I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 16 16:55:39 +14 2023 I: pbuilder-time-stamp: 1678935339 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_1.6.3+dfsg-3.dsc] I: copying [./plasmidid_1.6.3+dfsg.orig.tar.xz] I: copying [./plasmidid_1.6.3+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Wu6VeS0a/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 11 22:19:05 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./plasmidid_1.6.3+dfsg-3.dsc dpkg-source: info: extracting plasmidid in plasmidid-1.6.3+dfsg dpkg-source: info: unpacking plasmidid_1.6.3+dfsg.orig.tar.xz dpkg-source: info: unpacking plasmidid_1.6.3+dfsg-3.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/3345609/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/3345609/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3345609/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(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,-fixfilepath parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=45ea92422c00496abca570ee92dd851e 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=3345609 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/tmp.OKlqpBxPuG/pbuilderrc_TbPR --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.OKlqpBxPuG/b2 --logfile b2/build.log plasmidid_1.6.3+dfsg-3.dsc' SUDO_GID=111 SUDO_UID=106 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 5.15.0-0.bpo.2-amd64 #1 SMP Debian 5.15.5-2~bpo11+1 (2022-01-02) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 2021 more -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Mar 16 16:56 sh -> bash lrwxrwxrwx 1 root root 4 Mar 13 05:46 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 2021 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/3345609/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 ... 19655 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: aragorn{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-config{a} fonts-circos-symbols{a} fonts-cmu{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hmmer{a} infernal{a} intltool-debian{a} java-common{a} less{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbio-searchio-hmmer-perl{a} libbrotli1{a} libbsd0{a} libcapnp-0.7.0{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} libdbus-1-3{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} libgd-perl{a} libgd3{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} libgsl25{a} libgslcblas0{a} libharfbuzz0b{a} libhts3{a} libicu67{a} libio-all-perl{a} libio-string-perl{a} libipc-system-simple-perl{a} libjbig0{a} libjpeg62-turbo{a} liblcms2-2{a} libldap-2.4-2{a} liblist-allutils-perl{a} liblist-someutils-perl{a} liblist-utilsby-perl{a} libllvm11{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} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmd0{a} libmodule-implementation-perl{a} libmodule-runtime-perl{a} libmpdec3{a} libmurmurhash2{a} libncbi6{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libnumber-format-perl{a} libparams-classify-perl{a} libparams-validate-perl{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpng16-16{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{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} libsigsegv2{a} libspiffy-perl{a} libssh2-1{a} libstatistics-basic-perl{a} libsub-override-perl{a} libsvg-perl{a} libswiss-perl{a} libtbb2{a} libtext-format-perl{a} libtiff5{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libvulkan1{a} libwebp6{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{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} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{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-11-jre{a} openjdk-11-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} python3.9{a} python3.9-minimal{a} readline-common{a} samtools{a} sensible-utils{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 libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl 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 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 mesa-vulkan-drivers perl-tk psmisc publicsuffix shared-mime-info systemd systemd-cron wget xdg-user-dirs 0 packages upgraded, 216 newly installed, 0 to remove and 0 not upgraded. Need to get 183 MB of archives. After unpacking 829 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 less amd64 551-2 [133 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1k-1+deb11u1 [851 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 aragorn amd64 1.2.38-4 [86.7 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 bedtools amd64 2.30.0+dfsg-1 [663 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5 [124 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5 [58.4 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.20-2 [219 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5 [62.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u1 [350 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u1 [1305 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.12+7-2 [37.3 MB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909 [15.7 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-3 [522 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 fonts-circos-symbols all 0.69.9+dfsg-2 [46.7 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 fonts-cmu all 0.7.0-4 [4891 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libregexp-common-perl all 2017060201-1 [177 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libcarp-always-perl all 0.16-1 [9620 B] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libconfig-general-perl all 2.63-1 [70.5 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libdata-dumper-simple-perl all 0.11-5.1 [13.1 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1 [289 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libgd3 amd64 2.3.0-2 [137 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libgd-perl amd64 2.73-1+b1 [141 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libgetopt-simple-perl all 1.52-5.1 [15.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libmath-bezier-perl all 0.01-2.1 [7096 B] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libmath-round-perl all 0.07-1.1 [10.1 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libparams-validate-perl amd64 1.30-1+b1 [68.2 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libreadonly-perl all 2.050-3 [23.1 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libset-intspan-perl all 1.19-1.1 [26.3 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 liblist-allutils-perl all 0.18-1 [40.7 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libmath-vec-perl all 1.01-3.1 [18.0 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libio-all-perl all 0.87-1 [66.7 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libmath-vecstat-perl all 0.08-2.1 [8648 B] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libgraphics-colornames-perl all 3.5.0-3 [32.1 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libgraphics-colorobject-perl all 0.5.0-10 [29.1 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libtext-format-perl all 0.62-1 [22.7 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libclone-perl amd64 0.45-1+b1 [15.4 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libnumber-format-perl all 1.75-1.1 [29.5 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libstatistics-basic-perl all 1.6611-1.1 [62.2 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libsvg-perl all 2.85-1 [64.4 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 circos all 0.69.9+dfsg-2 [14.0 MB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1 [203 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libgif7 amd64 5.1.9-2 [45.1 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre amd64 11.0.12+7-2 [176 kB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 default-jre amd64 2:1.11-72 [1044 B] Get: 173 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 174 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 176 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 177 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 178 http://deb.debian.org/debian bullseye/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get: 179 http://deb.debian.org/debian bullseye/main amd64 infernal amd64 1.1.4-1 [5523 kB] Get: 180 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 181 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 182 http://deb.debian.org/debian bullseye/main amd64 libbio-searchio-hmmer-perl all 1.7.3-2 [95.9 kB] Get: 183 http://deb.debian.org/debian bullseye/main amd64 libcapnp-0.7.0 amd64 0.7.0-7 [1048 kB] Get: 184 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 185 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 186 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 187 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 188 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 189 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 190 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 191 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 192 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get: 193 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get: 194 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 195 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 196 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get: 197 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get: 198 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get: 199 http://deb.debian.org/debian bullseye/main amd64 libmurmurhash2 amd64 1.5-2 [5780 B] Get: 200 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 201 http://deb.debian.org/debian bullseye/main amd64 libncbi6 amd64 6.1.20170106+dfsg1-9 [4066 kB] Get: 202 http://deb.debian.org/debian bullseye/main amd64 libswiss-perl all 1.79-3 [773 kB] Get: 203 http://deb.debian.org/debian bullseye/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get: 204 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get: 205 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get: 206 http://deb.debian.org/debian bullseye/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB] Get: 207 http://deb.debian.org/debian bullseye/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get: 208 http://deb.debian.org/debian bullseye/main amd64 mash amd64 2.2.2+dfsg-2 [153 kB] Get: 209 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get: 210 http://deb.debian.org/debian bullseye/main amd64 ncbi-tools-bin amd64 6.1.20170106+dfsg1-9 [1943 kB] Get: 211 http://deb.debian.org/debian bullseye/main amd64 sysstat amd64 12.5.2-2 [603 kB] Get: 212 http://deb.debian.org/debian bullseye/main amd64 parallel all 20161222-1.1 [306 kB] Get: 213 http://deb.debian.org/debian bullseye/main amd64 prodigal amd64 1:2.6.3-4 [695 kB] Get: 214 http://deb.debian.org/debian bullseye/main amd64 prokka amd64 1.14.6+dfsg-3 [9968 kB] Get: 215 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 216 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Fetched 183 MB in 5s (35.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Selecting previously unselected package samtools. Preparing to unpack .../198-samtools_1.11-1_amd64.deb ... Unpacking samtools (1.11-1) ... Setting up cd-hit (4.8.1-3) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up liblmdb0:amd64 (0.9.24-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up aragorn (1.2.38-4) ... Setting up liblcms2-2:amd64 (2.12~rc1-2) ... Setting up ncbi-data (6.1.20170106+dfsg1-9) ... Setting up libpciaccess0:amd64 (0.16-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libconfig-general-perl (2.63-1) ... Setting up libset-intspan-perl (1.19-1.1) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up java-common (0.72) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libdynaloader-functions-perl (0.003-1.1) ... Setting up libgslcblas0:amd64 (2.6+dfsg-2) ... Setting up libmurmurhash2:amd64 (1.5-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libgsl25:amd64 (2.6+dfsg-2) ... Setting up prodigal (1:2.6.3-4) ... Setting up libclone-perl (0.45-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libgetopt-simple-perl (1.52-5.1) ... Setting up libglib2.0-0:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libglvnd0:amd64 (1.3.2-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libtbb2:amd64 (2020.3-1) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.30-1) ... Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up less (551-2) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up libsvg-perl (2.85-1) ... Setting up gettext-base (0.21-4) ... Setting up libnumber-format-perl (1.75-1.1) ... Setting up file (1:5.39-3) ... Setting up libcapnp-0.7.0:amd64 (0.7.0-7) ... Setting up liblist-utilsby-perl (0.11-1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libregexp-common-perl (2017060201-1) ... Setting up libmath-bezier-perl (0.01-2.1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up libasound2-data (1.2.4-1.1) ... Setting up infernal (1.1.4-1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up libreadonly-perl (2.050-3) ... Setting up fonts-cmu (0.7.0-4) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:amd64 (4.8.10-1) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1) ... Setting up libnspr4:amd64 (2:4.29-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libavahi-common-data:amd64 (0.8-5) ... Setting up libncurses6:amd64 (6.2+20201114-2) ... Setting up libdbus-1-3:amd64 (1.12.20-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libdata-dumper-simple-perl (0.11-5.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up mash (2.2.2+dfsg-2) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libmath-vecstat-perl (0.08-2.1) ... Setting up libpcsclite1:amd64 (1.9.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libglapi-mesa:amd64 (20.3.5-1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up libvulkan1:amd64 (1.2.162.0-1) ... Setting up libmath-round-perl (0.07-1.1) ... Setting up libgif7:amd64 (5.1.9-2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libasound2:amd64 (1.2.4-1.1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libtext-format-perl (0.62-1) ... Setting up libswiss-perl (1.79-3) ... Setting up libcarp-always-perl (0.16-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libtiff5:amd64 (4.2.0-1) ... Setting up libgraphics-colornames-perl (3.5.0-3) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up fonts-circos-symbols (0.69.9+dfsg-2) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up openssl (1.1.1k-1+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libdrm-common (2.4.104-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up bedtools (2.30.0+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libmath-vec-perl (1.01-3.1) ... Setting up libstatistics-basic-perl (1.6611-1.1) ... Setting up libncbi6:amd64 (6.1.20170106+dfsg1-9) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.14-3) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up gettext (0.21-4) ... Setting up libxcb-xfixes0:amd64 (1.14-3) ... Setting up libtool (2.4.6-15) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libxcb-glx0:amd64 (1.14-3) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libavahi-common3:amd64 (0.8-5) ... Setting up libgraphics-colorobject-perl (0.5.0-10) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Setting up libnss3:amd64 (2:3.61-1+deb11u1) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up libio-all-perl (0.87-1) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up libxcb-present0:amd64 (1.14-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libbio-searchio-hmmer-perl (1.7.3-2) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1) ... Setting up libxcb-sync1:amd64 (1.14-3) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up libxcb-dri2-0:amd64 (1.14-3) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libdrm2:amd64 (2.4.104-1) ... Setting up dwz (0.13+20210201-1) ... Setting up ncbi-tools-bin (6.1.20170106+dfsg1-9) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up sysstat (12.5.2-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libavahi-client3:amd64 (0.8-5) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.104-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:amd64 (1.14-3) ... Setting up libx11-xcb1:amd64 (2:1.7.2-1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libdrm-nouveau2:amd64 (2.4.104-1) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libdrm-radeon1:amd64 (2.4.104-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libdrm-intel1:amd64 (2.4.104-1) ... Setting up libgl1-mesa-dri:amd64 (20.3.5-1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... 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 samtools (1.11-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dh-autoreconf (20) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up parallel (20161222-1.1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+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 (2.3.3op2-3+deb11u1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up liblist-allutils-perl (0.18-1) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libparams-validate-perl:amd64 (1.30-1+b1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-all (3.9.2-3) ... Setting up libgd-perl (2.73-1+b1) ... Setting up circos (0.69.9+dfsg-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:amd64 (11.0.12+7-2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:amd64 (11.0.12+7-2) ... Setting up default-jre (2:1.11-72) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up prokka (1.14.6+dfsg-3) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 I: Building the package hostname: Name or service not known I: Running cd /build/plasmidid-1.6.3+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_1.6.3+dfsg-3_source.changes dpkg-buildpackage: info: source package plasmidid dpkg-buildpackage: info: source version 1.6.3+dfsg-3 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-1.6.3+dfsg' dh_auto_clean rm -f debian/plasmidID.1 rm -rf NO_GROUP/ TEST_DATA/plasmids_TEST_database.fasta.length TEST_DATA/plasmids_TEST_database.length debian/patches/fixTest.patch path make[1]: Leaving directory '/build/plasmidid-1.6.3+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-1.6.3+dfsg' PATH=$PATH:/build/plasmidid-1.6.3+dfsg/bin TEST_DATA/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:1.6.3 ------------------ CHECKING DEPENDENCIES AND MANDATORY FILES DEPENDENCY STATUS ---------- ------ blastn INSTALLED bowtie2-build INSTALLED bowtie2 INSTALLED bedtools INSTALLED prokka INSTALLED samtools INSTALLED mash INSTALLED circos INSTALLED Default output directory is: /build/plasmidid-1.6.3+dfsg Log will be saved in: /build/plasmidid-1.6.3+dfsg/NO_GROUP/KPN/logs/plasmidID.log No trim selected, skipping trimming step Contigs supplied, ommiting assembly step ------------------ #Pipeline summary# ------------------ Reads R1 KPN_TEST_R1.fastq.gz Reads R2 KPN_TEST_R2.fastq.gz Will be mapped with ddbb plasmids_TEST_database.fasta Entries covered more than 80 % Will be clustered by 0.5 % identity And used to reconstruct contigs in contigs_KPN_TEST.fasta  STARTING KMER FILTERING, CLUSTERING and MAPPING  SCREENING READS WITH KMERS (Thu Mar 16 17:00:30 +14 2023) Reads will be screened against database supplied for further filtering and mapping, this will reduce the input sequences to map against KPN CLUSTERING SEQUENCES BY KMER DISTANCE (Thu Mar 16 17:00:47 +14 2023) Sequences obtained after screen will be clustered to reduce redundancy, one representative, the largest, will be considered for further analysis KPN --------------------------------------- ERROR in Script plasmidID on or near line 602; exiting with status 1 MESSAGE: See /build/plasmidid-1.6.3+dfsg/logs/plasmidID.log for more information. command:mashclust.py -i /build/plasmidid-1.6.3+dfsg/NO_GROUP/KPN/kmer/database.filtered_0.95_term.fasta -d 0.5 --------------------------------------- make[1]: Leaving directory '/build/plasmidid-1.6.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/plasmidid-1.6.3+dfsg' dh_auto_install help2man -i debian/plasmidID.h2m ./plasmidID > debian/plasmidID.1 make[1]: Leaving directory '/build/plasmidid-1.6.3+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_1.6.3+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../plasmidid_1.6.3+dfsg-3_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/3345609/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3345609/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/3345609 and its subdirectories I: Current time: Thu Mar 16 17:01:07 +14 2023 I: pbuilder-time-stamp: 1678935667