Start: 2024-03-03 23:46:43 GMT [bullseye] Package: plasmidid Version: 1.6.3+dfsg-3 Installed-Size: 329 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos Recommends: trimmomatic, spades, python3-biopython, python3-numpy, python3-pandas Description: mapping-based, assembly-assisted plasmid identification tool Homepage: https://github.com/BU-ISCIII/plasmidID Description-md5: d2e67d45c872bf3607006dab611aef29 Section: science Priority: optional Filename: pool/main/p/plasmidid/plasmidid_1.6.3+dfsg-3_amd64.deb Size: 46260 MD5sum: 65edb80eb775247aefd5c4723726237c SHA256: f0f9333c1598a988b82bf851f6397017ac5acb1b12448862ddd57b71ba4dd0a8 [bullseye-next] Package: plasmidid Version: 1.6.3+dfsg-3 Installed-Size: 329 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos Recommends: trimmomatic, spades, python3-biopython, python3-numpy, python3-pandas Description: mapping-based, assembly-assisted plasmid identification tool Homepage: https://github.com/BU-ISCIII/plasmidID Description-md5: d2e67d45c872bf3607006dab611aef29 Section: science Priority: optional Filename: pool/main/p/plasmidid/plasmidid_1.6.3+dfsg-3_amd64.deb Size: 46260 MD5sum: 65edb80eb775247aefd5c4723726237c SHA256: f0f9333c1598a988b82bf851f6397017ac5acb1b12448862ddd57b71ba4dd0a8 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt plasmidid=1.6.3+dfsg-3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.3.1~202401311836~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt plasmidid=1.6.3+dfsg-3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpzzf932kc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpzzf932kc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpzzf932kc/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s INFO: Running scripts post_setup 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m3.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 0m4.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 0m4.2s INFO: Running scripts is_testable 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s INFO: Running scripts pre_test 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_test_root_password'] 0m4.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_test_root_password'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m4.5s DUMP: Package: plasmidid Version: 1.6.3+dfsg-3 Installed-Size: 329 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos Recommends: trimmomatic, spades, python3-biopython, python3-numpy, python3-pandas Description-en: mapping-based, assembly-assisted plasmid identification tool PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. . PlasmidID is a computational pipeline that maps Illumina reads over plasmid database sequences. The k-mer filtered, most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a circular image which allow user to determine plasmidic composition in any bacterial sample. Description-md5: d2e67d45c872bf3607006dab611aef29 Homepage: https://github.com/BU-ISCIII/plasmidID Section: science Priority: optional Filename: pool/main/p/plasmidid/plasmidid_1.6.3+dfsg-3_amd64.deb Size: 46260 MD5sum: 65edb80eb775247aefd5c4723726237c SHA256: f0f9333c1598a988b82bf851f6397017ac5acb1b12448862ddd57b71ba4dd0a8 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m4.5s INFO: apt-cache knows about the following packages: plasmidid 0m4.5s INFO: Running scripts pre_install 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy'] 0m4.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy', 'plasmidid'] 0m4.6s DUMP: plasmidid: Installed: (none) Candidate: 1.6.3+dfsg-3 Version table: 1.6.3+dfsg-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy', 'plasmidid'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-y', 'install', 'plasmidid'] 0m58.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: aragorn bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos default-jre default-jre-headless fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core hmmer infernal java-common less libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libbsd0 libcapnp-0.7.0 libcarp-always-perl libclone-perl libconfig-general-perl libcups2 libcurl3-gnutls libdata-dumper-simple-perl libdata-stag-perl libdbus-1-3 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdynaloader-functions-perl libedit2 libelf1 libexpat1 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libgd-perl libgd3 libgdbm-compat4 libgdbm6 libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl25 libgslcblas0 libharfbuzz0b libhts3 libicu67 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo liblcms2-2 libldap-2.4-2 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm11 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmodule-implementation-perl libmodule-runtime-perl libmpdec3 libmurmurhash2 libncbi6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libnumber-format-perl libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.32 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libspiffy-perl libsqlite3-0 libssh2-1 libstatistics-basic-perl libsvg-perl libswiss-perl libtbb2 libtext-format-perl libtiff5 libtry-tiny-perl libvulkan1 libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libz3-4 mash media-types ncbi-blast+ ncbi-data ncbi-tools-bin openjdk-11-jre openjdk-11-jre-headless openssl parallel perl perl-modules-5.32 procps prodigal prokka python3 python3-minimal python3.9 python3.9-minimal readline-common samtools sensible-utils sysstat ucf x11-common xz-utils Suggested packages: bowtie2-examples hmmer-doc libasound2-plugins alsa-utils bioperl libxml-sax-expatxs-perl cups-common libxml-parser-perl libgd-tools gdbm-l10n gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libdb-file-lock-perl libfile-mimeinfo-perl libfile-readbackwards-perl libfreezethaw-perl libmldbm-perl liblcms2-utils libscalar-number-perl pciutils pcscd lm-sensors libvibrant6b ncbi-cn3d ncbi-tools-x11 libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binutils binfmt-support readline-doc cwltool isag Recommended packages: circos-tools alsa-ucm-conf alsa-topology-conf bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl libwww-perl perl-tk libxml-libxslt-perl libmldbm-perl libxml-perl dbus libglib2.0-data shared-mime-info xdg-user-dirs libpod-coverage-perl libtest-pod-perl libldap-common liblist-someutils-xs-perl libgpm2 publicsuffix libsasl2-modules libcgi-pm-perl mesa-vulkan-drivers | vulkan-icd libxml-sax-expat-perl libatk-wrapper-java-jni fonts-dejavu-extra netbase trimmomatic spades python3-biopython python3-numpy python3-pandas psmisc systemd | cron | cron-daemon The following NEW packages will be installed: aragorn bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos default-jre default-jre-headless fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core hmmer infernal java-common less libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libbsd0 libcapnp-0.7.0 libcarp-always-perl libclone-perl libconfig-general-perl libcups2 libcurl3-gnutls libdata-dumper-simple-perl libdata-stag-perl libdbus-1-3 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdynaloader-functions-perl libedit2 libelf1 libexpat1 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libgd-perl libgd3 libgdbm-compat4 libgdbm6 libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl25 libgslcblas0 libharfbuzz0b libhts3 libicu67 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo liblcms2-2 libldap-2.4-2 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm11 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmodule-implementation-perl libmodule-runtime-perl libmpdec3 libmurmurhash2 libncbi6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libnumber-format-perl libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.32 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libspiffy-perl libsqlite3-0 libssh2-1 libstatistics-basic-perl libsvg-perl libswiss-perl libtbb2 libtext-format-perl libtiff5 libtry-tiny-perl libvulkan1 libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libz3-4 mash media-types ncbi-blast+ ncbi-data ncbi-tools-bin openjdk-11-jre openjdk-11-jre-headless openssl parallel perl perl-modules-5.32 plasmidid procps prodigal prokka python3 python3-minimal python3.9 python3.9-minimal readline-common samtools sensible-utils sysstat ucf x11-common xz-utils 0 upgraded, 193 newly installed, 0 to remove and 0 not upgraded. Need to get 183 MB of archives. After this operation, 852 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 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 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 less amd64 551-2 [133 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 xz-utils amd64 5.2.5-2.1~deb11u1 [220 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 aragorn amd64 1.2.38-4 [86.7 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 bedtools amd64 2.30.0+dfsg-1 [663 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5+deb11u2 [124 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5+deb11u2 [58.7 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.28-0+deb11u1 [223 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5+deb11u2 [62.6 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u6 [351 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u3 [1305 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.22+7-1~deb11u1 [38.2 MB] Get:56 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909+deb11u1 [15.9 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-3 [522 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 fonts-circos-symbols all 0.69.9+dfsg-2 [46.7 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 fonts-cmu all 0.7.0-4 [4891 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libregexp-common-perl all 2017060201-1 [177 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libcarp-always-perl all 0.16-1 [9620 B] Get:64 http://deb.debian.org/debian bullseye/main amd64 libconfig-general-perl all 2.63-1 [70.5 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libdata-dumper-simple-perl all 0.11-5.1 [13.1 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libxpm4 amd64 1:3.5.12-1.1+deb11u1 [50.0 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libgd3 amd64 2.3.0-2 [137 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libgd-perl amd64 2.73-1+b1 [141 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libgetopt-simple-perl all 1.52-5.1 [15.7 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libmath-bezier-perl all 0.01-2.1 [7096 B] Get:82 http://deb.debian.org/debian bullseye/main amd64 libmath-round-perl all 0.07-1.1 [10.1 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 libparams-validate-perl amd64 1.30-1+b1 [68.2 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 libreadonly-perl all 2.050-3 [23.1 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 libset-intspan-perl all 1.19-1.1 [26.3 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 liblist-allutils-perl all 0.18-1 [40.7 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 libmath-vec-perl all 1.01-3.1 [18.0 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libio-all-perl all 0.87-1 [66.7 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 libmath-vecstat-perl all 0.08-2.1 [8648 B] Get:102 http://deb.debian.org/debian bullseye/main amd64 libgraphics-colornames-perl all 3.5.0-3 [32.1 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libgraphics-colorobject-perl all 0.5.0-10 [29.1 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libtext-format-perl all 0.62-1 [22.7 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 libclone-perl amd64 0.45-1+b1 [15.4 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 libnumber-format-perl all 1.75-1.1 [29.5 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 libstatistics-basic-perl all 1.6611-1.1 [62.2 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 libsvg-perl all 2.85-1 [64.4 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 circos all 0.69.9+dfsg-2 [14.0 MB] Get:112 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1+deb11u2 [204 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:128 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get:138 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 libgif7 amd64 5.1.9-2 [45.1 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre amd64 11.0.22+7-1~deb11u1 [194 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 default-jre amd64 2:1.11-72 [1044 B] Get:152 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 infernal amd64 1.1.4-1 [5523 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 libbio-searchio-hmmer-perl all 1.7.3-2 [95.9 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 libcapnp-0.7.0 amd64 0.7.0-7 [1048 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u11 [344 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 libmurmurhash2 amd64 1.5-2 [5780 B] Get:176 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 libncbi6 amd64 6.1.20170106+dfsg1-9 [4066 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 libswiss-perl all 1.79-3 [773 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:181 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:182 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:183 http://deb.debian.org/debian bullseye/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB] Get:184 http://deb.debian.org/debian bullseye/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:185 http://deb.debian.org/debian bullseye/main amd64 mash amd64 2.2.2+dfsg-2 [153 kB] Get:186 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get:187 http://deb.debian.org/debian bullseye/main amd64 ncbi-tools-bin amd64 6.1.20170106+dfsg1-9 [1943 kB] Get:188 http://deb.debian.org/debian bullseye/main amd64 sysstat amd64 12.5.2-2 [603 kB] Get:189 http://deb.debian.org/debian bullseye/main amd64 parallel all 20161222-1.1 [306 kB] Get:190 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:191 http://deb.debian.org/debian bullseye/main amd64 prodigal amd64 1:2.6.3-4 [695 kB] Get:192 http://deb.debian.org/debian bullseye/main amd64 prokka amd64 1.14.6+dfsg-3 [9968 kB] Get:193 http://deb.debian.org/debian bullseye/main amd64 plasmidid amd64 1.6.3+dfsg-3 [46.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 183 MB in 15s (12.5 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6672 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.19-2_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.19-2) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../3-libperl5.32_5.32.1-4+deb11u3_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4+deb11u3) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl (5.32.1-4+deb11u3) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 8937 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.2+20201114-2+deb11u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.34.1-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.34.1-3) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 9375 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package less. Preparing to unpack .../001-less_551-2_amd64.deb ... Unpacking less (551-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../002-libncurses6_6.2+20201114-2+deb11u2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../003-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_1.1.1w-0+deb11u1_amd64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package ucf. Preparing to unpack .../008-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package xz-utils. Preparing to unpack .../009-xz-utils_5.2.5-2.1~deb11u1_amd64.deb ... Unpacking xz-utils (5.2.5-2.1~deb11u1) ... Selecting previously unselected package aragorn. Preparing to unpack .../010-aragorn_1.2.38-4_amd64.deb ... Unpacking aragorn (1.2.38-4) ... Selecting previously unselected package bedtools. Preparing to unpack .../011-bedtools_2.30.0+dfsg-1_amd64.deb ... Unpacking bedtools (2.30.0+dfsg-1) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../012-libtbb2_2020.3-1_amd64.deb ... Unpacking libtbb2:amd64 (2020.3-1) ... Selecting previously unselected package bowtie2. Preparing to unpack .../013-bowtie2_2.4.2-2+b3_amd64.deb ... Unpacking bowtie2 (2.4.2-2+b3) ... Selecting previously unselected package java-common. Preparing to unpack .../014-java-common_0.72_all.deb ... Unpacking java-common (0.72) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../015-libavahi-common-data_0.8-5+deb11u2_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.8-5+deb11u2) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../016-libavahi-common3_0.8-5+deb11u2_amd64.deb ... Unpacking libavahi-common3:amd64 (0.8-5+deb11u2) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../017-libdbus-1-3_1.12.28-0+deb11u1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.12.28-0+deb11u1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../018-libavahi-client3_0.8-5+deb11u2_amd64.deb ... Unpacking libavahi-client3:amd64 (0.8-5+deb11u2) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../019-libcups2_2.3.3op2-3+deb11u6_amd64.deb ... Unpacking libcups2:amd64 (2.3.3op2-3+deb11u6) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../020-liblcms2-2_2.12~rc1-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.12~rc1-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../021-libjpeg62-turbo_1%3a2.0.6-4_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.0.6-4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../022-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../023-libpng16-16_1.6.37-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../024-libfreetype6_2.10.4+dfsg-1+deb11u1_amd64.deb ... Unpacking libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../025-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../026-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../027-libfontconfig1_2.13.1-4.2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-4.2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../028-libnspr4_2%3a4.29-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.29-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../029-libnss3_2%3a3.61-1+deb11u3_amd64.deb ... Unpacking libnss3:amd64 (2:3.61-1+deb11u3) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../030-libasound2-data_1.2.4-1.1_all.deb ... Unpacking libasound2-data (1.2.4-1.1) ... Selecting previously unselected package libasound2:amd64. Preparing to unpack .../031-libasound2_1.2.4-1.1_amd64.deb ... Unpacking libasound2:amd64 (1.2.4-1.1) ... Selecting previously unselected package libglib2.0-0:amd64. 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Unpacking libmurmurhash2:amd64 (1.5-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../157-ncbi-data_6.1.20170106+dfsg1-9_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-9) ... Selecting previously unselected package libncbi6:amd64. Preparing to unpack .../158-libncbi6_6.1.20170106+dfsg1-9_amd64.deb ... Unpacking libncbi6:amd64 (6.1.20170106+dfsg1-9) ... Selecting previously unselected package libswiss-perl. Preparing to unpack .../159-libswiss-perl_1.79-3_all.deb ... Unpacking libswiss-perl (1.79-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../160-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../161-libxml-namespacesupport-perl_1.12-1.1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1.1) ... Selecting previously unselected package libxml-sax-base-perl. 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Setting up libglvnd0:amd64 (1.3.2-1) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u3) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libtbb2:amd64 (2020.3-1) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up less (551-2) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libcapnp-0.7.0:amd64 (0.7.0-7) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libasound2-data (1.2.4-1.1) ... Setting up infernal (1.1.4-1) ... Setting up fonts-cmu (0.7.0-4) ... 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+deb11u2) ... Setting up libnspr4:amd64 (2:4.29-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:amd64 (0.8-5+deb11u2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libdbus-1-3:amd64 (1.12.28-0+deb11u1) ... Setting up xz-utils (5.2.5-2.1~deb11u1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up mash (2.2.2+dfsg-2) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libpcsclite1:amd64 (1.9.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libglapi-mesa:amd64 (20.3.5-1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libvulkan1:amd64 (1.2.162.0-1) ... Setting up libgif7:amd64 (5.1.9-2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libasound2:amd64 (1.2.4-1.1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u5) ... Setting up fonts-circos-symbols (0.69.9+dfsg-2) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... 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+deb11u4) ... Setting up bedtools (2.30.0+dfsg-1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libncbi6:amd64 (6.1.20170106+dfsg1-9) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.14-3) ... Setting up libxcb-xfixes0:amd64 (1.14-3) ... 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+deb11u2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Setting up libnss3:amd64 (2:3.61-1+deb11u3) ... Setting up libxcb-shm0:amd64 (1.14-3) ... 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 libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libxcb-sync1:amd64 (1.14-3) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up ucf (3.0043) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up libxcb-dri2-0:amd64 (1.14-3) ... Setting up libdrm2:amd64 (2.4.104-1) ... Setting up ncbi-tools-bin (6.1.20170106+dfsg1-9) ... 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+deb11u2) ... 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+deb11u2) ... 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 libxcb-dri3-0:amd64 (1.14-3) ... Setting up libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... 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 (1:3.5.12-1.1+deb11u1) ... 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 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 samtools (1.11-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up perl (5.32.1-4+deb11u3) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libdata-dumper-simple-perl (0.11-5.1) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up libmath-vecstat-perl (0.08-2.1) ... Setting up parallel (20161222-1.1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libmath-round-perl (0.07-1.1) ... Setting up libcups2:amd64 (2.3.3op2-3+deb11u6) ... 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 libgraphics-colornames-perl (3.5.0-3) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up libmath-vec-perl (1.01-3.1) ... Setting up cd-hit (4.8.1-3) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up libconfig-general-perl (2.63-1) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libset-intspan-perl (1.19-1.1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up libdynaloader-functions-perl (0.003-1.1) ... Setting up libclone-perl (0.45-1+b1) ... Setting up libgetopt-simple-perl (1.52-5.1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libgraphics-colorobject-perl (0.5.0-10) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up libsvg-perl (2.85-1) ... Setting up python3 (3.9.2-3) ... Setting up libnumber-format-perl (1.75-1.1) ... Setting up libio-all-perl (0.87-1) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up liblist-utilsby-perl (0.11-1) ... Setting up libregexp-common-perl (2017060201-1) ... Setting up libmath-bezier-perl (0.01-2.1) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up ncbi-blast+ (2.11.0+ds-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 libgl1:amd64 (1.3.2-1) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libstatistics-basic-perl (1.6611-1.1) ... Setting up libparams-classify-perl (0.015-1+b3) ... 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 libgd-perl (2.73-1+b1) ... Setting up libbio-searchio-hmmer-perl (1.7.3-2) ... Setting up libmodule-runtime-perl (0.016-1) ... 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 libmodule-implementation-perl (0.09-1.1) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up liblist-allutils-perl (0.18-1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libparams-validate-perl:amd64 (1.30-1+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 (11.0.22+7-1~deb11u1) ... 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 (11.0.22+7-1~deb11u1) ... Setting up default-jre (2:1.11-72) ... Setting up ca-certificates-java (20190909+deb11u1) ... 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) ... Setting up plasmidid (1.6.3+dfsg-3) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 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. 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-y', 'install', 'plasmidid'] 0m58.0s INFO: Running scripts post_install 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_install_exceptions'] 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_install_exceptions'] 0m58.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 0m58.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 0m58.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpzzf932kc to bullseye-next 0m58.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m58.7s INFO: Running scripts pre_distupgrade 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'update'] 1m0.5s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Get:2 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:3 http://security.debian.org bullseye-security InRelease [48.4 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:6 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:7 http://security.debian.org bullseye-security/main amd64 Packages [269 kB] Get:8 http://security.debian.org bullseye-security/main Translation-en [174 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [15.6 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [11.6 kB] Fetched 646 kB in 1s (699 kB/s) Reading package lists... 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'update'] 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-yf', 'dist-upgrade'] 1m0.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-yf', 'dist-upgrade'] 1m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m1.2s DUMP: e8da8b99e6a2f501b5aeecfc4f2a03a0 - 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 1m1.4s DUMP: Package: plasmidid Version: 1.6.3+dfsg-3 Installed-Size: 329 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos Recommends: trimmomatic, spades, python3-biopython, python3-numpy, python3-pandas Description-en: mapping-based, assembly-assisted plasmid identification tool PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. . PlasmidID is a computational pipeline that maps Illumina reads over plasmid database sequences. The k-mer filtered, most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a circular image which allow user to determine plasmidic composition in any bacterial sample. Description-md5: d2e67d45c872bf3607006dab611aef29 Homepage: https://github.com/BU-ISCIII/plasmidID Section: science Priority: optional Filename: pool/main/p/plasmidid/plasmidid_1.6.3+dfsg-3_amd64.deb Size: 46260 MD5sum: 65edb80eb775247aefd5c4723726237c SHA256: f0f9333c1598a988b82bf851f6397017ac5acb1b12448862ddd57b71ba4dd0a8 1m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 1m1.4s INFO: apt-cache knows about the following packages: plasmidid 1m1.4s INFO: Running scripts pre_install 1m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_database-server'] 1m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_database-server'] 1m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_exceptions'] 1m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_exceptions'] 1m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_extras'] 1m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_extras'] 1m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy'] 1m1.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy'] 1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy', 'plasmidid'] 1m1.6s DUMP: plasmidid: Installed: 1.6.3+dfsg-3 Candidate: 1.6.3+dfsg-3 Version table: *** 1.6.3+dfsg-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy', 'plasmidid'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-y', 'install', 'plasmidid'] 1m2.1s DUMP: Reading package lists... Building dependency tree... Reading state information... plasmidid is already the newest version (1.6.3+dfsg-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-y', 'install', 'plasmidid'] 1m2.1s INFO: Running scripts post_install 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_install_exceptions'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_install_exceptions'] 1m2.1s INFO: Running scripts post_distupgrade 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_exceptions'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_exceptions'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_zz_backports'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_distupgrade_zz_backports'] 1m2.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m2.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m2.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m3.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m3.4s INFO: Running scripts pre_install 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_database-server'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_database-server'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_exceptions'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_exceptions'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_extras'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_extras'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy'] 1m3.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy', 'plasmidid'] 1m3.5s DUMP: plasmidid: Installed: 1.6.3+dfsg-3 Candidate: 1.6.3+dfsg-3 Version table: *** 1.6.3+dfsg-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-cache', 'policy', 'plasmidid'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-y', 'install', 'plasmidid=1.6.3+dfsg-3'] 1m3.9s DUMP: Reading package lists... Building dependency tree... Reading state information... plasmidid is already the newest version (1.6.3+dfsg-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', '-y', 'install', 'plasmidid=1.6.3+dfsg-3'] 1m3.9s INFO: Running scripts post_install 1m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_install_exceptions'] 1m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_install_exceptions'] 1m4.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m4.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m4.8s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 1m4.8s INFO: /bin converted to /usr/bin by /usr merge 1m4.8s INFO: /lib converted to /usr/lib by /usr merge 1m4.8s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m4.8s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m4.8s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m4.8s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m4.8s INFO: /lib/systemd/system-sleep converted to /usr/lib/systemd/system-sleep by /usr merge 1m4.8s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m4.8s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 1m4.8s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 1m4.8s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 1m4.8s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 1m4.8s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 1m4.8s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 1m4.8s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 1m4.8s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 1m4.8s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 1m4.8s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 1m4.8s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 1m4.8s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 1m4.8s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 1m4.8s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 1m4.8s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 1m4.8s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m4.8s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m4.8s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m4.8s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m4.8s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m4.8s INFO: /sbin converted to /usr/sbin by /usr merge 1m5.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', '-ac', '--ignore-obsolete'] 1m9.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', '-ac', '--ignore-obsolete'] 1m9.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.4s DUMP: 0.15.6 1m9.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m9.4s INFO: Running adequate version 0.15.6 now. 1m9.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'plasmidid'] 1m9.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'plasmidid'] 1m9.5s INFO: Running scripts pre_remove 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_exceptions'] 1m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/pre_remove_exceptions'] 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m15.8s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed aragorn aragorn 1.2.38-4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bedtools bedtools 2.30.0+dfsg-1 install ok installed bowtie2 bowtie2 2.4.2-2+b3 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed ca-certificates ca-certificates 20210119 install ok installed ca-certificates-java ca-certificates-java 20190909+deb11u1 install ok installed cd-hit cd-hit 4.8.1-3 install ok installed circos circos 0.69.9+dfsg-2 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed default-jre default-jre 2:1.11-72 install ok installed default-jre-headless default-jre-headless 2:1.11-72 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed fontconfig-config fontconfig-config 2.13.1-4.2 install ok installed fonts-circos-symbols fonts-circos-symbols 0.69.9+dfsg-2 install ok installed fonts-cmu fonts-cmu 0.7.0-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hmmer hmmer 3.3.2+dfsg-1 install ok installed hostname hostname 3.23 install ok installed infernal infernal 1.1.4-1 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed java-common java-common 0.72 install ok installed less less 551-2 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libasound2:amd64 libasound2 1.2.4-1.1 install ok installed libasound2-data libasound2-data 1.2.4-1.1 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-5+deb11u2 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-5+deb11u2 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-5+deb11u2 install ok installed libb-hooks-op-check-perl libb-hooks-op-check-perl 0.22-1+b3 install ok installed libbio-perl-perl libbio-perl-perl 1.7.7-2 install ok installed libbio-searchio-hmmer-perl libbio-searchio-hmmer-perl 1.7.3-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbsd0:amd64 libbsd0 0.11.3-1+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcapnp-0.7.0:amd64 libcapnp-0.7.0 0.7.0-7 install ok installed libcarp-always-perl libcarp-always-perl 0.16-1 install ok installed libclone-perl libclone-perl 0.45-1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libconfig-general-perl libconfig-general-perl 2.63-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libcups2:amd64 libcups2 2.3.3op2-3+deb11u6 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.74.0-1.3+deb11u11 install ok installed libdata-dumper-simple-perl libdata-dumper-simple-perl 0.11-5.1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.12.28-0+deb11u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libdeflate0:amd64 libdeflate0 1.7-1 install ok installed libdevel-callchecker-perl libdevel-callchecker-perl 0.008-1+b2 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-5 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.104-1 install ok installed libdrm-common libdrm-common 2.4.104-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.104-1 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.104-1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.104-1 install ok installed libdrm2:amd64 libdrm2 2.4.104-1 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.003-1.1 install ok installed libedit2:amd64 libedit2 3.1-20191231-2+b1 install ok installed libelf1:amd64 libelf1 0.183-1 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfile-basedir-perl libfile-basedir-perl 0.08-1 install ok installed libfont-ttf-perl libfont-ttf-perl 1.06-1.1 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-4.2 install ok installed libfreetype6:amd64 libfreetype6 2.10.4+dfsg-1+deb11u1 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgd-perl libgd-perl 2.73-1+b1 install ok installed libgd3:amd64 libgd3 2.3.0-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.19-2 install ok installed libgdbm6:amd64 libgdbm6 1.19-2 install ok installed libgetopt-simple-perl libgetopt-simple-perl 1.52-5.1 install ok installed libgif7:amd64 libgif7 5.1.9-2 install ok installed libgl1:amd64 libgl1 1.3.2-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 20.3.5-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 20.3.5-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.66.8-1+deb11u1 install ok installed libglvnd0:amd64 libglvnd0 1.3.2-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 20.3.5-1 install ok installed libglx0:amd64 libglx0 1.3.2-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgomp1:amd64 libgomp1 10.2.1-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgraphics-colornames-perl libgraphics-colornames-perl 3.5.0-3 install ok installed libgraphics-colorobject-perl libgraphics-colorobject-perl 0.5.0-10 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgsl25:amd64 libgsl25 2.6+dfsg-2 install ok installed libgslcblas0:amd64 libgslcblas0 2.6+dfsg-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.7.4-1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhts3:amd64 libhts3 1.11-4 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libio-all-perl libio-all-perl 0.87-1 install ok installed libio-string-perl libio-string-perl 1.08-3.1 install ok installed libipc-system-simple-perl libipc-system-simple-perl 1.30-1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.0.6-4 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblcms2-2:amd64 liblcms2-2 2.12~rc1-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed liblist-allutils-perl liblist-allutils-perl 0.18-1 install ok installed liblist-someutils-perl liblist-someutils-perl 0.58-1 install ok installed liblist-utilsby-perl liblist-utilsby-perl 0.11-1 install ok installed libllvm11:amd64 libllvm11 1:11.0.1-2 install ok installed liblmdb0:amd64 liblmdb0 0.9.24-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmath-bezier-perl libmath-bezier-perl 0.01-2.1 install ok installed libmath-round-perl libmath-round-perl 0.07-1.1 install ok installed libmath-vec-perl libmath-vec-perl 1.01-3.1 install ok installed libmath-vecstat-perl libmath-vecstat-perl 0.08-2.1 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmd0:amd64 libmd0 1.0.3-3 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-1.1 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libmurmurhash2:amd64 libmurmurhash2 1.5-2 install ok installed libncbi6:amd64 libncbi6 6.1.20170106+dfsg1-9 install ok installed libncurses6:amd64 libncurses6 6.2+20201114-2+deb11u2 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1+deb11u1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.29-1 install ok installed libnss3:amd64 libnss3 2:3.61-1+deb11u3 install ok installed libnumber-format-perl libnumber-format-perl 1.75-1.1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libparams-classify-perl libparams-classify-perl 0.015-1+b3 install ok installed libparams-validate-perl:amd64 libparams-validate-perl 1.30-1+b1 install ok installed libpciaccess0:amd64 libpciaccess0 0.16-1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libpcsclite1:amd64 libpcsclite1 1.9.1-1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libprocps8:amd64 libprocps8 2:3.3.17-5 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed libreadonly-perl libreadonly-perl 2.050-3 install ok installed libregexp-common-perl libregexp-common-perl 2017060201-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1+deb11u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1+deb11u1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsensors-config libsensors-config 1:3.6.0-7 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-7 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libset-intspan-perl libset-intspan-perl 1.19-1.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssh2-1:amd64 libssh2-1 1.9.0-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstatistics-basic-perl libstatistics-basic-perl 1.6611-1.1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsvg-perl libsvg-perl 2.85-1 install ok installed libswiss-perl libswiss-perl 1.79-3 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtbb2:amd64 libtbb2 2020.3-1 install ok installed libtext-format-perl libtext-format-perl 0.62-1 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.30-1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libvulkan1:amd64 libvulkan1 1.2.162.0-1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libx11-6:amd64 libx11-6 2:1.7.2-1+deb11u2 install ok installed libx11-data libx11-data 2:1.7.2-1+deb11u2 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.7.2-1+deb11u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.14-3 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.14-3 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.14-3 install ok installed libxcb-present0:amd64 libxcb-present0 1.14-3 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.14-3 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.14-3 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.14-3 install ok installed libxcb1:amd64 libxcb1 1.14-3 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.5-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1.1 install ok installed libxfixes3:amd64 libxfixes3 1:5.0.3-2 install ok installed libxi6:amd64 libxi6 2:1.7.10-1 install ok installed libxml-libxml-perl libxml-libxml-perl 2.0134+dfsg-2+b1 install ok installed libxml-namespacesupport-perl libxml-namespacesupport-perl 1.12-1.1 install ok installed libxml-sax-base-perl libxml-sax-base-perl 1.09-1.1 install ok installed libxml-sax-perl libxml-sax-perl 1.02+dfsg-1 install ok installed libxml-simple-perl libxml-simple-perl 2.25-1 install ok installed libxml2:amd64 libxml2 2.9.10+dfsg-6.7+deb11u4 install ok installed libxpm4:amd64 libxpm4 1:3.5.12-1.1+deb11u1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libz3-4:amd64 libz3-4 4.8.10-1 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mash mash 2.2.2+dfsg-2 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncbi-blast+ ncbi-blast+ 2.11.0+ds-1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-9 install ok installed ncbi-tools-bin ncbi-tools-bin 6.1.20170106+dfsg1-9 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed openjdk-11-jre:amd64 openjdk-11-jre 11.0.22+7-1~deb11u1 install ok installed openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.22+7-1~deb11u1 install ok installed openssl openssl 1.1.1w-0+deb11u1 install ok installed parallel parallel 20161222-1.1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.32.1-4+deb11u3 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed plasmidid plasmidid 1.6.3+dfsg-3 install ok installed procps procps 2:3.3.17-5 install ok installed prodigal prodigal 1:2.6.3-4 install ok installed prokka prokka 1.14.6+dfsg-3 install ok installed python3 python3 3.9.2-3 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.1-1 install ok installed samtools samtools 1.11-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.14 install ok installed sysstat sysstat 12.5.2-2 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed ucf ucf 3.0043 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed x11-common x11-common 1:7.7+22 install ok installed xz-utils xz-utils 5.2.5-2.1~deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 1m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'remove', 'aragorn', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'default-jre', 'default-jre-headless', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'hmmer', 'infernal', 'java-common', 'less', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-op-check-perl', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcapnp-0.7.0:amd64', 'libcarp-always-perl', 'libclone-perl', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libicu67:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libparams-classify-perl', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libtiff5:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-tools-bin', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'x11-common', 'xz-utils', 'plasmidid'] 1m19.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: aragorn bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos default-jre default-jre-headless fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core hmmer infernal java-common less libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libbsd0 libcapnp-0.7.0 libcarp-always-perl libclone-perl libconfig-general-perl libcups2 libcurl3-gnutls libdata-dumper-simple-perl libdata-stag-perl libdbus-1-3 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdynaloader-functions-perl libedit2 libelf1 libexpat1 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libgd-perl libgd3 libgdbm-compat4 libgdbm6 libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl25 libgslcblas0 libharfbuzz0b libhts3 libicu67 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo liblcms2-2 libldap-2.4-2 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm11 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmodule-implementation-perl libmodule-runtime-perl libmpdec3 libmurmurhash2 libncbi6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libnumber-format-perl libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.32 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libspiffy-perl libsqlite3-0 libssh2-1 libstatistics-basic-perl libsvg-perl libswiss-perl libtbb2 libtext-format-perl libtiff5 libtry-tiny-perl libvulkan1 libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libz3-4 mash media-types ncbi-blast+ ncbi-data ncbi-tools-bin openjdk-11-jre openjdk-11-jre-headless openssl parallel perl perl-modules-5.32 plasmidid procps prodigal prokka python3 python3-minimal python3.9 python3.9-minimal readline-common samtools sensible-utils sysstat ucf x11-common xz-utils 0 upgraded, 0 newly installed, 193 to remove and 0 not upgraded. After this operation, 852 MB disk space will be freed. (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 ... 15289 files and directories currently installed.) Removing plasmidid (1.6.3+dfsg-3) ... Removing prokka (1.14.6+dfsg-3) ... Removing aragorn (1.2.38-4) ... Removing bedtools (2.30.0+dfsg-1) ... Removing bowtie2 (2.4.2-2+b3) ... Removing default-jre (2:1.11-72) ... Removing openjdk-11-jre:amd64 (11.0.22+7-1~deb11u1) ... Removing default-jre-headless (2:1.11-72) ... Removing cd-hit (4.8.1-3) ... Removing circos (0.69.9+dfsg-2) ... Removing libgd-perl (2.73-1+b1) ... Removing libgd3:amd64 (2.3.0-2) ... Removing fonts-circos-symbols (0.69.9+dfsg-2) ... Removing fonts-cmu (0.7.0-4) ... Removing hmmer (3.3.2+dfsg-1) ... Removing infernal (1.1.4-1) ... Removing less (551-2) ... Removing libparams-validate-perl:amd64 (1.30-1+b1) ... Removing liblist-allutils-perl (0.18-1) ... Removing liblist-someutils-perl (0.58-1) ... Removing libmodule-implementation-perl (0.09-1.1) ... Removing libmodule-runtime-perl (0.016-1) ... Removing libparams-classify-perl (0.015-1+b3) ... Removing libdevel-callchecker-perl (0.008-1+b2) ... Removing libb-hooks-op-check-perl (0.22-1+b3) ... Removing libbio-searchio-hmmer-perl (1.7.3-2) ... Removing libbio-perl-perl (1.7.7-2) ... Removing samtools (1.11-1) ... Removing libhts3:amd64 (1.11-4) ... Removing libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Removing libgl1:amd64 (1.3.2-1) ... Removing libglx0:amd64 (1.3.2-1) ... Removing libglx-mesa0:amd64 (20.3.5-1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libgl1-mesa-dri:amd64 (20.3.5-1) ... Removing libllvm11:amd64 (1:11.0.1-2) ... Removing libedit2:amd64 (3.1-20191231-2+b1) ... Removing mash (2.2.2+dfsg-2) ... Removing libcapnp-0.7.0:amd64 (0.7.0-7) ... Removing libcarp-always-perl (0.16-1) ... Removing libclone-perl (0.45-1+b1) ... Removing libconfig-general-perl (2.63-1) ... Removing libdata-dumper-simple-perl (0.11-5.1) ... Removing libdata-stag-perl (0.14-2) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libdeflate0:amd64 (1.7-1) ... Removing libdivsufsort3:amd64 (2.0.1-5) ... Removing libdrm-amdgpu1:amd64 (2.4.104-1) ... Removing libdrm-intel1:amd64 (2.4.104-1) ... Removing libdrm-radeon1:amd64 (2.4.104-1) ... Removing libdrm-nouveau2:amd64 (2.4.104-1) ... Removing libdynaloader-functions-perl (0.003-1.1) ... Removing libelf1:amd64 (0.183-1) ... Removing ncbi-blast+ (2.11.0+ds-1) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libfile-basedir-perl (0.08-1) ... Removing libfont-ttf-perl (1.06-1.1) ... Removing parallel (20161222-1.1) ... Removing 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Removing 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Removing libswiss-perl (1.79-3) ... Removing libgraphics-colorobject-perl (0.5.0-10) ... Removing libgraphics-colornames-perl (3.5.0-3) ... Removing libxml-simple-perl (2.25-1) ... Removing libxml-libxml-perl (2.0134+dfsg-2+b1) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Unregistering 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 Removing libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::PurePerl with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Removing libxml-sax-base-perl (1.09-1.1) ... Removing libgetopt-simple-perl (1.52-5.1) ... Removing libgif7:amd64 (5.1.9-2) ... Removing libglapi-mesa:amd64 (20.3.5-1) ... Removing libglvnd0:amd64 (1.3.2-1) ... Removing libgomp1:amd64 (10.2.1-6) ... Removing libgsl25:amd64 (2.6+dfsg-2) ... Removing libgslcblas0:amd64 (2.6+dfsg-2) ... Removing libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Removing libicu67:amd64 (67.1-7) ... Removing libio-all-perl (0.87-1) ... Removing libio-string-perl (1.08-3.1) ... Removing libipc-system-simple-perl (1.30-1) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing liblist-utilsby-perl (0.11-1) ... Removing liblmdb0:amd64 (0.9.24-1) ... Removing libmath-bezier-perl (0.01-2.1) ... Removing libmath-round-perl (0.07-1.1) ... Removing libmath-vec-perl (1.01-3.1) ... Removing libmath-vecstat-perl (0.08-2.1) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-1) ... Removing libmurmurhash2:amd64 (1.5-2) ... Removing ncbi-tools-bin (6.1.20170106+dfsg1-9) ... Removing libncbi6:amd64 (6.1.20170106+dfsg1-9) ... Removing procps (2:3.3.17-5) ... Removing libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Removing libstatistics-basic-perl (1.6611-1.1) ... Removing libnumber-format-perl (1.75-1.1) ... Removing libpciaccess0:amd64 (0.16-1) ... Removing libprocps8:amd64 (2:3.3.17-5) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1-1) ... Removing libreadonly-perl (2.050-3) ... Removing libregexp-common-perl (2017060201-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing sysstat (12.5.2-2) ... Removing libsensors5:amd64 (1:3.6.0-7) ... Removing libsensors-config (1:3.6.0-7) ... Removing libset-intspan-perl (1.19-1.1) ... Removing libspiffy-perl (0.46-1) ... Removing libssh2-1:amd64 (1.9.0-2) ... Removing libsvg-perl (2.85-1) ... Removing libtbb2:amd64 (2020.3-1) ... Removing libtext-format-perl (0.62-1) ... Removing libtry-tiny-perl (0.30-1) ... Removing libvulkan1:amd64 (1.2.162.0-1) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... Removing libxcb-dri2-0:amd64 (1.14-3) ... Removing libxcb-dri3-0:amd64 (1.14-3) ... Removing libxcb-glx0:amd64 (1.14-3) ... Removing libxcb-present0:amd64 (1.14-3) ... Removing libxcb-shm0:amd64 (1.14-3) ... Removing libxcb-sync1:amd64 (1.14-3) ... Removing libxcb-xfixes0:amd64 (1.14-3) ... Removing libxdamage1:amd64 (1:1.1.5-2) ... Removing libxtst6:amd64 (2:1.2.3-1) ... Removing libxi6:amd64 (2:1.7.10-1) ... Removing libxext6:amd64 (2:1.3.3-1.1) ... Removing libxfixes3:amd64 (1:5.0.3-2) ... Removing libxml-namespacesupport-perl (1.12-1.1) ... Removing libxpm4:amd64 (1:3.5.12-1.1+deb11u1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libz3-4:amd64 (4.8.10-1) ... Removing media-types (4.0.0) ... Removing ncbi-data (6.1.20170106+dfsg1-9) ... Removing prodigal (1:2.6.3-4) ... Removing readline-common (8.1-1) ... Removing x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xz-utils (5.2.5-2.1~deb11u1) ... Removing libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Removing libxcb1:amd64 (1.14-3) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.3-1+deb11u1) ... Removing libdrm2:amd64 (2.4.104-1) ... Removing libdrm-common (2.4.104-1) ... Removing perl (5.32.1-4+deb11u3) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libgdbm-compat4:amd64 (1.19-2) ... Removing libgdbm6:amd64 (1.19-2) ... Removing libmd0:amd64 (1.0.3-3) ... Removing libx11-data (2:1.7.2-1+deb11u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing ca-certificates-java (20190909+deb11u1) ... Removing openjdk-11-jre-headless:amd64 (11.0.22+7-1~deb11u1) ... Removing ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libfontconfig1:amd64 (2.13.1-4.2) ... Removing fontconfig-config (2.13.1-4.2) ... Removing fonts-dejavu-core (2.37-2) ... Removing java-common (0.72) ... Removing libasound2:amd64 (1.2.4-1.1) ... Removing libasound2-data (1.2.4-1.1) ... Removing libcups2:amd64 (2.3.3op2-3+deb11u6) ... Removing libavahi-client3:amd64 (0.8-5+deb11u2) ... Removing libavahi-common3:amd64 (0.8-5+deb11u2) ... Removing libavahi-common-data:amd64 (0.8-5+deb11u2) ... Removing libharfbuzz0b:amd64 (2.7.4-1) ... Removing libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Removing libdbus-1-3:amd64 (1.12.28-0+deb11u1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing libglib2.0-0:amd64 (2.66.8-1+deb11u1) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libjpeg62-turbo:amd64 (1:2.0.6-4) ... Removing liblcms2-2:amd64 (2.12~rc1-2) ... Removing libnss3:amd64 (2:3.61-1+deb11u3) ... Removing libnspr4:amd64 (2:4.29-1) ... Removing libpcsclite1:amd64 (1.9.1-1) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libsqlite3-0:amd64 (3.34.1-3) ... Removing openssl (1.1.1w-0+deb11u1) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.14) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 1m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'remove', 'aragorn', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'default-jre', 'default-jre-headless', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'hmmer', 'infernal', 'java-common', 'less', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-op-check-perl', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcapnp-0.7.0:amd64', 'libcarp-always-perl', 'libclone-perl', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libicu67:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libparams-classify-perl', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libtiff5:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'ncbi-tools-bin', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'x11-common', 'xz-utils', 'plasmidid'] 1m19.9s INFO: Running scripts post_remove 1m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_remove_exceptions'] 1m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_remove_exceptions'] 1m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--purge', 'aragorn', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'default-jre', 'default-jre-headless', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'hmmer', 'infernal', 'java-common', 'less', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-op-check-perl', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcapnp-0.7.0:amd64', 'libcarp-always-perl', 'libclone-perl', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libicu67:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libparams-classify-perl', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libtiff5:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-tools-bin', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'x11-common', 'xz-utils'] 1m21.3s DUMP: dpkg: warning: ignoring request to remove aragorn which isn't installed dpkg: warning: ignoring request to remove bedtools which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed (Reading database ... 6831 files and directories currently installed.) Purging configuration files for ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20190909+deb11u1) ... dpkg: warning: ignoring request to remove cd-hit which isn't installed Purging configuration files for circos (0.69.9+dfsg-2) ... dpkg: warning: ignoring request to remove default-jre which isn't installed dpkg: warning: ignoring request to remove default-jre-headless which isn't installed Purging configuration files for fontconfig-config (2.13.1-4.2) ... dpkg: warning: ignoring request to remove fonts-circos-symbols which isn't installed dpkg: warning: ignoring request to remove fonts-cmu which isn't installed Purging configuration files for fonts-dejavu-core (2.37-2) ... dpkg: warning: ignoring request to remove hmmer which isn't installed dpkg: warning: ignoring request to remove infernal which isn't installed Purging configuration files for java-common (0.72) ... dpkg: warning: ignoring request to remove less which isn't installed dpkg: warning: ignoring request to remove libasound2 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libb-hooks-op-check-perl which isn't installed dpkg: warning: ignoring request to remove libbio-perl-perl which isn't installed dpkg: warning: ignoring request to remove libbio-searchio-hmmer-perl which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcapnp-0.7.0 which isn't installed dpkg: warning: ignoring request to remove libcarp-always-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libconfig-general-perl which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdata-dumper-simple-perl which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdevel-callchecker-perl which isn't installed dpkg: warning: ignoring request to remove libdivsufsort3 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm-intel1 which isn't installed dpkg: warning: ignoring request to remove libdrm-nouveau2 which isn't installed dpkg: warning: ignoring request to remove libdrm-radeon1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libdynaloader-functions-perl which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfile-basedir-perl which isn't installed dpkg: warning: ignoring request to remove libfont-ttf-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgd-perl which isn't installed dpkg: warning: ignoring request to remove libgd3 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgetopt-simple-perl which isn't installed dpkg: warning: ignoring request to remove libgif7 which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (20.3.5-1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.66.8-1+deb11u1) ... dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't installed dpkg: warning: ignoring request to remove libglx0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphics-colornames-perl which isn't installed dpkg: warning: ignoring request to remove libgraphics-colorobject-perl which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgsl25 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libio-all-perl which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libipc-system-simple-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove liblist-allutils-perl which isn't installed dpkg: warning: ignoring request to remove liblist-someutils-perl which isn't installed dpkg: warning: ignoring request to remove liblist-utilsby-perl which isn't installed dpkg: warning: ignoring request to remove libllvm11 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmath-bezier-perl which isn't installed dpkg: warning: ignoring request to remove libmath-round-perl which isn't installed dpkg: warning: ignoring request to remove libmath-vec-perl which isn't installed dpkg: warning: ignoring request to remove libmath-vecstat-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmd0 which isn't installed dpkg: warning: ignoring request to remove libmodule-implementation-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libmurmurhash2 which isn't installed dpkg: warning: ignoring request to remove libncbi6 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libnumber-format-perl which isn't installed dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libparams-validate-perl which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libprocps8 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libreadonly-perl which isn't installed dpkg: warning: ignoring request to remove libregexp-common-perl which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-7) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libset-intspan-perl which isn't installed dpkg: warning: ignoring request to remove libspiffy-perl which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libstatistics-basic-perl which isn't installed dpkg: warning: ignoring request to remove libsvg-perl which isn't installed dpkg: warning: ignoring request to remove libswiss-perl which isn't installed dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libtext-format-perl which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libx11-xcb1 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri2-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri3-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-glx0 which isn't installed dpkg: warning: ignoring request to remove libxcb-present0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb-sync1 which isn't installed dpkg: warning: ignoring request to remove libxcb-xfixes0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdamage1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxml-libxml-perl which isn't installed dpkg: warning: ignoring request to remove libxml-namespacesupport-perl which isn't installed dpkg: warning: ignoring request to remove libxml-sax-base-perl which isn't installed Purging configuration files for libxml-sax-perl (1.02+dfsg-1) ... dpkg: warning: ignoring request to remove libxml-simple-perl which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxpm4 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxshmfence1 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove mash which isn't installed Purging configuration files for media-types (4.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-9) ... dpkg: warning: ignoring request to remove ncbi-tools-bin which isn't installed dpkg: warning: ignoring request to remove openjdk-11-jre which isn't installed Purging configuration files for openjdk-11-jre-headless:amd64 (11.0.22+7-1~deb11u1) ... Purging configuration files for openssl (1.1.1w-0+deb11u1) ... Purging configuration files for parallel (20161222-1.1) ... Purging configuration files for perl (5.32.1-4+deb11u3) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for procps (2:3.3.17-5) ... dpkg: warning: ignoring request to remove prodigal which isn't installed dpkg: warning: ignoring request to remove prokka which isn't installed Purging configuration files for python3 (3.9.2-3) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.1-1) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sysstat (12.5.2-2) ... Purging configuration files for ucf (3.0043) ... Purging configuration files for x11-common (1:7.7+22) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed 1m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--purge', 'aragorn', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'default-jre', 'default-jre-headless', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'hmmer', 'infernal', 'java-common', 'less', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-op-check-perl', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcapnp-0.7.0:amd64', 'libcarp-always-perl', 'libclone-perl', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libicu67:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmd0:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libparams-classify-perl', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libspiffy-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libtiff5:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'ncbi-blast+', 'ncbi-data', 'ncbi-tools-bin', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'x11-common', 'xz-utils'] 1m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--purge', 'plasmidid'] 1m21.4s DUMP: (Reading database ... 6679 files and directories currently installed.) Purging configuration files for plasmidid (1.6.3+dfsg-3) ... 1m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--purge', 'plasmidid'] 1m21.4s INFO: Running scripts post_purge 1m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_purge_exceptions'] 1m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_purge_exceptions'] 1m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--purge', '--pending'] 1m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--purge', '--pending'] 1m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--remove', '--pending'] 1m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg', '--remove', '--pending'] 1m21.4s INFO: Running scripts post_test 1m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_test_exceptions'] 1m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'tmp/scripts/post_test_exceptions'] 1m21.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m21.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg-divert', '--list'] 1m21.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'dpkg-divert', '--list'] 1m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'clean'] 1m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzzf932kc', 'apt-get', 'clean'] 1m21.8s DEBUG: Recording chroot state 1m22.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/shm'] 1m22.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/shm'] 1m22.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/console'] 1m22.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/console'] 1m22.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/ptmx'] 1m22.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/ptmx'] 1m22.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/pts'] 1m22.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/dev/pts'] 1m22.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/proc'] 1m22.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzzf932kc/proc'] 1m22.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m22.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzzf932kc'] 1m22.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpzzf932kc 1m22.9s INFO: PASS: Upgrading between Debian distributions. 1m22.9s INFO: PASS: All tests. 1m22.9s INFO: piuparts run ends. ret=0 End: 2024-03-03 23:48:06 GMT