Unpacking openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../062-default-jre-headless_2%3a1.17-74_amd64.deb ... Unpacking default-jre-headless (2:1.17-74) ... 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Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up bedtools (2.30.0+dfsg-3) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up libmath-vec-perl (1.01-5) ... Setting up libstatistics-basic-perl (1.6611-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libncbi6:amd64 (6.1.20170106+dfsg1-10) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up gettext (0.21-12) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libavif15:amd64 (0.11.1-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libgraphics-colorobject-perl (0.5.0-10) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libio-all-perl (0.87-2) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libbio-searchio-hmmer-perl (1.7.3-2) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up mash (2.3+dfsg-3+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libx265-199:amd64 (3.5-2+b1) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up ncbi-tools-bin (6.1.20170106+dfsg1-10) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up sysstat (12.6.1-1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.37-2) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxpm4:amd64 (1:3.5.12-1.1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libheif1:amd64 (1.15.1-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libgd3:amd64 (2.3.3-9) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up parallel (20221122+ds-2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libcups2:amd64 (2.4.2-3) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up samtools (1.16.1-1) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up libgd-perl (2.76-4+b1) ... Setting up liblist-allutils-perl (0.19-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libparams-validate-perl:amd64 (1.31-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up circos (0.69.9+dfsg-2) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up ca-certificates-java (20230103) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-17-jre:amd64 (17.0.6+10-1) ... Setting up default-jre (2:1.17-74) ... Setting up prokka (1.14.6+dfsg-4) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... 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 (20230103) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/plasmidid-1.6.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plasmidid_1.6.5+dfsg-2_source.changes dpkg-buildpackage: info: source package plasmidid dpkg-buildpackage: info: source version 1.6.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with=python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/plasmidid-1.6.5+dfsg' dh_auto_clean rm -f debian/plasmidID.1 rm -rf NO_GROUP/ test/plasmids_TEST_database.fasta.length test/plasmids_TEST_database.length debian/patches/fixTest.patch path make[1]: Leaving directory '/build/plasmidid-1.6.5+dfsg' dh_clean debian/rules binary dh binary --with=python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/build/plasmidid-1.6.5+dfsg' PATH=$PATH:/build/plasmidid-1.6.5+dfsg/bin test/test.sh || true Executing:../plasmidID -1 KPN_TEST_R1.fastq.gz -2 KPN_TEST_R2.fastq.gz -d plasmids_TEST_database.fasta -c contigs_KPN_TEST.fasta -s KPN --no-trim Forward reads: KPN_TEST_R1.fastq.gz Reverse reads: KPN_TEST_R2.fastq.gz PlasmidDatabase: plasmids_TEST_database.fasta Contigs: contigs_KPN_TEST.fasta Options: --no-trim ------------------ Starting plasmidID version:1.6.4 ------------------ CHECKING DEPENDENCIES AND MANDATORY FILES DEPENDENCY STATUS ---------- ------ gawk NOT INSTALLED blastn INSTALLED bowtie2-build INSTALLED bowtie2 INSTALLED bedtools INSTALLED prokka INSTALLED samtools INSTALLED mash INSTALLED circos INSTALLED ERROR: 1 missing dependencies, aborting execution make[1]: Leaving directory '/build/plasmidid-1.6.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/plasmidid-1.6.5+dfsg' dh_auto_install help2man -i debian/plasmidID.h2m ./plasmidID > debian/plasmidID.1 make[1]: Leaving directory '/build/plasmidid-1.6.5+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installman dh_python3 dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package plasmidid: substitution variable ${perl:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'plasmidid' in '../plasmidid_1.6.5+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plasmidid_1.6.5+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../plasmidid_1.6.5+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3149875/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3149875 and its subdirectories I: Current time: Sat Jun 15 06:01:27 +14 2024 I: pbuilder-time-stamp: 1718380887