Start: 2025-08-12 11:24:53 GMT [trixie] Package: plasmidid Version: 1.6.5+dfsg-2 Installed-Size: 331 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_1.6.5+dfsg-2_amd64.deb Size: 47212 MD5sum: fa7b528e02d2aacb387b176a5356e052 SHA256: e0ec3f8d2467bd4f685d0c2c32b08c57c3cf170714b522094b657a1f11f9336f [trixie-next] Package: plasmidid Version: 1.6.5+dfsg-2 Installed-Size: 331 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_1.6.5+dfsg-2_amd64.deb Size: 47212 MD5sum: fa7b528e02d2aacb387b176a5356e052 SHA256: e0ec3f8d2467bd4f685d0c2c32b08c57c3cf170714b522094b657a1f11f9336f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt plasmidid=1.6.5+dfsg-2 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 1.6.1~202508101417~1.6.0-7-g17c4ea32 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt plasmidid=1.6.5+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpcplg7zwx 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpcplg7zwx 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpcplg7zwx/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'update'] 0m2.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [138 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9668 kB] Fetched 9805 kB in 1s (9068 kB/s) Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.4s DUMP: 8fc0def95551deb38dc214d6c9cce720 - 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.4s INFO: Running scripts post_setup 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.2s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_minimize'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_minimize'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_zz_backports'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_setup_zz_backports'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat 0m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m4.8s INFO: Running scripts is_testable 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s INFO: Running scripts pre_test 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_test_root_password'] 0m4.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_test_root_password'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m5.2s DUMP: Package: plasmidid Version: 1.6.5+dfsg-2 Installed-Size: 331 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_1.6.5+dfsg-2_amd64.deb Size: 47212 MD5sum: fa7b528e02d2aacb387b176a5356e052 SHA256: e0ec3f8d2467bd4f685d0c2c32b08c57c3cf170714b522094b657a1f11f9336f 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m5.2s INFO: apt-cache knows about the following packages: plasmidid 0m5.2s INFO: Running scripts pre_install 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy'] 0m5.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy', 'plasmidid'] 0m5.4s DUMP: plasmidid: Installed: (none) Candidate: 1.6.5+dfsg-2 Version table: 1.6.5+dfsg-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy', 'plasmidid'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-y', 'install', 'plasmidid'] 0m41.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: adwaita-icon-theme aragorn at-spi2-common bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme hmmer infernal java-common less libabsl20240722 libaom3 libapparmor1 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libavif16 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libcairo-gobject2 libcairo2 libcapnp-1.1.0 libcarp-always-perl libclone-perl libcloudproviders0 libcolord2 libcom-err2 libconfig-general-perl libcups2t64 libcurl3t64-gnutls libdata-dumper-simple-perl libdata-stag-perl libdatrie1 libdav1d7 libdbus-1-3 libdconf1 libde265-0 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libdynaloader-functions-perl libedit2 libelf1t64 libepoxy0 libexpat1 libffi8 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libfribidi0 libgav1-1 libgbm1 libgd-perl libgd3 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl28 libgslcblas0 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap2 liblerc4 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm19 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-implementation-perl libmodule-runtime-perl libmurmurhash2 libncbi-vdb3 libncbi6t64 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnspr4 libnss3 libnumber-format-perl libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librav1e0.7 libreadline8t64 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libsharpyuv0 libspiffy-perl libssh2-1t64 libstatistics-basic-perl libsvg-perl libsvtav1enc2 libswiss-perl libsystemd-shared libtasn1-6 libtext-charwidth-perl libtext-format-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtry-tiny-perl libunistring5 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxkbcommon0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libyuv0 libz3-4 mash media-types mesa-libgallium ncbi-blast+ ncbi-data ncbi-tools-bin ncbi-vdb-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parallel perl perl-modules-5.40 procps prodigal prokka python3 python3-minimal python3.13 python3.13-minimal readline-common samtools sensible-utils shared-mime-info sysstat systemd systemd-sysv ucf x11-common xkb-data xz-utils Suggested packages: adwaita-icon-theme-legacy bowtie2-examples hmmer-doc alsa-utils libasound2-plugins bioperl libxml-sax-expatxs-perl colord cups-common libxml-parser-perl libgd-tools gdbm-l10n low-memory-monitor gnutls-bin gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user gvfs libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar libheif-plugin-rav1e libheif-plugin-svtenc libdb-file-lock-perl libfile-mimeinfo-perl libfile-readbackwards-perl libfreezethaw-perl libmldbm-perl liblcms2-utils libcryptsetup12 libtss2-rc0t64 libscalar-number-perl pciutils pcscd lm-sensors libarchive13t64 libbpf1 libdw1t64 libfido2-1 libgcrypt20 libip4tc2 libpwquality1 libqrencode4 libsub-name-perl libvibrant6t64 ncbi-cn3d ncbi-tools-x11 libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic csh fish ksh tcsh zsh perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binutils binfmt-support readline-doc cwltool isag systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved systemd-repart libtss2-tcti-device0 polkitd Recommended packages: librsvg2-common circos-tools alsa-ucm-conf alsa-topology-conf at-spi2-core bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl 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 libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libpod-coverage-perl libtest-pod-perl libgtk-3-bin libheif-plugin-x265 libheif-plugin-aomenc krb5-locales libldap-common liblist-someutils-xs-perl libgpm2 publicsuffix libsasl2-modules libcgi-pm-perl libkmod2 mesa-vulkan-drivers | vulkan-icd libxml-sax-expat-perl libatk-wrapper-java-jni fonts-dejavu-extra trimmomatic spades python3-biopython python3-numpy python3-pandas psmisc linux-sysctl-defaults systemd-timesyncd | time-daemon systemd-cryptsetup libnss-systemd The following NEW packages will be installed: adwaita-icon-theme aragorn at-spi2-common bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme hmmer infernal java-common less libabsl20240722 libaom3 libapparmor1 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libavif16 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libcairo-gobject2 libcairo2 libcapnp-1.1.0 libcarp-always-perl libclone-perl libcloudproviders0 libcolord2 libcom-err2 libconfig-general-perl libcups2t64 libcurl3t64-gnutls libdata-dumper-simple-perl libdata-stag-perl libdatrie1 libdav1d7 libdbus-1-3 libdconf1 libde265-0 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libdynaloader-functions-perl libedit2 libelf1t64 libepoxy0 libexpat1 libffi8 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libfribidi0 libgav1-1 libgbm1 libgd-perl libgd3 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl28 libgslcblas0 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap2 liblerc4 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm19 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-implementation-perl libmodule-runtime-perl libmurmurhash2 libncbi-vdb3 libncbi6t64 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnspr4 libnss3 libnumber-format-perl libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librav1e0.7 libreadline8t64 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libsharpyuv0 libspiffy-perl libssh2-1t64 libstatistics-basic-perl libsvg-perl libsvtav1enc2 libswiss-perl libsystemd-shared libtasn1-6 libtext-charwidth-perl libtext-format-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtry-tiny-perl libunistring5 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxkbcommon0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libyuv0 libz3-4 mash media-types mesa-libgallium ncbi-blast+ ncbi-data ncbi-tools-bin ncbi-vdb-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parallel perl perl-modules-5.40 plasmidid procps prodigal prokka python3 python3-minimal python3.13 python3.13-minimal readline-common samtools sensible-utils shared-mime-info sysstat systemd systemd-sysv ucf x11-common xkb-data xz-utils 0 upgraded, 276 newly installed, 0 to remove and 0 not upgraded. Need to get 235 MB of archives. After this operation, 1103 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257.7-1 [2151 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 4.1.0-1 [43.7 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257.7-1 [3099 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257.7-1 [64.2 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.16.2-2 [80.0 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.16.2-2 [159 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.16.2-2 [71.6 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 less amd64 668-1 [161 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.5.1-1 [1494 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20250419 [162 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257.7-1 [297 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.1-6 [267 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:38 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:39 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0052 [43.3 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 xz-utils amd64 5.8.1-1 [660 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-4 [311 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:43 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.3-1 [1515 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1 [282 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-4 [141 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.18.6+ds-2 [52.7 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 48.1-1 [504 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 aragorn amd64 1.2.41-3 [88.0 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.56.2-1 [171 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 bowtie2 amd64 2.5.4-1+b2 [1505 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 fonts-circos-symbols all 0.69.9+dfsg-2 [46.7 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 fonts-cmu all 0.7.0-5 [4892 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libregexp-common-perl all 2024080801-1 [167 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libcarp-always-perl all 0.16-1 [9620 B] Get:69 http://deb.debian.org/debian trixie/main amd64 libconfig-general-perl all 2.67-1 [71.3 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libdata-dumper-simple-perl all 0.11-7 [12.5 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0.1904.20250204-1 [174 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.2.1-1.2 [133 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.19.8-1 [11.7 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b3 [189 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.19.8-1 [15.3 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.19.8-1 [520 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-13 [126 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libgd-perl amd64 2.78-1+b3 [131 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libgetopt-simple-perl all 1.52-7 [15.5 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libmath-bezier-perl all 0.01-4 [7032 B] Get:100 http://deb.debian.org/debian trixie/main amd64 libmath-round-perl all 0.08-1 [9172 B] Get:101 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-2 [15.6 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libparams-validate-perl amd64 1.31-2+b3 [63.4 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libreadonly-perl all 2.050-3 [23.1 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libset-intspan-perl all 1.19-3 [25.3 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 liblist-allutils-perl all 0.19-1 [42.0 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libmath-vec-perl all 1.01-5 [17.1 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libmath-vecstat-perl all 0.08-3 [8408 B] Get:120 http://deb.debian.org/debian trixie/main amd64 libgraphics-colornames-perl all 3.5.0-3.1 [29.0 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libgraphics-colorobject-perl all 0.5.0-10.1 [28.1 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libtext-format-perl all 0.63-1 [19.5 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libnumber-format-perl all 1.76-1 [29.4 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libstatistics-basic-perl all 1.6611-3 [61.5 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libsvg-perl all 2.87-1 [64.3 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 circos all 0.69.9+dfsg-2 [14.0 MB] Get:130 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.16.2-2 [52.1 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get:135 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.110-1 [1393 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.3-1 [55.2 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.8+9-1 [41.8 MB] Get:140 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:141 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.56.2-1 [51.9 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.56.2-1 [80.7 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.56.2-1 [68.5 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.4-1+b1 [130 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-2 [29.2 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-3 [139 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:166 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-3 [251 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2.3 [463 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.3-1 [226 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [55.6 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [35.7 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.1-3 [26.8 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.1-3 [11.9 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.1-3 [5860 B] Get:183 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b4 [16.0 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.49-3 [4908 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.49-3 [2769 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.124-2 [8288 B] Get:195 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.124-2 [39.0 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.124-2 [22.6 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.124-2 [64.1 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-3+b1 [26.0 MB] Get:209 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get:212 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 25.0.7-2 [9629 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 25.0.7-2 [44.4 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.4.309.0-1 [130 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 25.0.7-2 [46.1 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 25.0.7-2 [143 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.14-1 [21.1 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.14-1 [381 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.8+9-1 [205 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get:229 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 infernal amd64 1.1.5-3 [5936 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 libbio-searchio-hmmer-perl all 1.7.3-2 [95.9 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 libcapnp-1.1.0 amd64 1.1.0-2 [1479 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:240 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get:248 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get:249 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:250 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get:254 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get:255 http://deb.debian.org/debian trixie/main amd64 libmurmurhash2 amd64 1.6-1+b1 [6180 B] Get:256 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:257 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:258 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get:259 http://deb.debian.org/debian trixie/main amd64 libncbi6t64 amd64 6.1.20170106+dfsg2-6 [4107 kB] Get:260 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:261 http://deb.debian.org/debian trixie/main amd64 libswiss-perl all 1.80-1 [776 kB] Get:262 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:263 http://deb.debian.org/debian trixie/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:264 http://deb.debian.org/debian trixie/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:265 http://deb.debian.org/debian trixie/main amd64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB] Get:266 http://deb.debian.org/debian trixie/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-5+b2 [314 kB] Get:267 http://deb.debian.org/debian trixie/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:268 http://deb.debian.org/debian trixie/main amd64 mash amd64 2.3+dfsg-6+b2 [192 kB] Get:269 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get:270 http://deb.debian.org/debian trixie/main amd64 ncbi-tools-bin amd64 6.1.20170106+dfsg2-6 [1931 kB] Get:271 http://deb.debian.org/debian trixie/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get:272 http://deb.debian.org/debian trixie/main amd64 parallel all 20240222+ds-2 [2163 kB] Get:273 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.21-1 [667 kB] Get:274 http://deb.debian.org/debian trixie/main amd64 prodigal amd64 1:2.6.3-6 [508 kB] Get:275 http://deb.debian.org/debian trixie/main amd64 prokka all 1.14.6+dfsg-6 [15.2 MB] Get:276 http://deb.debian.org/debian trixie/main amd64 plasmidid amd64 1.6.5+dfsg-2 [47.2 kB] Preconfiguring packages ... Fetched 235 MB in 2s (96.0 MB/s) Selecting previously unselected package libsystemd-shared:amd64. (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 ... 4938 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.7-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.7-1) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_4.1.0-1_amd64.deb ... Unpacking libapparmor1:amd64 (4.1.0-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up x11-common (1:7.7+24) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.2-2) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up less (668-1) ... Setting up xkb-data (2.42-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libabsl20240722:amd64 (20240722.0-4) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up libasound2-data (1.2.14-1) ... Setting up infernal (1.1.5-3) ... Setting up fonts-cmu (0.7.0-5) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libasound2t64:amd64 (1.2.14-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libavahi-common-data:amd64 (0.8-16) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up libdbus-1-3:amd64 (1.16.2-2) ... Setting up xz-utils (5.8.1-1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.48-1) ... Setting up libatomic1:amd64 (14.2.0-19) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgav1-1:amd64 (0.19.0-3+b1) ... Setting up libpcsclite1:amd64 (2.3.3-1) ... Setting up libsensors5:amd64 (1:3.6.2-2) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libvulkan1:amd64 (1.4.309.0-1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up libdav1d7:amd64 (1.5.1-1) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up sensible-utils (0.0.25) ... Setting up libxshmfence1:amd64 (1.3.3-1) ... Setting up at-spi2-common (2.56.2-1) ... Setting up libtiff6:amd64 (4.7.0-3) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.16.2-2) ... Setting up librav1e0.7:amd64 (0.7.1-9+b2) ... Setting up procps (2:4.0.4-9) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libcapnp-1.1.0:amd64 (1.1.0-2) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libwayland-egl1:amd64 (1.23.1-3) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up fonts-circos-symbols (0.69.9+dfsg-2) ... Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libde265-0:amd64 (1.0.15-1+b3) ... Setting up libdivsufsort3:amd64 (2.0.1-6+b1) ... Setting up openssl (3.5.1-1) ... Setting up libdrm-common (2.4.124-2) ... Setting up libyuv0:amd64 (0.0.1904.20250204-1) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up dbus-bin (1.16.2-2) ... Setting up libxkbcommon0:amd64 (1.7.0-2) ... Setting up libwayland-client0:amd64 (1.23.1-3) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.7-3+b1) ... Setting up libwayland-server0:amd64 (1.23.1-3) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libavif16:amd64 (1.2.1-1.2) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libxpm4:amd64 (1:3.5.17-1+b3) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libavahi-common3:amd64 (0.8-16) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libnss3:amd64 (2:3.110-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up libperl5.40:amd64 (5.40.1-6) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up perl (5.40.1-6) ... Setting up libglib2.0-0t64:amd64 (2.84.3-1) ... Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b4) ... Setting up libdata-dumper-simple-perl (0.11-7) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up mash (2.3+dfsg-6+b2) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up libmath-vecstat-perl (0.08-3) ... Setting up ucf (3.0052) ... Setting up libspiffy-perl (0.46-1) ... Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libmath-round-perl (0.08-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libdrm2:amd64 (2.4.124-2) ... Setting up libwayland-cursor0:amd64 (1.23.1-3) ... Setting up libtext-format-perl (0.63-1) ... Setting up libswiss-perl (1.80-1) ... Setting up libpam-systemd:amd64 (257.7-1) ... Setting up libcarp-always-perl (0.16-1) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-4) ... Setting up libgraphics-colornames-perl (3.5.0-3.1) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up sysstat (12.7.5-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-collect.timer' → '/usr/lib/systemd/system/sysstat-collect.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-rotate.timer' → '/usr/lib/systemd/system/sysstat-rotate.timer'. Created symlink '/etc/systemd/system/sysstat.service.wants/sysstat-summary.timer' → '/usr/lib/systemd/system/sysstat-summary.timer'. Created symlink '/etc/systemd/system/multi-user.target.wants/sysstat.service' → '/usr/lib/systemd/system/sysstat.service'. Setting up libavahi-client3:amd64 (0.8-16) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libmath-vec-perl (1.01-5) ... Setting up libdrm-amdgpu1:amd64 (2.4.124-2) ... Setting up cd-hit (4.8.1-4) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up gtk-update-icon-cache (4.18.6+ds-2) ... Setting up fontconfig (2.15.0-2.3) ... Regenerating fonts cache... done. Setting up libfile-basedir-perl (0.09-2) ... Setting up libconfig-general-perl (2.67-1) ... Setting up libset-intspan-perl (1.19-3) ... Setting up libatk1.0-0t64:amd64 (2.56.2-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.8+9-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up python3.13 (3.13.5-2) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libgetopt-simple-perl (1.52-7) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libpango-1.0-0:amd64 (1.56.3-1) ... Setting up libdrm-intel1:amd64 (2.4.124-2) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-2) ... Setting up libgraphics-colorobject-perl (0.5.0-10.1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up libsvg-perl (2.87-1) ... Setting up python3 (3.13.5-1) ... Setting up libnumber-format-perl (1.76-1) ... Setting up libio-all-perl (0.87-2) ... Setting up libdevel-callchecker-perl:amd64 (0.009-2) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up libregexp-common-perl (2024080801-1) ... Setting up libmath-bezier-perl (0.01-4) ... Setting up libcolord2:amd64 (1.4.7-3) ... Setting up bowtie2 (2.5.4-1+b2) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up libncbi6t64:amd64 (6.1.20170106+dfsg2-6) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up libreadonly-perl (2.050-3) ... Setting up dbus-user-session (1.16.2-2) ... Setting up adwaita-icon-theme (48.1-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libatspi2.0-0t64:amd64 (2.56.2-1) ... Setting up parallel (20240222+ds-2) ... Setting up libdata-stag-perl (0.14-3) ... Setting up ncbi-tools-bin (6.1.20170106+dfsg2-6) ... Setting up libcairo-gobject2:amd64 (1.18.4-1+b1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up libcups2t64:amd64 (2.4.10-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... Setting up libstatistics-basic-perl (1.6611-3) ... Setting up libatk-bridge2.0-0t64:amd64 (2.56.2-1) ... Setting up mesa-libgallium:amd64 (25.0.7-2) ... Setting up libgbm1:amd64 (25.0.7-2) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up libgl1-mesa-dri:amd64 (25.0.7-2) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up dconf-service (0.40.0-5) ... Setting up libxml-sax-perl (1.02+dfsg-4) ... 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 libbio-searchio-hmmer-perl (1.7.3-2) ... Setting up libmodule-runtime-perl (0.018-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b2) ... 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 libhts3t64:amd64 (1.21+ds-1) ... Setting up libglx-mesa0:amd64 (25.0.7-2) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up samtools (1.21-1) ... Setting up liblist-allutils-perl (0.19-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libparams-validate-perl:amd64 (1.31-2+b3) ... Setting up libgtk-3-common (3.24.49-3) ... Setting up libgtk-3-0t64:amd64 (3.24.49-3) ... Setting up libheif1:amd64 (1.19.8-1) ... Setting up libgd3:amd64 (2.3.3-13) ... Setting up libheif-plugin-dav1d:amd64 (1.19.8-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.8-1) ... Setting up libgd-perl (2.78-1+b3) ... Setting up circos (0.69.9+dfsg-2) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for systemd (257.7-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.8+9-1) ... Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up prokka (1.14.6+dfsg-6) ... Setting up plasmidid (1.6.5+dfsg-2) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-y', 'install', 'plasmidid'] 0m41.6s INFO: Running scripts post_install 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_install_exceptions'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_install_exceptions'] 0m41.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m42.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m42.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpcplg7zwx to trixie-next 0m42.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main deb http://security.debian.org trixie-security main deb http://deb.debian.org/debian/ trixie-updates main deb http://deb.debian.org/debian/ trixie-proposed-updates main 0m42.7s INFO: Running scripts pre_distupgrade 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_exceptions'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_exceptions'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'update'] 0m43.8s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Get:2 http://security.debian.org trixie-security InRelease [43.4 kB] Get:3 http://deb.debian.org/debian trixie-updates InRelease [47.1 kB] Get:4 http://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:5 http://security.debian.org trixie-security/main amd64 Packages [5304 B] Get:6 http://deb.debian.org/debian trixie-updates/main amd64 Packages [2432 B] Get:7 http://deb.debian.org/debian trixie-updates/main Translation-en [396 B] Get:8 http://security.debian.org trixie-security/main Translation-en [6724 B] Get:9 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages [7300 B] Get:10 http://deb.debian.org/debian trixie-proposed-updates/main Translation-en [3288 B] Fetched 172 kB in 0s (903 kB/s) Reading package lists... 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'update'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-yf', 'dist-upgrade'] 0m44.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-yf', 'dist-upgrade'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m45.3s DUMP: 5c6a884f0339ba51c78a9d3f50b19f1b - 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m45.6s DUMP: Package: plasmidid Version: 1.6.5+dfsg-2 Installed-Size: 331 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_1.6.5+dfsg-2_amd64.deb Size: 47212 MD5sum: fa7b528e02d2aacb387b176a5356e052 SHA256: e0ec3f8d2467bd4f685d0c2c32b08c57c3cf170714b522094b657a1f11f9336f 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m45.6s INFO: apt-cache knows about the following packages: plasmidid 0m45.6s INFO: Running scripts pre_install 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_database-server'] 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_database-server'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_exceptions'] 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_exceptions'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_extras'] 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_extras'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture'] 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy'] 0m45.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy'] 0m45.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy', 'plasmidid'] 0m45.8s DUMP: plasmidid: Installed: 1.6.5+dfsg-2 Candidate: 1.6.5+dfsg-2 Version table: *** 1.6.5+dfsg-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m45.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy', 'plasmidid'] 0m45.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-y', 'install', 'plasmidid'] 0m46.2s DUMP: Reading package lists... Building dependency tree... Reading state information... plasmidid is already the newest version (1.6.5+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m46.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-y', 'install', 'plasmidid'] 0m46.2s INFO: Running scripts post_install 0m46.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_install_exceptions'] 0m46.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_install_exceptions'] 0m46.2s INFO: Running scripts post_distupgrade 0m46.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m46.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m46.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_exceptions'] 0m46.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_exceptions'] 0m46.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m46.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m46.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m46.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m46.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_zz_backports'] 0m46.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_distupgrade_zz_backports'] 0m46.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m47.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m47.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m48.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m48.6s INFO: Running scripts pre_install 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_database-server'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_database-server'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_exceptions'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_exceptions'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_extras'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_extras'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy'] 0m48.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy'] 0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy', 'plasmidid'] 0m48.8s DUMP: plasmidid: Installed: 1.6.5+dfsg-2 Candidate: 1.6.5+dfsg-2 Version table: *** 1.6.5+dfsg-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-cache', 'policy', 'plasmidid'] 0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-y', 'install', 'plasmidid=1.6.5+dfsg-2'] 0m49.3s DUMP: Reading package lists... Building dependency tree... Reading state information... plasmidid is already the newest version (1.6.5+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', '-y', 'install', 'plasmidid=1.6.5+dfsg-2'] 0m49.3s INFO: Running scripts post_install 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_install_exceptions'] 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_install_exceptions'] 0m49.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m50.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 0m51.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', '-ac', '--ignore-obsolete'] 0m55.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', '-ac', '--ignore-obsolete'] 0m55.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m55.1s DUMP: 0.15.9~deb12u1 0m55.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m55.1s INFO: Running adequate version 0.15.9~deb12u1 now. 0m55.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'plasmidid'] 0m55.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'plasmidid'] 0m55.2s INFO: Running scripts pre_remove 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_exceptions'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/pre_remove_exceptions'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m3.4s DUMP: install ok installed adwaita-icon-theme adwaita-icon-theme 48.1-1 install ok installed apt apt 3.0.3 install ok installed aragorn aragorn 1.2.41-3 install ok installed at-spi2-common at-spi2-common 2.56.2-1 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bedtools bedtools 2.31.1+dfsg-2 install ok installed bowtie2 bowtie2 2.5.4-1+b2 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed ca-certificates ca-certificates 20250419 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed cd-hit cd-hit 4.8.1-4 install ok installed circos circos 0.69.9+dfsg-2 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed dbus dbus 1.16.2-2 install ok installed dbus-bin dbus-bin 1.16.2-2 install ok installed dbus-daemon dbus-daemon 1.16.2-2 install ok installed dbus-session-bus-common dbus-session-bus-common 1.16.2-2 install ok installed dbus-system-bus-common dbus-system-bus-common 1.16.2-2 install ok installed dbus-user-session dbus-user-session 1.16.2-2 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.40.0-5 install ok installed dconf-service dconf-service 0.40.0-5 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed default-jre default-jre 2:1.21-76 install ok installed default-jre-headless default-jre-headless 2:1.21-76 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-2.3 install ok installed fontconfig-config fontconfig-config 2.15.0-2.3 install ok installed fonts-circos-symbols fonts-circos-symbols 0.69.9+dfsg-2 install ok installed fonts-cmu fonts-cmu 0.7.0-5 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 4.18.6+ds-2 install ok installed gzip gzip 1.13-1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.18-2 install ok installed hmmer hmmer 3.4+dfsg-2 install ok installed hostname hostname 3.25 install ok installed infernal infernal 1.1.5-3 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed java-common java-common 0.76 install ok installed less less 668-1 install ok installed libabsl20240722:amd64 libabsl20240722 20240722.0-4 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libaom3:amd64 libaom3 3.12.1-1 install ok installed libapparmor1:amd64 libapparmor1 4.1.0-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libasound2-data libasound2-data 1.2.14-1 install ok installed libasound2t64:amd64 libasound2t64 1.2.14-1 install ok installed libatk-bridge2.0-0t64:amd64 libatk-bridge2.0-0t64 2.56.2-1 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.56.2-1 install ok installed libatomic1:amd64 libatomic1 14.2.0-19 install ok installed libatspi2.0-0t64:amd64 libatspi2.0-0t64 2.56.2-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-16 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-16 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-16 install ok installed libavif16:amd64 libavif16 1.2.1-1.2 install ok installed libb-hooks-op-check-perl:amd64 libb-hooks-op-check-perl 0.22-3+b2 install ok installed libbio-perl-perl libbio-perl-perl 1.7.8-1 install ok installed libbio-searchio-hmmer-perl libbio-searchio-hmmer-perl 1.7.3-2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcairo-gobject2:amd64 libcairo-gobject2 1.18.4-1+b1 install ok installed libcairo2:amd64 libcairo2 1.18.4-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcapnp-1.1.0:amd64 libcapnp-1.1.0 1.1.0-2 install ok installed libcarp-always-perl libcarp-always-perl 0.16-1 install ok installed libclone-perl:amd64 libclone-perl 0.47-1+b1 install ok installed libcloudproviders0:amd64 libcloudproviders0 0.3.6-2 install ok installed libcolord2:amd64 libcolord2 1.4.7-3 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-3+b3 install ok installed libconfig-general-perl libconfig-general-perl 2.67-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcups2t64:amd64 libcups2t64 2.4.10-3 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.14.1-2 install ok installed libdata-dumper-simple-perl libdata-dumper-simple-perl 0.11-7 install ok installed libdata-stag-perl libdata-stag-perl 0.14-3 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1 install ok installed libdav1d7:amd64 libdav1d7 1.5.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.16.2-2 install ok installed libdconf1:amd64 libdconf1 0.40.0-5 install ok installed libde265-0:amd64 libde265-0 1.0.15-1+b3 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libdeflate0:amd64 libdeflate0 1.23-2 install ok installed libdevel-callchecker-perl:amd64 libdevel-callchecker-perl 0.009-2 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-6+b1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.124-2 install ok installed libdrm-common libdrm-common 2.4.124-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.124-2 install ok installed libdrm2:amd64 libdrm2 2.4.124-2 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.004-2 install ok installed libedit2:amd64 libedit2 3.1-20250104-1 install ok installed libelf1t64:amd64 libelf1t64 0.192-4 install ok installed libepoxy0:amd64 libepoxy0 1.5.10-2 install ok installed libexpat1:amd64 libexpat1 2.7.1-2 install ok installed libffi8:amd64 libffi8 3.4.8-2 install ok installed libfile-basedir-perl libfile-basedir-perl 0.09-2 install ok installed libfont-ttf-perl libfont-ttf-perl 1.06-2 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.3 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgav1-1:amd64 libgav1-1 0.19.0-3+b1 install ok installed libgbm1:amd64 libgbm1 25.0.7-2 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgd-perl libgd-perl 2.78-1+b3 install ok installed libgd3:amd64 libgd3 2.3.3-13 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.12+dfsg-4 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.12+dfsg-4 install ok installed libgetopt-simple-perl libgetopt-simple-perl 1.52-7 install ok installed libgif7:amd64 libgif7 5.2.2-1+b1 install ok installed libgl1:amd64 libgl1 1.7.0-1+b2 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 25.0.7-2 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.3-1 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1+b2 install ok installed libglx-mesa0:amd64 libglx-mesa0 25.0.7-2 install ok installed libglx0:amd64 libglx0 1.7.0-1+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgraphics-colornames-perl libgraphics-colornames-perl 3.5.0-3.1 install ok installed libgraphics-colorobject-perl libgraphics-colorobject-perl 0.5.0-10.1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgsl28:amd64 libgsl28 2.8+dfsg-5 install ok installed libgslcblas0:amd64 libgslcblas0 2.8+dfsg-5 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libgtk-3-0t64:amd64 libgtk-3-0t64 3.24.49-3 install ok installed libgtk-3-common libgtk-3-common 3.24.49-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1 install ok installed libheif-plugin-dav1d:amd64 libheif-plugin-dav1d 1.19.8-1 install ok installed libheif-plugin-libde265:amd64 libheif-plugin-libde265 1.19.8-1 install ok installed libheif1:amd64 libheif1 1.19.8-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libhts3t64:amd64 libhts3t64 1.21+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libio-all-perl libio-all-perl 0.87-2 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed libipc-system-simple-perl libipc-system-simple-perl 1.30-2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-4 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap2:amd64 libldap2 2.6.10+dfsg-1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblist-allutils-perl liblist-allutils-perl 0.19-1 install ok installed liblist-someutils-perl liblist-someutils-perl 0.59-1 install ok installed liblist-utilsby-perl liblist-utilsby-perl 0.12-2 install ok installed libllvm19:amd64 libllvm19 1:19.1.7-3+b1 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmath-bezier-perl libmath-bezier-perl 0.01-4 install ok installed libmath-round-perl libmath-round-perl 0.08-1 install ok installed libmath-vec-perl libmath-vec-perl 1.01-5 install ok installed libmath-vecstat-perl libmath-vecstat-perl 0.08-3 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.4-2 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.4-2 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.4-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-2 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.018-1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libmurmurhash2:amd64 libmurmurhash2 1.6-1+b1 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.2.1+dfsg-2 install ok installed libncbi6t64:amd64 libncbi6t64 6.1.20170106+dfsg2-6 install ok installed libncurses6:amd64 libncurses6 6.5+20250216-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1.1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.8.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.11.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.11.0-1 install ok installed libnspr4:amd64 libnspr4 2:4.36-1 install ok installed libnss3:amd64 libnss3 2:3.110-1 install ok installed libnumber-format-perl libnumber-format-perl 1.76-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam-systemd:amd64 libpam-systemd 257.7-1 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.56.3-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.56.3-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.56.3-1 install ok installed libparams-classify-perl:amd64 libparams-classify-perl 0.015-2+b4 install ok installed libparams-validate-perl:amd64 libparams-validate-perl 1.31-2+b3 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpcsclite1:amd64 libpcsclite1 2.3.3-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-6 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.48-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-9 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.5-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.5-2 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.5-2 install ok installed librav1e0.7:amd64 librav1e0.7 0.7.1-9+b2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed libreadonly-perl libreadonly-perl 2.050-3 install ok installed libregexp-common-perl libregexp-common-perl 2024080801-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-9 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsensors-config libsensors-config 1:3.6.2-2 install ok installed libsensors5:amd64 libsensors5 1:3.6.2-2 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libset-intspan-perl libset-intspan-perl 1.19-3 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstatistics-basic-perl libstatistics-basic-perl 1.6611-3 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsvg-perl libsvg-perl 2.87-1 install ok installed libsvtav1enc2:amd64 libsvtav1enc2 2.3.0+dfsg-1 install ok installed libswiss-perl libswiss-perl 1.80-1 install ok installed libsystemd-shared:amd64 libsystemd-shared 257.7-1 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-format-perl libtext-format-perl 0.63-1 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2+b1 install ok installed libtiff6:amd64 libtiff6 4.7.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libtry-tiny-perl libtry-tiny-perl 0.32-1 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libuv1t64:amd64 libuv1t64 1.50.0-2 install ok installed libvulkan1:amd64 libvulkan1 1.4.309.0-1 install ok installed libwayland-client0:amd64 libwayland-client0 1.23.1-3 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.23.1-3 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.23.1-3 install ok installed libwayland-server0:amd64 libwayland-server0 1.23.1-3 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1 install ok installed libx11-data libx11-data 2:1.8.12-1 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.12-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.17.0-2+b1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.17.0-2+b1 install ok installed libxcb-present0:amd64 libxcb-present0 1.17.0-2+b1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.17.0-2+b1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.17.0-2+b1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.6-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.3-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1+b2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2+b4 install ok installed libxi6:amd64 libxi6 2:1.8.2-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3+b4 install ok installed libxkbcommon0:amd64 libxkbcommon0 1.7.0-2 install ok installed libxml-libxml-perl libxml-libxml-perl 2.0207+dfsg+really+2.0134-5+b2 install ok installed libxml-namespacesupport-perl libxml-namespacesupport-perl 1.12-2 install ok installed libxml-sax-base-perl libxml-sax-base-perl 1.09-3 install ok installed libxml-sax-perl libxml-sax-perl 1.02+dfsg-4 install ok installed libxml-simple-perl libxml-simple-perl 2.25-2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-2.1 install ok installed libxpm4:amd64 libxpm4 1:3.5.17-1+b3 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1+b3 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3.3-1 install ok installed libxtst6:amd64 libxtst6 2:1.2.5-1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libyuv0:amd64 libyuv0 0.0.1904.20250204-1 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mash mash 2.3+dfsg-6+b2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed mesa-libgallium:amd64 mesa-libgallium 25.0.7-2 install ok installed mount mount 2.41-5 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-7 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-6 install ok installed ncbi-tools-bin ncbi-tools-bin 6.1.20170106+dfsg2-6 install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed netbase netbase 6.5 install ok installed openjdk-21-jre:amd64 openjdk-21-jre 21.0.8+9-1 install ok installed openjdk-21-jre-headless:amd64 openjdk-21-jre-headless 21.0.8+9-1 install ok installed openssl openssl 3.5.1-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed parallel parallel 20240222+ds-2 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl perl 5.40.1-6 install ok installed perl-base perl-base 5.40.1-6 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-6 install ok installed plasmidid plasmidid 1.6.5+dfsg-2 install ok installed procps procps 2:4.0.4-9 install ok installed prodigal prodigal 1:2.6.3-6 install ok installed prokka prokka 1.14.6+dfsg-6 install ok installed python3 python3 3.13.5-1 install ok installed python3-minimal python3-minimal 3.13.5-1 install ok installed python3.13 python3.13 3.13.5-2 install ok installed python3.13-minimal python3.13-minimal 3.13.5-2 install ok installed readline-common readline-common 8.2-6 install ok installed samtools samtools 1.21-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.25 install ok installed shared-mime-info shared-mime-info 2.4-5+b2 install ok installed sqv sqv 1.3.0-3 install ok installed sysstat sysstat 12.7.5-2 install ok installed systemd systemd 257.7-1 install ok installed systemd-sysv systemd-sysv 257.7-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed ucf ucf 3.0052 install ok installed util-linux util-linux 2.41-5 install ok installed x11-common x11-common 1:7.7+24 install ok installed xkb-data xkb-data 2.42-1 install ok installed xz-utils xz-utils 5.8.1-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'remove', '--allow-remove-essential', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hmmer', 'infernal', 'java-common', 'less', 'libabsl20240722:amd64', 'libaom3:amd64', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libavif16:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libconfig-general-perl', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgbm1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm19:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmurmurhash2:amd64', 'libncbi-vdb3:amd64', 'libncbi6t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libparams-classify-perl:amd64', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libsharpyuv0:amd64', 'libspiffy-perl', 'libssh2-1t64:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc2:amd64', 'libswiss-perl', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-format-perl', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libunistring5:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyuv0:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'mesa-libgallium:amd64', 'ncbi-blast+-', 'ncbi-data', 'ncbi-tools-bin', 'ncbi-vdb-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'systemd', 'systemd-sysv', 'ucf', 'x11-common', 'xkb-data', 'xz-utils', 'plasmidid'] 1m7.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adwaita-icon-theme aragorn at-spi2-common bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme hmmer infernal java-common less libabsl20240722 libaom3 libapparmor1 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libavif16 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libcairo-gobject2 libcairo2 libcapnp-1.1.0 libcarp-always-perl libclone-perl libcloudproviders0 libcolord2 libcom-err2 libconfig-general-perl libcups2t64 libcurl3t64-gnutls libdata-dumper-simple-perl libdata-stag-perl libdatrie1 libdav1d7 libdbus-1-3 libdconf1 libde265-0 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libdynaloader-functions-perl libedit2 libelf1t64 libepoxy0 libexpat1 libffi8 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libfribidi0 libgav1-1 libgbm1 libgd-perl libgd3 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl28 libgslcblas0 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap2 liblerc4 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm19 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-implementation-perl libmodule-runtime-perl libmurmurhash2 libncbi-vdb3 libncbi6t64 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnspr4 libnss3 libnumber-format-perl libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librav1e0.7 libreadline8t64 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libsharpyuv0 libspiffy-perl libssh2-1t64 libstatistics-basic-perl libsvg-perl libsvtav1enc2 libswiss-perl libsystemd-shared libtasn1-6 libtext-charwidth-perl libtext-format-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtry-tiny-perl libunistring5 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxkbcommon0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libyuv0 libz3-4 mash media-types mesa-libgallium ncbi-blast+ ncbi-data ncbi-tools-bin ncbi-vdb-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parallel perl perl-modules-5.40 plasmidid procps prodigal prokka python3 python3-minimal python3.13 python3.13-minimal readline-common samtools sensible-utils shared-mime-info sysstat systemd systemd-sysv ucf x11-common xkb-data xz-utils WARNING: The following essential packages will be removed. This should NOT be done unless you know exactly what you are doing! systemd-sysv systemd (due to systemd-sysv) 0 upgraded, 0 newly installed, 276 to remove and 0 not upgraded. After this operation, 1103 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 ... 18756 files and directories currently installed.) Removing plasmidid (1.6.5+dfsg-2) ... Removing prokka (1.14.6+dfsg-6) ... Removing default-jre (2:1.21-76) ... Removing openjdk-21-jre:amd64 (21.0.8+9-1) ... Removing libgtk-3-0t64:amd64 (3.24.49-3) ... Removing adwaita-icon-theme (48.1-1) ... Removing aragorn (1.2.41-3) ... Removing libatk-bridge2.0-0t64:amd64 (2.56.2-1) ... Removing libatk1.0-0t64:amd64 (2.56.2-1) ... Removing at-spi2-common (2.56.2-1) ... Removing bedtools (2.31.1+dfsg-2) ... Removing bowtie2 (2.5.4-1+b2) ... Removing default-jre-headless (2:1.21-76) ... Removing openjdk-21-jre-headless:amd64 (21.0.8+9-1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cd-hit (4.8.1-4) ... Removing circos (0.69.9+dfsg-2) ... Removing libgtk-3-common (3.24.49-3) ... Removing dconf-gsettings-backend:amd64 (0.40.0-5) ... Removing dconf-service (0.40.0-5) ... Removing dbus-user-session (1.16.2-2) ... Removing libpam-systemd:amd64 (257.7-1) ... Removing dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus-daemon (1.16.2-2) ... Removing dbus-bin (1.16.2-2) ... Removing dbus-session-bus-common (1.16.2-2) ... Removing dbus-system-bus-common (1.16.2-2) ... Removing libpangocairo-1.0-0:amd64 (1.56.3-1) ... Removing libpangoft2-1.0-0:amd64 (1.56.3-1) ... Removing libpango-1.0-0:amd64 (1.56.3-1) ... Removing fontconfig (2.15.0-2.3) ... Removing libgd-perl (2.78-1+b3) ... Removing libgd3:amd64 (2.3.3-13) ... Removing libcairo-gobject2:amd64 (1.18.4-1+b1) ... Removing libcairo2:amd64 (1.18.4-1+b1) ... Removing libfontconfig1:amd64 (2.15.0-2.3) ... Removing fontconfig-config (2.15.0-2.3) ... Removing fonts-circos-symbols (0.69.9+dfsg-2) ... Removing fonts-cmu (0.7.0-5) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing gtk-update-icon-cache (4.18.6+ds-2) ... Removing hicolor-icon-theme (0.18-2) ... Removing hmmer (3.4+dfsg-2) ... Removing infernal (1.1.5-3) ... Removing java-common (0.76) ... Removing less (668-1) ... Removing libavif16:amd64 (1.2.1-1.2) ... Removing libgav1-1:amd64 (0.19.0-3+b1) ... Removing libabsl20240722:amd64 (20240722.0-4) ... Removing libaom3:amd64 (3.12.1-1) ... dpkg: warning: overriding problem because --force enabled: dpkg: warning: this is a protected package; it should not be removed Removing systemd-sysv (257.7-1) ... Removing systemd (257.7-1) ... Removing libapparmor1:amd64 (4.1.0-1) ... Removing libasound2t64:amd64 (1.2.14-1) ... Removing libasound2-data (1.2.14-1) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-4) ... Removing shared-mime-info (2.4-5+b2) ... Removing libcloudproviders0:amd64 (0.3.6-2) ... Removing libatspi2.0-0t64:amd64 (2.56.2-1) ... Removing libcups2t64:amd64 (2.4.10-3) ... Removing libavahi-client3:amd64 (0.8-16) ... Removing libavahi-common3:amd64 (0.8-16) ... Removing libavahi-common-data:amd64 (0.8-16) ... Removing libparams-validate-perl:amd64 (1.31-2+b3) ... Removing liblist-allutils-perl (0.19-1) ... Removing liblist-someutils-perl (0.59-1) ... Removing libmodule-implementation-perl (0.09-2) ... Removing libmodule-runtime-perl (0.018-1) ... Removing libparams-classify-perl:amd64 (0.015-2+b4) ... Removing libdevel-callchecker-perl:amd64 (0.009-2) ... Removing libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Removing libbio-searchio-hmmer-perl (1.7.3-2) ... Removing libbio-perl-perl (1.7.8-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing samtools (1.21-1) ... Removing libhts3t64:amd64 (1.21+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.14.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing mash (2.3+dfsg-6+b2) ... Removing libcapnp-1.1.0:amd64 (1.1.0-2) ... Removing libcarp-always-perl (0.16-1) ... Removing libclone-perl:amd64 (0.47-1+b1) ... Removing libcolord2:amd64 (1.4.7-3) ... Removing libgssapi-krb5-2:amd64 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-3+b3) ... Removing libconfig-general-perl (2.67-1) ... Removing libdata-dumper-simple-perl (0.11-7) ... Removing libdata-stag-perl (0.14-3) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libdbus-1-3:amd64 (1.16.2-2) ... Removing libdconf1:amd64 (0.40.0-5) ... Removing libtiff6:amd64 (4.7.0-3) ... Removing libdeflate0:amd64 (1.23-2) ... Removing libdivsufsort3:amd64 (2.0.1-6+b1) ... Removing libgl1:amd64 (1.7.0-1+b2) ... Removing libglx0:amd64 (1.7.0-1+b2) ... Removing libglx-mesa0:amd64 (25.0.7-2) ... Removing libgl1-mesa-dri:amd64 (25.0.7-2) ... Removing libgbm1:amd64 (25.0.7-2) ... Removing mesa-libgallium:amd64 (25.0.7-2) ... Removing libdrm-amdgpu1:amd64 (2.4.124-2) ... Removing libdrm-intel1:amd64 (2.4.124-2) ... Removing libdrm2:amd64 (2.4.124-2) ... Removing libdrm-common (2.4.124-2) ... Removing libdynaloader-functions-perl (0.004-2) ... Removing libllvm19:amd64 (1:19.1.7-3+b1) ... Removing libedit2:amd64 (3.1-20250104-1) ... Removing libelf1t64:amd64 (0.192-4) ... Removing libepoxy0:amd64 (1.5.10-2) ... Removing ncbi-blast+ (2.16.0+ds-7) ... Removing python3 (3.13.5-1) ... Removing python3.13 (3.13.5-2) ... Removing python3-minimal (3.13.5-1) ... Removing python3.13-minimal (3.13.5-2) ... Removing libexpat1:amd64 (2.7.1-2) ... Removing libwayland-server0:amd64 (1.23.1-3) ... Removing libwayland-cursor0:amd64 (1.23.1-3) ... Removing libwayland-client0:amd64 (1.23.1-3) ... Removing libfile-basedir-perl (0.09-2) ... Removing libfont-ttf-perl (1.06-2) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libxml-simple-perl (2.25-2) ... Removing libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b2) ... 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 libswiss-perl (1.80-1) ... Removing libgraphics-colorobject-perl (0.5.0-10.1) ... Removing libgraphics-colornames-perl (3.5.0-3.1) ... Removing libio-all-perl (0.87-2) ... Removing libspiffy-perl (0.46-1) ... Removing parallel (20240222+ds-2) ... 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 libgdk-pixbuf2.0-common (2.42.12+dfsg-4) ... Removing libgetopt-simple-perl (1.52-7) ... Removing libgif7:amd64 (5.2.2-1+b1) ... Removing libglvnd0:amd64 (1.7.0-1+b2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libgsl28:amd64 (2.8+dfsg-5) ... Removing libgslcblas0:amd64 (2.8+dfsg-5) ... Removing libhtscodecs2:amd64 (1.6.1-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libio-string-perl (1.08-4) ... Removing libipc-system-simple-perl (1.30-2) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libyuv0:amd64 (0.0.1904.20250204-1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-4) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-6) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap2:amd64 (2.6.10+dfsg-1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing liblist-utilsby-perl (0.12-2) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libmath-bezier-perl (0.01-4) ... Removing libmath-round-perl (0.08-1) ... Removing libmath-vec-perl (1.01-5) ... Removing libmath-vecstat-perl (0.08-3) ... Removing libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.4-2) ... Removing libmbedx509-7:amd64 (3.6.4-2) ... Removing libmbedcrypto16:amd64 (3.6.4-2) ... Removing libmurmurhash2:amd64 (1.6-1+b1) ... Removing ncbi-tools-bin (6.1.20170106+dfsg2-6) ... Removing libncbi6t64:amd64 (6.1.20170106+dfsg2-6) ... Removing libncurses6:amd64 (6.5+20250216-2) ... Removing libpython3-stdlib:amd64 (3.13.5-1) ... Removing libpython3.13-stdlib:amd64 (3.13.5-2) ... Removing sysstat (12.7.5-2) ... Removing libnghttp2-14:amd64 (1.64.0-1.1) ... Removing libnghttp3-9:amd64 (1.8.0-1) ... Removing libngtcp2-16:amd64 (1.11.0-1) ... Removing libnss3:amd64 (2:3.110-1) ... Removing libnspr4:amd64 (2:4.36-1) ... Removing libstatistics-basic-perl (1.6611-3) ... Removing libnumber-format-perl (1.76-1) ... Removing libpciaccess0:amd64 (0.17-3+b3) ... Removing libpcsclite1:amd64 (2.3.3-1) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.48-1) ... Removing libpython3.13-minimal:amd64 (3.13.5-2) ... Removing librav1e0.7:amd64 (0.7.1-9+b2) ... Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libreadonly-perl (2.050-3) ... Removing libregexp-common-perl (2024080801-1) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Removing libsensors5:amd64 (1:3.6.2-2) ... Removing libsensors-config (1:3.6.2-2) ... Removing libset-intspan-perl (1.19-3) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libsvg-perl (2.87-1) ... Removing libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Removing libsystemd-shared:amd64 (257.7-1) ... Removing libtext-format-perl (0.63-1) ... Removing libthai-data (0.1.29-2) ... Removing libtry-tiny-perl (0.32-1) ... Removing libuv1t64:amd64 (1.50.0-2) ... Removing libvulkan1:amd64 (1.4.309.0-1) ... Removing libwayland-egl1:amd64 (1.23.1-3) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Removing libxtst6:amd64 (2:1.2.5-1) ... Removing libx11-xcb1:amd64 (2:1.8.12-1) ... Removing libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Removing libxcb-sync1:amd64 (1.17.0-2+b1) ... Removing libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Removing libxcb-glx0:amd64 (1.17.0-2+b1) ... Removing libxcb-present0:amd64 (1.17.0-2+b1) ... Removing libxcb-randr0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcomposite1:amd64 (1:0.4.6-1) ... Removing libxcursor1:amd64 (1:1.2.3-1) ... Removing libxdamage1:amd64 (1:1.1.6-1+b2) ... Removing libxrandr2:amd64 (2:1.5.4-1+b3) ... Removing libxfixes3:amd64 (1:6.0.0-2+b4) ... Removing libxi6:amd64 (2:1.8.2-1) ... Removing libxinerama1:amd64 (2:1.1.4-3+b4) ... Removing libxkbcommon0:amd64 (1.7.0-2) ... Removing libxml-sax-perl (1.02+dfsg-4) ... 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-namespacesupport-perl (1.12-2) ... Removing libxml-sax-base-perl (1.09-3) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Removing libxpm4:amd64 (1:3.5.17-1+b3) ... Removing libxrender1:amd64 (1:0.9.12-1) ... Removing libxshmfence1:amd64 (1.3.3-1) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing media-types (13.0.0) ... Removing ncbi-data (6.1.20170106+dfsg2-6) ... Removing ncbi-vdb-data (3.2.1+dfsg-2) ... Removing netbase (6.5) ... Removing openssl (3.5.1-1) ... Removing prodigal (1:2.6.3-6) ... Removing readline-common (8.2-6) ... Removing x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xkb-data (2.42-1) ... Removing xz-utils (5.8.1-1) ... Removing libglib2.0-0t64:amd64 (2.84.3-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing perl (5.40.1-6) ... Removing libperl5.40:amd64 (5.40.1-6) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgnutls30t64:amd64 (3.8.9-3) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing ucf (3.0052) ... Removing procps (2:4.0.4-9) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libproc2-0:amd64 (2:4.0.4-9) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libtext-wrapi18n-perl (0.06-10) ... Removing libtext-charwidth-perl:amd64 (0.04-11+b4) ... Removing libunistring5:amd64 (1.3-2) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing perl-modules-5.40 (5.40.1-6) ... Removing sensible-utils (0.0.25) ... Removing libffi8:amd64 (3.4.8-2) ... Removing libx11-6:amd64 (2:1.8.12-1) ... Removing libx11-data (2:1.8.12-1) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing libheif1:amd64 (1.19.8-1) ... Removing libheif-plugin-libde265:amd64 (1.19.8-1) ... Removing libde265-0:amd64 (1.0.15-1+b3) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libheif-plugin-dav1d:amd64 (1.19.8-1) ... Removing libdav1d7:amd64 (1.5.1-1) ... Processing triggers for libc-bin (2.41-12) ... 1m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'remove', '--allow-remove-essential', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hmmer', 'infernal', 'java-common', 'less', 'libabsl20240722:amd64', 'libaom3:amd64', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libavif16:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libconfig-general-perl', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgbm1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm19:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmurmurhash2:amd64', 'libncbi-vdb3:amd64', 'libncbi6t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libparams-classify-perl:amd64', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libsharpyuv0:amd64', 'libspiffy-perl', 'libssh2-1t64:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc2:amd64', 'libswiss-perl', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-format-perl', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libunistring5:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyuv0:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'mesa-libgallium:amd64', 'ncbi-blast+-', 'ncbi-data', 'ncbi-tools-bin', 'ncbi-vdb-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'systemd', 'systemd-sysv', 'ucf', 'x11-common', 'xkb-data', 'xz-utils', 'plasmidid'] 1m7.0s INFO: Running scripts post_remove 1m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_remove_exceptions'] 1m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_remove_exceptions'] 1m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--purge', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hmmer', 'infernal', 'java-common', 'less', 'libabsl20240722:amd64', 'libaom3:amd64', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libavif16:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libconfig-general-perl', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgbm1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm19:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmurmurhash2:amd64', 'libncbi-vdb3:amd64', 'libncbi6t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libparams-classify-perl:amd64', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libsharpyuv0:amd64', 'libspiffy-perl', 'libssh2-1t64:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc2:amd64', 'libswiss-perl', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-format-perl', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libunistring5:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyuv0:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'mesa-libgallium:amd64', 'ncbi-blast+', 'ncbi-data', 'ncbi-tools-bin', 'ncbi-vdb-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'systemd', 'systemd-sysv', 'ucf', 'x11-common', 'xkb-data', 'xz-utils'] 1m8.0s DUMP: (Reading database ... 5130 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (48.1-1) ... dpkg: warning: ignoring request to remove aragorn which isn't installed dpkg: warning: ignoring request to remove at-spi2-common 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 Purging configuration files for ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... dpkg: warning: ignoring request to remove cd-hit which isn't installed Purging configuration files for circos (0.69.9+dfsg-2) ... Purging configuration files for dbus (1.16.2-2) ... rmdir: failed to remove '/var/run/dbus': No such file or directory rmdir: failed to remove '/var/lib/dbus': Directory not empty dpkg: warning: while removing dbus, directory '/var/lib/dbus' not empty so not removed dpkg: warning: ignoring request to remove dbus-bin which isn't installed Purging configuration files for dbus-daemon (1.16.2-2) ... dpkg: warning: ignoring request to remove dbus-session-bus-common which isn't installed dpkg: warning: ignoring request to remove dbus-system-bus-common which isn't installed Purging configuration files for dbus-user-session (1.16.2-2) ... dpkg: warning: ignoring request to remove dconf-gsettings-backend which isn't installed dpkg: warning: ignoring request to remove dconf-service which isn't installed 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 (2.15.0-2.3) ... Purging configuration files for fontconfig-config (2.15.0-2.3) ... 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 (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: ignoring request to remove gtk-update-icon-cache which isn't installed dpkg: warning: ignoring request to remove hicolor-icon-theme which isn't installed 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 (0.76) ... dpkg: warning: ignoring request to remove less which isn't installed dpkg: warning: ignoring request to remove libabsl20240722 which isn't installed dpkg: warning: ignoring request to remove libaom3 which isn't installed dpkg: warning: ignoring request to remove libapparmor1 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libasound2t64 which isn't installed dpkg: warning: ignoring request to remove libatk-bridge2.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libatspi2.0-0t64 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 libavif16 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 libcairo-gobject2 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcapnp-1.1.0 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 libcloudproviders0 which isn't installed dpkg: warning: ignoring request to remove libcolord2 which isn't installed dpkg: warning: ignoring request to remove libcom-err2 which isn't installed dpkg: warning: ignoring request to remove libconfig-general-perl which isn't installed dpkg: warning: ignoring request to remove libcups2t64 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-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 libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdav1d7 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdconf1 which isn't installed dpkg: warning: ignoring request to remove libde265-0 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 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 libelf1t64 which isn't installed dpkg: warning: ignoring request to remove libepoxy0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 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 libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgav1-1 which isn't installed dpkg: warning: ignoring request to remove libgbm1 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-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-4) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common 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 (25.0.7-2) ... Purging configuration files for libglib2.0-0t64:amd64 (2.84.3-1) ... 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 libgnutls30t64 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 libgsl28 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-5) ... Purging configuration files for libgtk-3-0t64:amd64 (3.24.49-3) ... Purging configuration files for libgtk-3-common (3.24.49-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libheif-plugin-dav1d which isn't installed dpkg: warning: ignoring request to remove libheif-plugin-libde265 which isn't installed dpkg: warning: ignoring request to remove libheif1 which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 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 libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 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 libllvm19 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 libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 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 libmurmurhash2 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libncbi6t64 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 libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 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 libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpam-systemd which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 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 libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.5-2) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove librav1e0.7 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... 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 (1:3.6.2-2) ... 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 libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libspiffy-perl which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 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 libsvtav1enc2 which isn't installed dpkg: warning: ignoring request to remove libswiss-perl which isn't installed dpkg: warning: ignoring request to remove libsystemd-shared which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtext-charwidth-perl which isn't installed dpkg: warning: ignoring request to remove libtext-format-perl which isn't installed dpkg: warning: ignoring request to remove libtext-wrapi18n-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwayland-client0 which isn't installed dpkg: warning: ignoring request to remove libwayland-cursor0 which isn't installed dpkg: warning: ignoring request to remove libwayland-egl1 which isn't installed dpkg: warning: ignoring request to remove libwayland-server0 which isn't installed dpkg: warning: ignoring request to remove libwebp7 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-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-randr0 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 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 libxcomposite1 which isn't installed dpkg: warning: ignoring request to remove libxcursor1 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 libxinerama1 which isn't installed dpkg: warning: ignoring request to remove libxkbcommon0 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-4) ... 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 libxrandr2 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 libyuv0 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 (13.0.0) ... dpkg: warning: ignoring request to remove mesa-libgallium which isn't installed dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-6) ... dpkg: warning: ignoring request to remove ncbi-tools-bin which isn't installed Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ... Purging configuration files for netbase (6.5) ... dpkg: warning: ignoring request to remove openjdk-21-jre which isn't installed Purging configuration files for openjdk-21-jre-headless:amd64 (21.0.8+9-1) ... Purging configuration files for openssl (3.5.1-1) ... Purging configuration files for parallel (20240222+ds-2) ... Purging configuration files for perl (5.40.1-6) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for procps (2:4.0.4-9) ... 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 (3.13.5-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.5-2) ... Purging configuration files for readline-common (8.2-6) ... 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 shared-mime-info (2.4-5+b2) ... Purging configuration files for sysstat (12.7.5-2) ... Purging configuration files for systemd (257.7-1) ... dpkg: warning: ignoring request to remove systemd-sysv which isn't installed Purging configuration files for ucf (3.0052) ... Purging configuration files for x11-common (1:7.7+24) ... dpkg: warning: ignoring request to remove xkb-data which isn't installed dpkg: warning: ignoring request to remove xz-utils which isn't installed 1m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--purge', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-circos-symbols', 'fonts-cmu', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hmmer', 'infernal', 'java-common', 'less', 'libabsl20240722:amd64', 'libaom3:amd64', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libavif16:amd64', 'libb-hooks-op-check-perl:amd64', 'libbio-perl-perl', 'libbio-searchio-hmmer-perl', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcom-err2:amd64', 'libconfig-general-perl', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgbm1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm19:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmurmurhash2:amd64', 'libncbi-vdb3:amd64', 'libncbi6t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnumber-format-perl', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libparams-classify-perl:amd64', 'libparams-validate-perl:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'librav1e0.7:amd64', 'libreadline8t64:amd64', 'libreadonly-perl', 'libregexp-common-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libset-intspan-perl', 'libsharpyuv0:amd64', 'libspiffy-perl', 'libssh2-1t64:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc2:amd64', 'libswiss-perl', 'libsystemd-shared:amd64', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-format-perl', 'libtext-wrapi18n-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libunistring5:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-sax-base-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyuv0:amd64', 'libz3-4:amd64', 'mash', 'media-types', 'mesa-libgallium:amd64', 'ncbi-blast+', 'ncbi-data', 'ncbi-tools-bin', 'ncbi-vdb-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parallel', 'perl', 'perl-modules-5.40', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'systemd', 'systemd-sysv', 'ucf', 'x11-common', 'xkb-data', 'xz-utils'] 1m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--purge', 'plasmidid'] 1m8.0s DUMP: (Reading database ... 4946 files and directories currently installed.) Purging configuration files for plasmidid (1.6.5+dfsg-2) ... 1m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--purge', 'plasmidid'] 1m8.0s INFO: Running scripts post_purge 1m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_purge_exceptions'] 1m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_purge_exceptions'] 1m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--purge', '--pending'] 1m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--purge', '--pending'] 1m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--remove', '--pending'] 1m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg', '--remove', '--pending'] 1m8.0s INFO: Running scripts post_test 1m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_test_exceptions'] 1m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'tmp/scripts/post_test_exceptions'] 1m8.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 1m8.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 1m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg-divert', '--list'] 1m8.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 1m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'dpkg-divert', '--list'] 1m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'clean'] 1m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx', 'apt-get', 'clean'] 1m8.4s DEBUG: Recording chroot state 1m9.0s INFO: Warning: Package purging left files on system: /etc/default/locale -> ../locale.conf not owned /etc/vconsole.conf -> default/keyboard not owned /root/.ssh/ not owned /var/cache/private/ not owned /var/lib/private/ not owned /var/log/private/ not owned 1m9.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/shm'] 1m9.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/shm'] 1m9.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/console'] 1m9.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/console'] 1m9.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/ptmx'] 1m9.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/ptmx'] 1m9.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/pts'] 1m9.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/dev/pts'] 1m9.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/proc'] 1m9.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx/proc'] 1m9.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 1m9.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcplg7zwx'] 1m9.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpcplg7zwx 1m9.5s INFO: PASS: Upgrading between Debian distributions. 1m9.5s INFO: PASS: All tests. 1m9.5s INFO: piuparts run ends. ret=0 End: 2025-08-12 11:26:03 GMT