Start: 2024-02-22 11:10:16 GMT [stable] Package: plasmidid Version: 1.6.3+dfsg-3 Installed-Size: 329 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos Recommends: trimmomatic, spades, python3-biopython, python3-numpy, python3-pandas Description: mapping-based, assembly-assisted plasmid identification tool Homepage: https://github.com/BU-ISCIII/plasmidID Description-md5: d2e67d45c872bf3607006dab611aef29 Section: science Priority: optional Filename: pool/main/p/plasmidid/plasmidid_1.6.3+dfsg-3_amd64.deb Size: 46260 MD5sum: 65edb80eb775247aefd5c4723726237c SHA256: f0f9333c1598a988b82bf851f6397017ac5acb1b12448862ddd57b71ba4dd0a8 [testing] 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 [sid] 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/sbin/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/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/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 1.3.1~202401311821~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt plasmidid=1.6.5+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpqduirf4p 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpqduirf4p 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/proc'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/proc'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/pts'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/pts'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/ptmx'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/console'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/console'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/shm'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/shm'] 0m2.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m2.0s DEBUG: Created policy-rc.d and chmodded it. 0m2.0s DEBUG: Created resolv.conf. 0m2.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpqduirf4p/tmp/scripts/ 0m2.0s INFO: Running scripts post_chroot_unpack 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'update'] 0m6.3s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 Packages [8068 kB] Get:3 http://deb.debian.org/debian bullseye/main Translation-en [6236 kB] Fetched 14.4 MB in 3s (4126 kB/s) Reading package lists... 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'update'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-yf', 'dist-upgrade'] 0m9.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libc-bin libc6 libgnutls30 perl-base tar tzdata 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7841 kB of archives. After this operation, 44.0 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 base-files amd64 11.1+deb11u9 [70.2 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 perl-base amd64 5.32.1-4+deb11u3 [1628 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 tar amd64 1.34+dfsg-1+deb11u1 [847 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libc6 amd64 2.31-13+deb11u8 [2823 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 libc-bin amd64 2.31-13+deb11u8 [829 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libgnutls30 amd64 3.7.1-5+deb11u4 [1340 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2024a-0+deb11u1 [304 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7841 kB in 0s (58.9 MB/s) (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 ... 6664 files and directories currently installed.) Preparing to unpack .../base-files_11.1+deb11u9_amd64.deb ... Unpacking base-files (11.1+deb11u9) over (11.1+deb11u8) ... Setting up base-files (11.1+deb11u9) ... Installing new version of config file /etc/debian_version ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../perl-base_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl-base (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Setting up perl-base (5.32.1-4+deb11u3) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1+deb11u1_amd64.deb ... Unpacking tar (1.34+dfsg-1+deb11u1) over (1.34+dfsg-1) ... Setting up tar (1.34+dfsg-1+deb11u1) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../libc6_2.31-13+deb11u8_amd64.deb ... Unpacking libc6:amd64 (2.31-13+deb11u8) over (2.31-13+deb11u6) ... Setting up libc6:amd64 (2.31-13+deb11u8) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-13+deb11u8_amd64.deb ... Unpacking libc-bin (2.31-13+deb11u8) over (2.31-13+deb11u6) ... Setting up libc-bin (2.31-13+deb11u8) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u4_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u4) over (3.7.1-5+deb11u3) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u4) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../tzdata_2024a-0+deb11u1_all.deb ... Unpacking tzdata (2024a-0+deb11u1) over (2021a-1+deb11u10) ... Setting up tzdata (2024a-0+deb11u1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Feb 22 11:10:26 UTC 2024. Universal Time is now: Thu Feb 22 11:10:26 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-yf', 'dist-upgrade'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.9s DUMP: 29fcf27583012b383113cec2bf757015 - 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.9s INFO: Running scripts post_setup 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_dummy_users'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_dummy_users'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_forbid_home'] 0m12.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_forbid_home'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_force-unsafe-io'] 0m12.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_force-unsafe-io'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_minimize'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_minimize'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_squeeze-backports'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_squeeze-backports'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_zz_backports'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_setup_zz_backports'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m12.3s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m12.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m12.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 0m12.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 0m12.7s INFO: Running scripts is_testable 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/is_testable_uninstallable'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/is_testable_uninstallable'] 0m12.7s INFO: Running scripts pre_test 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_test_exceptions'] 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_test_exceptions'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_test_root_password'] 0m12.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_test_root_password'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m13.0s DUMP: Package: plasmidid Version: 1.6.3+dfsg-3 Installed-Size: 329 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos Recommends: trimmomatic, spades, python3-biopython, python3-numpy, python3-pandas Description-en: mapping-based, assembly-assisted plasmid identification tool PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. . PlasmidID is a computational pipeline that maps Illumina reads over plasmid database sequences. The k-mer filtered, most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a circular image which allow user to determine plasmidic composition in any bacterial sample. Description-md5: d2e67d45c872bf3607006dab611aef29 Homepage: https://github.com/BU-ISCIII/plasmidID Section: science Priority: optional Filename: pool/main/p/plasmidid/plasmidid_1.6.3+dfsg-3_amd64.deb Size: 46260 MD5sum: 65edb80eb775247aefd5c4723726237c SHA256: f0f9333c1598a988b82bf851f6397017ac5acb1b12448862ddd57b71ba4dd0a8 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 0m13.0s INFO: apt-cache knows about the following packages: plasmidid 0m13.0s INFO: Running scripts pre_install 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 0m13.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 0m13.2s DUMP: plasmidid: Installed: (none) Candidate: 1.6.3+dfsg-3 Version table: 1.6.3+dfsg-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid'] 0m54.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: aragorn bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos default-jre default-jre-headless fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core hmmer infernal java-common less libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libbsd0 libcapnp-0.7.0 libcarp-always-perl libclone-perl libconfig-general-perl libcups2 libcurl3-gnutls libdata-dumper-simple-perl libdata-stag-perl libdbus-1-3 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdynaloader-functions-perl libedit2 libelf1 libexpat1 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libgd-perl libgd3 libgdbm-compat4 libgdbm6 libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl25 libgslcblas0 libharfbuzz0b libhts3 libicu67 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo liblcms2-2 libldap-2.4-2 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm11 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmodule-implementation-perl libmodule-runtime-perl libmpdec3 libmurmurhash2 libncbi6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libnumber-format-perl libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.32 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libspiffy-perl libsqlite3-0 libssh2-1 libstatistics-basic-perl libsvg-perl libswiss-perl libtbb2 libtext-format-perl libtiff5 libtry-tiny-perl libvulkan1 libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libz3-4 mash media-types ncbi-blast+ ncbi-data ncbi-tools-bin openjdk-11-jre openjdk-11-jre-headless openssl parallel perl perl-modules-5.32 procps prodigal prokka python3 python3-minimal python3.9 python3.9-minimal readline-common samtools sensible-utils sysstat ucf x11-common xz-utils Suggested packages: bowtie2-examples hmmer-doc libasound2-plugins alsa-utils bioperl libxml-sax-expatxs-perl cups-common libxml-parser-perl libgd-tools gdbm-l10n gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libdb-file-lock-perl libfile-mimeinfo-perl libfile-readbackwards-perl libfreezethaw-perl libmldbm-perl liblcms2-utils libscalar-number-perl pciutils pcscd lm-sensors libvibrant6b ncbi-cn3d ncbi-tools-x11 libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binutils binfmt-support readline-doc cwltool isag Recommended packages: circos-tools alsa-ucm-conf alsa-topology-conf bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl libwww-perl perl-tk libxml-libxslt-perl libmldbm-perl libxml-perl dbus libglib2.0-data shared-mime-info xdg-user-dirs libpod-coverage-perl libtest-pod-perl libldap-common liblist-someutils-xs-perl libgpm2 publicsuffix libsasl2-modules libcgi-pm-perl mesa-vulkan-drivers | vulkan-icd libxml-sax-expat-perl libatk-wrapper-java-jni fonts-dejavu-extra netbase trimmomatic spades python3-biopython python3-numpy python3-pandas psmisc systemd | cron | cron-daemon The following NEW packages will be installed: aragorn bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos default-jre default-jre-headless fontconfig-config fonts-circos-symbols fonts-cmu fonts-dejavu-core hmmer infernal java-common less libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libbsd0 libcapnp-0.7.0 libcarp-always-perl libclone-perl libconfig-general-perl libcups2 libcurl3-gnutls libdata-dumper-simple-perl libdata-stag-perl libdbus-1-3 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdynaloader-functions-perl libedit2 libelf1 libexpat1 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libgd-perl libgd3 libgdbm-compat4 libgdbm6 libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl25 libgslcblas0 libharfbuzz0b libhts3 libicu67 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo liblcms2-2 libldap-2.4-2 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm11 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmodule-implementation-perl libmodule-runtime-perl libmpdec3 libmurmurhash2 libncbi6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libnumber-format-perl libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.32 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libspiffy-perl libsqlite3-0 libssh2-1 libstatistics-basic-perl libsvg-perl libswiss-perl libtbb2 libtext-format-perl libtiff5 libtry-tiny-perl libvulkan1 libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 libz3-4 mash media-types ncbi-blast+ ncbi-data ncbi-tools-bin openjdk-11-jre openjdk-11-jre-headless openssl parallel perl perl-modules-5.32 plasmidid procps prodigal prokka python3 python3-minimal python3.9 python3.9-minimal readline-common samtools sensible-utils sysstat ucf x11-common xz-utils 0 upgraded, 193 newly installed, 0 to remove and 0 not upgraded. Need to get 183 MB of archives. After this operation, 852 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 less amd64 551-2 [133 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 xz-utils amd64 5.2.5-2.1~deb11u1 [220 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 aragorn amd64 1.2.38-4 [86.7 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 bedtools amd64 2.30.0+dfsg-1 [663 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5+deb11u2 [124 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5+deb11u2 [58.7 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.28-0+deb11u1 [223 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5+deb11u2 [62.6 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u6 [351 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u3 [1305 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.22+7-1~deb11u1 [38.2 MB] Get:56 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909+deb11u1 [15.9 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-3 [522 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 fonts-circos-symbols all 0.69.9+dfsg-2 [46.7 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 fonts-cmu all 0.7.0-4 [4891 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libregexp-common-perl all 2017060201-1 [177 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libcarp-always-perl all 0.16-1 [9620 B] Get:64 http://deb.debian.org/debian bullseye/main amd64 libconfig-general-perl all 2.63-1 [70.5 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libdata-dumper-simple-perl all 0.11-5.1 [13.1 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libxpm4 amd64 1:3.5.12-1.1+deb11u1 [50.0 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libgd3 amd64 2.3.0-2 [137 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libgd-perl amd64 2.73-1+b1 [141 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libgetopt-simple-perl all 1.52-5.1 [15.7 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libmath-bezier-perl all 0.01-2.1 [7096 B] Get:82 http://deb.debian.org/debian bullseye/main amd64 libmath-round-perl all 0.07-1.1 [10.1 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 libparams-validate-perl amd64 1.30-1+b1 [68.2 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 libreadonly-perl all 2.050-3 [23.1 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 libset-intspan-perl all 1.19-1.1 [26.3 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 liblist-allutils-perl all 0.18-1 [40.7 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 libmath-vec-perl all 1.01-3.1 [18.0 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libspiffy-perl all 0.46-1 [25.7 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libio-all-perl all 0.87-1 [66.7 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 libmath-vecstat-perl all 0.08-2.1 [8648 B] Get:102 http://deb.debian.org/debian bullseye/main amd64 libgraphics-colornames-perl all 3.5.0-3 [32.1 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libgraphics-colorobject-perl all 0.5.0-10 [29.1 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libtext-format-perl all 0.62-1 [22.7 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 libclone-perl amd64 0.45-1+b1 [15.4 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 libnumber-format-perl all 1.75-1.1 [29.5 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 libstatistics-basic-perl all 1.6611-1.1 [62.2 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 libsvg-perl all 2.85-1 [64.4 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 circos all 0.69.9+dfsg-2 [14.0 MB] Get:112 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1+deb11u2 [204 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:128 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get:138 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 libgif7 amd64 5.1.9-2 [45.1 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre amd64 11.0.22+7-1~deb11u1 [194 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 default-jre amd64 2:1.11-72 [1044 B] Get:152 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 infernal amd64 1.1.4-1 [5523 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 libbio-searchio-hmmer-perl all 1.7.3-2 [95.9 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 libcapnp-0.7.0 amd64 0.7.0-7 [1048 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u11 [344 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 libmurmurhash2 amd64 1.5-2 [5780 B] Get:176 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 libncbi6 amd64 6.1.20170106+dfsg1-9 [4066 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 libswiss-perl all 1.79-3 [773 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:181 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:182 http://deb.debian.org/debian bullseye/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:183 http://deb.debian.org/debian bullseye/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB] Get:184 http://deb.debian.org/debian bullseye/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:185 http://deb.debian.org/debian bullseye/main amd64 mash amd64 2.2.2+dfsg-2 [153 kB] Get:186 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get:187 http://deb.debian.org/debian bullseye/main amd64 ncbi-tools-bin amd64 6.1.20170106+dfsg1-9 [1943 kB] Get:188 http://deb.debian.org/debian bullseye/main amd64 sysstat amd64 12.5.2-2 [603 kB] Get:189 http://deb.debian.org/debian bullseye/main amd64 parallel all 20161222-1.1 [306 kB] Get:190 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:191 http://deb.debian.org/debian bullseye/main amd64 prodigal amd64 1:2.6.3-4 [695 kB] Get:192 http://deb.debian.org/debian bullseye/main amd64 prokka amd64 1.14.6+dfsg-3 [9968 kB] Get:193 http://deb.debian.org/debian bullseye/main amd64 plasmidid amd64 1.6.3+dfsg-3 [46.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 183 MB in 2s (97.2 MB/s) Selecting previously unselected package perl-modules-5.32. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6672 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8937 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. 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Setting up libglvnd0:amd64 (1.3.2-1) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u3) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libtbb2:amd64 (2020.3-1) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up less (551-2) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libcapnp-0.7.0:amd64 (0.7.0-7) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libasound2-data (1.2.4-1.1) ... Setting up infernal (1.1.4-1) ... Setting up fonts-cmu (0.7.0-4) ... Setting up libz3-4:amd64 (4.8.10-1) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1+deb11u2) ... Setting up libnspr4:amd64 (2:4.29-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:amd64 (0.8-5+deb11u2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libdbus-1-3:amd64 (1.12.28-0+deb11u1) ... Setting up xz-utils (5.2.5-2.1~deb11u1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up mash (2.2.2+dfsg-2) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libpcsclite1:amd64 (1.9.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libglapi-mesa:amd64 (20.3.5-1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libvulkan1:amd64 (1.2.162.0-1) ... Setting up libgif7:amd64 (5.1.9-2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libasound2:amd64 (1.2.4-1.1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u5) ... Setting up fonts-circos-symbols (0.69.9+dfsg-2) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up libdrm-common (2.4.104-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up bedtools (2.30.0+dfsg-1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libncbi6:amd64 (6.1.20170106+dfsg1-9) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.14-3) ... Setting up libxcb-xfixes0:amd64 (1.14-3) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libxcb-glx0:amd64 (1.14-3) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libavahi-common3:amd64 (0.8-5+deb11u2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Setting up libnss3:amd64 (2:3.61-1+deb11u3) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up libxcb-present0:amd64 (1.14-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libxcb-sync1:amd64 (1.14-3) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up ucf (3.0043) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up libxcb-dri2-0:amd64 (1.14-3) ... Setting up libdrm2:amd64 (2.4.104-1) ... Setting up ncbi-tools-bin (6.1.20170106+dfsg1-9) ... Setting up procps (2:3.3.17-5) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up sysstat (12.5.2-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libavahi-client3:amd64 (0.8-5+deb11u2) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.104-1) ... Setting up libxcb-dri3-0:amd64 (1.14-3) ... Setting up libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libdrm-nouveau2:amd64 (2.4.104-1) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up libxpm4:amd64 (1:3.5.12-1.1+deb11u1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libdrm-radeon1:amd64 (2.4.104-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libdrm-intel1:amd64 (2.4.104-1) ... Setting up libgl1-mesa-dri:amd64 (20.3.5-1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up samtools (1.11-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up perl (5.32.1-4+deb11u3) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libdata-dumper-simple-perl (0.11-5.1) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up libmath-vecstat-perl (0.08-2.1) ... Setting up parallel (20161222-1.1) ... Setting up libspiffy-perl (0.46-1) ... Setting up libmath-round-perl (0.07-1.1) ... Setting up libcups2:amd64 (2.3.3op2-3+deb11u6) ... Setting up libtext-format-perl (0.62-1) ... Setting up libswiss-perl (1.79-3) ... Setting up libcarp-always-perl (0.16-1) ... Setting up libgraphics-colornames-perl (3.5.0-3) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up libmath-vec-perl (1.01-3.1) ... Setting up cd-hit (4.8.1-3) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up libconfig-general-perl (2.63-1) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libset-intspan-perl (1.19-1.1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up libdynaloader-functions-perl (0.003-1.1) ... Setting up libclone-perl (0.45-1+b1) ... Setting up libgetopt-simple-perl (1.52-5.1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libgraphics-colorobject-perl (0.5.0-10) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up libsvg-perl (2.85-1) ... Setting up python3 (3.9.2-3) ... Setting up libnumber-format-perl (1.75-1.1) ... Setting up libio-all-perl (0.87-1) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up liblist-utilsby-perl (0.11-1) ... Setting up libregexp-common-perl (2017060201-1) ... Setting up libmath-bezier-perl (0.01-2.1) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up libreadonly-perl (2.050-3) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libstatistics-basic-perl (1.6611-1.1) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgd-perl (2.73-1+b1) ... Setting up libbio-searchio-hmmer-perl (1.7.3-2) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up liblist-allutils-perl (0.18-1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libparams-validate-perl:amd64 (1.30-1+b1) ... Setting up circos (0.69.9+dfsg-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:amd64 (11.0.22+7-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:amd64 (11.0.22+7-1~deb11u1) ... Setting up default-jre (2:1.11-72) ... Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up prokka (1.14.6+dfsg-3) ... Setting up plasmidid (1.6.3+dfsg-3) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid'] 0m54.5s INFO: Running scripts post_install 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 0m54.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 0m55.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 0m55.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpqduirf4p to testing 0m55.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m55.4s INFO: Running scripts pre_distupgrade 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_exceptions'] 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_exceptions'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'update'] 0m58.9s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8786 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 2s (6205 kB/s) Reading package lists... 0m58.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'update'] 0m58.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-yf', 'dist-upgrade'] 2m2.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libcapnp-0.7.0 libicu67 libldap-2.4-2 libllvm11 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libprocps8 libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libvulkan1 libwebp6 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libgsl25 libsemanage1 The following NEW packages will be installed: adwaita-icon-theme at-spi2-common fontconfig gcc-12-base gtk-update-icon-cache hicolor-icon-theme libabsl20220623 libaom3 libatk1.0-0 libavif15 libcairo2 libcap2 libcapnp-0.9.2 libdatrie1 libdav1d6 libde265-0 libffi8 libfile-find-rule-perl libfribidi0 libgav1-1 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgsl27 libgtk2.0-0 libgtk2.0-common libheif1 libhtscodecs2 libicu72 libldap-2.5-0 liblerc4 libllvm15 libmbedcrypto7 libmbedtls14 libmbedx509-1 libnuma1 libnumber-compare-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libperl5.36 libpixman-1-0 libproc2-0 libpython3.11-minimal libpython3.11-stdlib librav1e0 libsemanage2 libsepol2 libssl3 libsvtav1enc1 libtext-glob-perl libthai-data libthai0 libtiff6 libwebp7 libx265-199 libxcb-randr0 libxcb-render0 libxcomposite1 libxcursor1 libxinerama1 libxrandr2 libyuv0 openjdk-17-jre openjdk-17-jre-headless perl-modules-5.36 python3.11 python3.11-minimal shared-mime-info usrmerge util-linux-extra The following packages will be upgraded: adduser apt base-files base-passwd bash bedtools bowtie2 bsdutils ca-certificates ca-certificates-java cd-hit coreutils dash debconf debian-archive-keyring debianutils default-jre default-jre-headless diffutils dpkg e2fsprogs findutils fontconfig-config fonts-cmu fonts-dejavu-core gpgv grep gzip hostname init-system-helpers java-common less libacl1 libapt-pkg6.0 libasound2 libasound2-data libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libbio-perl-perl libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcap-ng0 libclone-perl libcom-err2 libconfig-general-perl libcrypt1 libcups2 libcurl3-gnutls libdata-dumper-simple-perl libdata-stag-perl libdb5.3 libdbus-1-3 libdebconfclient0 libdeflate0 libdevel-callchecker-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdynaloader-functions-perl libedit2 libelf1 libexpat1 libext2fs2 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libgcc-s1 libgcrypt20 libgd-perl libgd3 libgdbm-compat4 libgdbm6 libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libhts3 libidn2-0 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl liblz4-1 liblzma5 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmd0 libmodule-implementation-perl libmodule-runtime-perl libmount1 libmurmurhash2 libncbi6 libncurses6 libncursesw6 libnettle8 libnghttp2-14 libnspr4 libnss3 libnumber-format-perl libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libparams-classify-perl libparams-validate-perl libpciaccess0 libpcre2-8-0 libpcre3 libpcsclite1 libpng16-16 libpsl5 libpython3-stdlib libreadline8 libregexp-common-perl libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsensors-config libsensors5 libset-intspan-perl libsmartcols1 libsqlite3-0 libss2 libssh2-1 libstatistics-basic-perl libstdc++6 libsvg-perl libswiss-perl libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libtry-tiny-perl libudev1 libunistring2 libuuid1 libvulkan1 libx11-6 libx11-data libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxpm4 libxrender1 libxtst6 libxxhash0 libz3-4 libzstd1 login logsave lsb-base mash mawk media-types mount ncbi-blast+ ncbi-data ncbi-tools-bin ncurses-base ncurses-bin openssl parallel passwd perl perl-base plasmidid procps prodigal prokka python3 python3-minimal readline-common samtools sed sensible-utils sysstat sysvinit-utils tar tzdata ucf util-linux x11-common xz-utils zlib1g 241 upgraded, 70 newly installed, 2 to remove and 0 not upgraded. Need to get 232 MB of archives. After this operation, 534 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u5 [70.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u4 [2748 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u4 [606 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libblkid1 amd64 2.38.1-5+b1 [147 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpcre2-8-0 amd64 10.42-1 [261 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libselinux1 amd64 3.4-1+b6 [73.7 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libmount1 amd64 2.38.1-5+b1 [166 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.38.1-5+b1 [107 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libaudit-common all 1:3.0.9-1 [10.4 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libcap-ng0 amd64 0.8.3-1+b3 [17.1 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.9-1 [46.8 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 login amd64 1:4.13+dfsg1-1+b1 [616 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 util-linux-extra amd64 2.38.1-5+b1 [111 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.38.1-5+b1 [1177 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 liblzma5 amd64 5.4.1-0.2 [205 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [290 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 tar amd64 1.34+dfsg-1.2+deb12u1 [836 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 dpkg amd64 1.21.22 [1567 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 sysvinit-utils amd64 3.06-4 [31.0 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 lsb-base all 11.6 [4584 B] Get:23 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 debianutils amd64 5.7-0.5~deb12u1 [103 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.2.15-2+b2 [1491 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.38.1-5+b1 [94.4 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.12-2 [91.8 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 diffutils amd64 1:3.8-4 [352 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 findutils amd64 4.9.0-4 [636 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.8-5 [421 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 gzip amd64 1.12-1 [140 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 hostname amd64 3.23+nmu1 [10.5 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libtinfo6 amd64 6.4-4 [331 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 ncurses-bin amd64 6.4-4 [421 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libparams-validate-perl amd64 1.31-1 [64.4 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libaom3 amd64 3.6.0-1 [1851 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libdav1d6 amd64 1.0.0-2 [495 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libabsl20220623 amd64 20220623.1-1 [391 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libgav1-1 amd64 0.18.0-1+b1 [332 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 librav1e0 amd64 0.5.1-6 [763 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libsvtav1enc1 amd64 1.4.1+dfsg-1 [2121 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libyuv0 amd64 0.0~git20230123.b2528b0-1 [168 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libavif15 amd64 0.11.1-1 [93.8 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libde265-0 amd64 1.0.11-1+deb12u2 [185 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libx265-199 amd64 3.5-2+b1 [1150 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libheif1 amd64 1.15.1-1 [215 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libgd3 amd64 2.3.3-9 [124 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libgd-perl amd64 2.76-4+b1 [132 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-7+deb12u1 [1608 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 debconf all 1.5.82 [121 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libpam0g amd64 1.5.2-6+deb12u1 [92.0 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [697 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u2 [192 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libxpm4 amd64 1:3.5.12-1.1+deb12u1 [48.6 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 sed amd64 4.9-1 [329 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libgcrypt20 amd64 1.10.1-3 [696 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 liblz4-1 amd64 1.9.4-1 [62.9 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libcap2 amd64 1:2.66-4 [27.0 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.22-1~deb12u1 [331 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.22-1~deb12u1 [108 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libxxhash0 amd64 0.8.1-1 [27.6 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.6.1 [907 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libnettle8 amd64 3.8.1-2 [288 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libp11-kit0 amd64 0.24.1-2 [345 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libtasn1-6 amd64 4.19.0-2 [56.6 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u2 [1404 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 libsemanage-common all 3.4-1 [21.6 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libsepol2 amd64 3.4-2.1 [276 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libsemanage2 amd64 3.4-1+b5 [89.9 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 passwd amd64 1:4.13+dfsg1-1+b1 [972 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libpam-modules-bin amd64 1.5.2-6+deb12u1 [75.6 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libpam-modules amd64 1.5.2-6+deb12u1 [291 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.134 [183 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 gpgv amd64 2.2.40-1.1 [648 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 debian-archive-keyring all 2023.3+deb12u1 [161 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.4-1+b3 [46.6 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.6.1 [1373 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libdebconfclient0 amd64 0.270 [9900 B] Get:130 http://deb.debian.org/debian bookworm/main amd64 base-passwd amd64 3.6.1 [60.0 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:132 http://deb.debian.org/debian bookworm/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:133 http://deb.debian.org/debian bookworm/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 usrmerge all 37~deb12u1 [13.3 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 init-system-helpers all 1.65.2 [49.8 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 ncurses-base all 6.4-4 [261 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libcapnp-0.9.2 amd64 0.9.2-2 [1305 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 mash amd64 2.3+dfsg-3+b1 [188 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-5 [108 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-5 [941 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libmurmurhash2 amd64 1.5-3 [5860 B] Get:143 http://deb.debian.org/debian bookworm/main amd64 logsave amd64 1.47.0-2 [19.6 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libext2fs2 amd64 1.47.0-2 [205 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 e2fsprogs amd64 1.47.0-2 [571 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 mount amd64 2.38.1-5+b1 [134 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:162 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libuuid1 amd64 2.38.1-5+b1 [28.8 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:167 http://deb.debian.org/debian bookworm/main amd64 libpam-runtime all 1.5.2-6+deb12u1 [161 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 libacl1 amd64 2.3.1-3 [31.5 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 libattr1 amd64 1:2.5.1-4 [22.2 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 mawk amd64 1.3.4.20200120-3.1 [119 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2024a-0+deb12u1 [297 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 less amd64 590-2 [131 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 xz-utils amd64 5.4.1-0.2 [471 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u1 [44.0 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 bedtools amd64 2.30.0+dfsg-3 [665 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.5.0-3+b2 [1409 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230710~deb12u1 [11.9 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get:194 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.10+7-1~deb12u1 [43.7 MB] Get:207 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get:208 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get:209 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get:234 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get:245 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get:251 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:254 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:257 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.10+7-1~deb12u1 [184 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 fonts-cmu all 0.7.0-5 [4892 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 libconfig-general-perl all 2.65-2 [71.8 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:269 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:274 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u5 [385 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 libdata-dumper-simple-perl all 0.11-7 [12.5 kB] Get:276 http://deb.debian.org/debian bookworm/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:277 http://deb.debian.org/debian bookworm/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:278 http://deb.debian.org/debian bookworm/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:279 http://deb.debian.org/debian bookworm/main amd64 libgetopt-simple-perl all 1.52-7 [15.5 kB] Get:280 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:281 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:282 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:283 http://deb.debian.org/debian bookworm/main amd64 libio-all-perl all 0.87-2 [67.3 kB] Get:284 http://deb.debian.org/debian bookworm/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:285 http://deb.debian.org/debian bookworm/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:286 http://deb.debian.org/debian bookworm/main amd64 liblist-allutils-perl all 0.19-1 [42.0 kB] Get:287 http://deb.debian.org/debian bookworm/main amd64 libmath-bezier-perl all 0.01-4 [7032 B] Get:288 http://deb.debian.org/debian bookworm/main amd64 libmath-round-perl all 0.07-3 [9312 B] Get:289 http://deb.debian.org/debian bookworm/main amd64 libmath-vec-perl all 1.01-5 [17.1 kB] Get:290 http://deb.debian.org/debian bookworm/main amd64 libmath-vecstat-perl all 0.08-3 [8408 B] Get:291 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:292 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:293 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:294 http://deb.debian.org/debian bookworm/main amd64 libncbi6 amd64 6.1.20170106+dfsg1-10 [4082 kB] Get:295 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get:296 http://deb.debian.org/debian bookworm/main amd64 libnumber-format-perl all 1.75-3 [28.9 kB] Get:297 http://deb.debian.org/debian bookworm/main amd64 libregexp-common-perl all 2017060201-3 [175 kB] Get:298 http://deb.debian.org/debian bookworm/main amd64 libset-intspan-perl all 1.19-3 [25.3 kB] Get:299 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.47.0-2 [24.5 kB] Get:300 http://deb.debian.org/debian bookworm/main amd64 libstatistics-basic-perl all 1.6611-3 [61.5 kB] Get:301 http://deb.debian.org/debian bookworm/main amd64 libsvg-perl all 2.87-1 [64.3 kB] Get:302 http://deb.debian.org/debian bookworm/main amd64 libswiss-perl all 1.80-1 [776 kB] Get:303 http://deb.debian.org/debian bookworm/main amd64 libvulkan1 amd64 1.3.239.0-1 [116 kB] Get:304 http://deb.debian.org/debian bookworm/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:305 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get:306 http://deb.debian.org/debian bookworm/main amd64 ncbi-tools-bin amd64 6.1.20170106+dfsg1-10 [1941 kB] Get:307 http://deb.debian.org/debian bookworm/main amd64 sysstat amd64 12.6.1-1 [596 kB] Get:308 http://deb.debian.org/debian bookworm/main amd64 parallel all 20221122+ds-2 [1873 kB] Get:309 http://deb.debian.org/debian bookworm/main amd64 prodigal amd64 1:2.6.3-6 [508 kB] Get:310 http://deb.debian.org/debian bookworm/main amd64 prokka amd64 1.14.6+dfsg-4 [9968 kB] Get:311 http://deb.debian.org/debian bookworm/main amd64 plasmidid amd64 1.6.5+dfsg-2 [47.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 232 MB in 2s (96.0 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15289 files and directories currently installed.) Preparing to unpack .../base-files_12.4+deb12u5_amd64.deb ... Unpacking base-files (12.4+deb12u5) over (11.1+deb11u9) ... Setting up base-files (12.4+deb12u5) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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Setting up libtinfo6:amd64 (6.4-4) ... (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 ... 15315 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4-4_amd64.deb ... Unpacking ncurses-bin (6.4-4) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4-4) ... (Reading database ... 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(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 ... 17493 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.6.1_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.6.1) over (2.2.4) ... Setting up libapt-pkg6.0:amd64 (2.6.1) ... (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 ... 17493 files and directories currently installed.) Preparing to unpack .../libnettle8_3.8.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libnettle8:amd64 (3.8.1-2) ... (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 ... 17493 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.8.1-2_amd64.deb ... Unpacking libhogweed6:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libhogweed6:amd64 (3.8.1-2) ... (Reading database ... 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(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 ... 17495 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-1) ... (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 ... 17500 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.24.1-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.24.1-2) over (0.23.22-1) ... Setting up libp11-kit0:amd64 (0.24.1-2) ... (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 ... 17500 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-2) over (4.16.0-2+deb11u1) ... Setting up libtasn1-6:amd64 (4.19.0-2) ... (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 ... 17500 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u2_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u2) over (3.7.1-5+deb11u4) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u2) ... (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 ... 17502 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.4-1_all.deb ... Unpacking libsemanage-common (3.4-1) over (3.1-1) ... Setting up libsemanage-common (3.4-1) ... Installing new version of config file /etc/selinux/semanage.conf ... Selecting previously unselected package libsepol2: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 ... 17502 files and directories currently installed.) Preparing to unpack .../libsepol2_3.4-2.1_amd64.deb ... Unpacking libsepol2:amd64 (3.4-2.1) ... Setting up libsepol2:amd64 (3.4-2.1) ... Selecting previously unselected package libsemanage2: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 ... 17506 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.4-1+b5_amd64.deb ... Unpacking libsemanage2:amd64 (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.4-1+b5) ... (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 ... 17511 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-1+b1_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-1+b1) over (1:4.8.1-1) ... Setting up passwd (1:4.13+dfsg1-1+b1) ... Installing new version of config file /etc/default/useradd ... (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 ... 17546 files and directories currently installed.) Removing libsemanage1:amd64 (3.1-1+b2) ... (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 ... 17541 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.2-6+deb12u1_amd64.deb ... Unpacking libpam-modules-bin (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Replacing files in old package libpam-modules:amd64 (1.4.0-9+deb11u1) ... Setting up libpam-modules-bin (1.5.2-6+deb12u1) ... (Reading database ... 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(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 ... 17517 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.3+deb12u1_all.deb ... Unpacking debian-archive-keyring (2023.3+deb12u1) over (2021.1.1+deb11u1) ... Setting up debian-archive-keyring (2023.3+deb12u1) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (Reading database ... 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(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 ... 17515 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.1_amd64.deb ... Unpacking base-passwd (3.6.1) over (3.5.51) ... Setting up base-passwd (3.6.1) ... Selecting previously unselected package libnumber-compare-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17515 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17521 files and directories currently installed.) Preparing to unpack .../libtext-glob-perl_0.11-3_all.deb ... Unpacking libtext-glob-perl (0.11-3) ... Setting up libtext-glob-perl (0.11-3) ... Selecting previously unselected package libfile-find-rule-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17527 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 17541 files and directories currently installed.) Preparing to unpack .../usrmerge_37~deb12u1_all.deb ... Unpacking usrmerge (37~deb12u1) ... Setting up usrmerge (37~deb12u1) ... (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 ... 17548 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.65.2_all.deb ... Unpacking init-system-helpers (1.65.2) over (1.60) ... Setting up init-system-helpers (1.65.2) ... (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 ... 17548 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4-4_all.deb ... Unpacking ncurses-base (6.4-4) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-base (6.4-4) ... Selecting previously unselected package libssl3: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 ... 17550 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libcapnp-0.9.2:amd64. Preparing to unpack .../libcapnp-0.9.2_0.9.2-2_amd64.deb ... Unpacking libcapnp-0.9.2:amd64 (0.9.2-2) ... Preparing to unpack .../mash_2.3+dfsg-3+b1_amd64.deb ... Unpacking mash (2.3+dfsg-3+b1) over (2.2.2+dfsg-2) ... (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 ... 17580 files and directories currently installed.) Removing libgsl25:amd64 (2.6+dfsg-2) ... (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 ... 17567 files and directories currently installed.) Preparing to unpack .../libgslcblas0_2.7.1+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.7.1+dfsg-5) over (2.6+dfsg-2) ... Selecting previously unselected package libgsl27:amd64. Preparing to unpack .../libgsl27_2.7.1+dfsg-5_amd64.deb ... Unpacking libgsl27:amd64 (2.7.1+dfsg-5) ... Preparing to unpack .../libmurmurhash2_1.5-3_amd64.deb ... Unpacking libmurmurhash2:amd64 (1.5-3) over (1.5-2) ... Preparing to unpack .../logsave_1.47.0-2_amd64.deb ... Unpacking logsave (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../libext2fs2_1.47.0-2_amd64.deb ... Unpacking libext2fs2:amd64 (1.47.0-2) over (1.46.2-2) ... Setting up libext2fs2:amd64 (1.47.0-2) ... (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 ... 17579 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2_amd64.deb ... Unpacking e2fsprogs (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../mount_2.38.1-5+b1_amd64.deb ... Unpacking mount (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u2) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... (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 ... 17886 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) over (3.9.2-3) ... Setting up python3-minimal (3.11.2-1+b1) ... (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 ... 17887 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) over (3.9.2-3) ... Preparing to unpack .../01-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) over (4.0.0) ... Preparing to unpack .../02-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) over (8.1-1) ... Preparing to unpack .../03-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) over (8.1-1) ... Preparing to unpack .../04-libsqlite3-0_3.40.1-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.40.1-2) over (3.34.1-3) ... Preparing to unpack .../05-libtirpc-common_1.3.3+ds-1_all.deb ... Unpacking libtirpc-common (1.3.3+ds-1) over (1.3.1-1+deb11u1) ... Preparing to unpack .../06-libgssapi-krb5-2_1.20.1-2+deb12u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../07-libkrb5-3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../08-libk5crypto3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../09-libkrb5support0_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../10-libcom-err2_1.47.0-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../11-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) over (1.6.1-2) ... Preparing to unpack .../12-libtirpc3_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.3+ds-1) over (1.3.1-1+deb11u1) ... Preparing to unpack .../13-libuuid1_2.38.1-5+b1_amd64.deb ... Unpacking libuuid1:amd64 (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Setting up libuuid1:amd64 (2.38.1-5+b1) ... Selecting previously unselected package libpython3.11-stdlib: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 ... 17893 files and directories currently installed.) Preparing to unpack .../libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Preparing to unpack .../libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) over (3.9.2-3) ... Preparing to unpack .../libpam-runtime_1.5.2-6+deb12u1_all.deb ... Unpacking libpam-runtime (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Setting up libpam-runtime (1.5.2-6+deb12u1) ... (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 ... 18267 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-3_amd64.deb ... Unpacking libacl1:amd64 (2.3.1-3) over (2.2.53-10) ... Setting up libacl1:amd64 (2.3.1-3) ... (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 ... 18268 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.1-4_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.1-4) over (1:2.4.48-6) ... Setting up libattr1:amd64 (1:2.5.1-4) ... Installing new version of config file /etc/xattr.conf ... (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 ... 18269 files and directories currently installed.) Preparing to unpack .../libmd0_1.0.4-2_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-2) over (1.0.3-3) ... Setting up libmd0:amd64 (1.0.4-2) ... (Reading database ... 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Removing debian:chambers_of_commerce_root_-_2008.pem Removing debian:cybertrust_global_root.pem Removing debian:dst_root_ca_x3.pem Removing debian:ec-acc.pem Removing debian:geotrust_primary_certification_authority_-_g2.pem Removing debian:global_chambersign_root_-_2008.pem Removing debian:globalsign_root_ca_-_r2.pem Removing debian:hellenic_academic_and_research_institutions_rootca_2011.pem Removing debian:network_solutions_certificate_authority.pem Removing debian:quovadis_root_ca.pem Removing debian:sonera_class_2_root_ca.pem Removing debian:staat_der_nederlanden_ev_root_ca.pem Removing debian:staat_der_nederlanden_root_ca_-_g3.pem Removing debian:trustis_fps_root_ca.pem Removing debian:verisign_universal_root_certification_authority.pem Replacing debian:ACCVRAIZ1.pem Replacing debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Replacing debian:Actalis_Authentication_Root_CA.pem Replacing 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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 Replacing debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Replacing debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Replacing debian:Hongkong_Post_Root_CA_1.pem Replacing debian:Hongkong_Post_Root_CA_3.pem Replacing debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Replacing debian:IdenTrust_Commercial_Root_CA_1.pem Replacing debian:IdenTrust_Public_Sector_Root_CA_1.pem Replacing debian:Izenpe.com.pem Replacing debian:Microsec_e-Szigno_Root_CA_2009.pem Replacing debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Replacing debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Replacing debian:NAVER_Global_Root_Certification_Authority.pem Replacing debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Replacing debian:OISTE_WISeKey_Global_Root_GB_CA.pem Replacing debian:OISTE_WISeKey_Global_Root_GC_CA.pem Replacing debian:QuoVadis_Root_CA_1_G3.pem Replacing debian:QuoVadis_Root_CA_2.pem Replacing debian:QuoVadis_Root_CA_2_G3.pem Replacing debian:QuoVadis_Root_CA_3.pem Replacing debian:QuoVadis_Root_CA_3_G3.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Replacing debian:SSL.com_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_Root_Certification_Authority_RSA.pem Replacing debian:SZAFIR_ROOT_CA2.pem Replacing debian:SecureSign_RootCA11.pem Replacing debian:SecureTrust_CA.pem Replacing debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Replacing debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Replacing debian:Security_Communication_Root_CA.pem Replacing debian:Starfield_Class_2_CA.pem Replacing debian:Starfield_Root_Certificate_Authority_-_G2.pem Replacing debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Replacing debian:SwissSign_Gold_CA_-_G2.pem Replacing debian:SwissSign_Silver_CA_-_G2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_3.pem Replacing debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Replacing debian:TWCA_Global_Root_CA.pem Replacing debian:TWCA_Root_Certification_Authority.pem Replacing debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Replacing debian:TrustCor_ECA-1.pem Replacing debian:TrustCor_RootCert_CA-1.pem Replacing debian:TrustCor_RootCert_CA-2.pem Replacing debian:Trustwave_Global_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Replacing debian:UCA_Extended_Validation_Root.pem Replacing debian:UCA_Global_G2_Root.pem Replacing debian:USERTrust_ECC_Certification_Authority.pem Replacing debian:USERTrust_RSA_Certification_Authority.pem Replacing debian:XRamp_Global_CA_Root.pem Replacing debian:certSIGN_ROOT_CA.pem Replacing debian:certSIGN_Root_CA_G2.pem Replacing debian:e-Szigno_Root_CA_2017.pem Replacing debian:ePKI_Root_Certification_Authority.pem Replacing debian:emSign_ECC_Root_CA_-_C3.pem Replacing debian:emSign_ECC_Root_CA_-_G3.pem Replacing debian:emSign_Root_CA_-_C1.pem Replacing debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up sysstat (12.6.1-1) ... Installing new version of config file /etc/sysstat/sysstat.ioconf ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libheif1:amd64 (1.15.1-1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libgd3:amd64 (2.3.3-9) ... Setting up parallel (20221122+ds-2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libcups2:amd64 (2.4.2-3+deb12u5) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up python3 (3.11.2-1+b1) ... Setting up samtools (1.16.1-1) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up libgd-perl (2.76-4+b1) ... Setting up liblist-allutils-perl (0.19-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up openjdk-17-jre-headless:amd64 (17.0.10+7-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libparams-validate-perl:amd64 (1.31-1) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... Processing triggers for debianutils (5.7-0.5~deb12u1) ... Processing triggers for ca-certificates-java (20230710~deb12u1) ... done. Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre:amd64 (17.0.10+7-1~deb12u1) ... Setting up default-jre (2:1.17-74) ... Setting up prokka (1.14.6+dfsg-4) ... Setting up plasmidid (1.6.5+dfsg-2) ... Installing new version of config file /etc/plasmidid/OR.conf ... Installing new version of config file /etc/plasmidid/circos_individual_1_3_3.conf ... Installing new version of config file /etc/plasmidid/circos_summary_1_3_3.conf ... Installing new version of config file /etc/plasmidid/simple.conf ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230710~deb12u1) ... done. 2m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-yf', 'dist-upgrade'] 2m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m3.6s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 2m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 2m3.8s 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 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 2m3.8s INFO: apt-cache knows about the following packages: plasmidid 2m3.8s INFO: Running scripts pre_install 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 2m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 2m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 2m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 2m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 2m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 2m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 2m3.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 2m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 2m4.0s 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 bookworm/main amd64 Packages 100 /var/lib/dpkg/status 2m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 2m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid'] 2m4.5s DUMP: Reading package lists... Building dependency tree... Reading state information... plasmidid is already the newest version (1.6.5+dfsg-2). The following packages were automatically installed and are no longer required: libcapnp-0.7.0 libicu67 libldap-2.4-2 libllvm11 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libprocps8 libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libvulkan1 libwebp6 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid'] 2m4.5s INFO: Running scripts post_install 2m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 2m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 2m4.5s INFO: Running scripts post_distupgrade 2m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_exceptions'] 2m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_exceptions'] 2m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_zz_backports'] 2m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_zz_backports'] 2m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 2m6.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 2m6.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpqduirf4p to sid 2m6.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 2m6.2s INFO: Running scripts pre_distupgrade 2m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_exceptions'] 2m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_exceptions'] 2m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'update'] 2m10.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9743 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7151 kB] Fetched 17.1 MB in 3s (6049 kB/s) Reading package lists... 2m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'update'] 2m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-yf', 'dist-upgrade'] 3m10.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gcc-12-base libcapnp-0.7.0 libcapnp-0.9.2 libdav1d6 libicu67 libldap-2.4-2 libllvm11 libllvm15 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libnuma1 libperl5.32 libperl5.36 libprocps8 libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 libx265-199 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 perl-modules-5.36 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libavif15 libsvtav1enc1 The following NEW packages will be installed: fonts-dejavu-mono gcc-14-base libavif16 libcapnp-1.0.1 libdav1d7 libheif-plugin-dav1d libheif-plugin-libde265 libllvm17 libperl5.38 libsharpyuv0 libsvtav1enc1d1 libunistring5 netbase perl-modules-5.38 The following packages will be upgraded: adduser adwaita-icon-theme apt aragorn at-spi2-common base-files base-passwd bash bedtools bowtie2 bsdutils ca-certificates ca-certificates-java coreutils dash debconf debian-archive-keyring debianutils default-jre default-jre-headless diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core gcc-10-base gcc-12-base gcc-9-base gpgv grep gtk-update-icon-cache hmmer hostname infernal init-system-helpers java-common libabsl20220623 libacl1 libaom3 libapt-pkg6.0 libasound2 libasound2-data libatk1.0-0 libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-op-check-perl libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcairo2 libcap-ng0 libcap2 libclone-perl libcom-err2 libcrypt1 libcups2 libcurl3-gnutls libdatrie1 libdb5.3 libdbus-1-3 libde265-0 libdebconfclient0 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1 libext2fs2 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgd-perl libgd3 libgdbm-compat4 libgdbm6 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgraphics-colorobject-perl libgraphite2-3 libgsl27 libgslcblas0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libheif1 libhogweed6 libhts3 libhtscodecs2 libicu72 libidn2-0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 liblmdb0 liblz4-1 liblzma5 libmath-round-perl libmbedcrypto7 libmbedtls14 libmbedx509-1 libmd0 libmount1 libmpdec3 libmurmurhash2 libncurses6 libncursesw6 libnettle8 libnghttp2-14 libnsl2 libnspr4 libnss3 libnuma1 libnumber-format-perl libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libparams-classify-perl libparams-validate-perl libpciaccess0 libpcre2-8-0 libpcsclite1 libpng16-16 libproc2-0 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librav1e0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsensors-config libsensors5 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libssl3 libstdc++6 libsystemd0 libtasn1-6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc3 libudev1 libuuid1 libvulkan1 libwebp7 libx11-6 libx11-data libx11-xcb1 libxi6 libxml-libxml-perl libxml2 libxpm4 libxxhash0 libyuv0 libz3-4 libzstd1 login logsave mash mawk media-types mount ncbi-blast+ ncurses-base ncurses-bin openjdk-11-jre openjdk-11-jre-headless openjdk-17-jre openjdk-17-jre-headless openssl parallel passwd perl perl-base procps prokka python3 python3-minimal python3.11 python3.11-minimal readline-common samtools sed sensible-utils shared-mime-info sysstat sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 249 upgraded, 14 newly installed, 2 to remove and 0 not upgraded. Need to get 282 MB of archives. After this operation, 210 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.16 [88.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-6 [96.9 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15 [2750 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15 [602 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240201-3 [42.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240201-3 [71.6 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:10 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240201-3 [714 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:16 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:17 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.3 [240 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.3-2 [362 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.3-2 [124 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:22 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3+b1 [87.8 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.12 [983 kB] Get:24 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:25 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.4 [1509 kB] Get:26 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:27 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:28 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:29 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:30 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:31 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:35 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libnumber-format-perl all 1.76-1 [29.4 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b2 [313 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libparams-validate-perl amd64 1.31-2+b1 [63.6 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libgd-perl amd64 2.78-1+b1 [131 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] Get:44 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:46 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:47 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5+b1 [72.8 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5+b1 [48.5 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libdav1d7 amd64 1.4.0-1 [546 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [108 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libgd3 amd64 2.3.3-9+b1 [125 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libaom3 amd64 3.8.1-1 [1868 kB] Get:59 http://deb.debian.org/debian sid/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libyuv0 amd64 0.0~git202401110.af6ac82-1 [169 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libavif16 amd64 1.0.4-1 [105 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4 [308 kB] Get:64 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:65 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:66 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:67 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1 [317 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.0-1 [101 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.42-1 [277 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1 [388 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libheif-plugin-dav1d amd64 1.17.6-1 [9592 B] Get:74 http://deb.debian.org/debian sid/main amd64 libde265-0 amd64 1.0.15-1 [187 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libheif-plugin-libde265 amd64 1.17.6-1 [12.9 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libheif1 amd64 1.17.6-1 [284 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:79 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [232 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libxpm4 amd64 1:3.5.17-1 [55.8 kB] Get:85 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-6 [159 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-6 [190 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2 [11.3 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2 [48.4 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-6 [117 kB] Get:94 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-6 [155 kB] Get:95 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-6 [1230 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2 [295 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2 [327 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.3-1 [1425 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271 [9940 B] Get:105 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-9.1+b1 [65.8 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:108 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1+b1 [50.1 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-9.1+b1 [265 kB] Get:112 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:113 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:114 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:115 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:117 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.12 [1368 kB] Get:118 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:119 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:120 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:121 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-6 [32.1 kB] Get:122 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2+b1 [19.9 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.47.0-2+b1 [205 kB] Get:124 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2+b1 [572 kB] Get:125 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-6 [143 kB] Get:126 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:127 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:128 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-1 [597 kB] Get:129 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5+b1 [135 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5+b1 [333 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5+b1 [80.0 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5+b1 [33.2 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:137 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.5-1 [2063 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:140 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-6 [29.7 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-1 [1825 kB] Get:145 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-1 [2037 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-1 [817 kB] Get:147 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:148 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:150 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-9.1 [134 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:154 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get:156 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get:157 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:158 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1 [1241 kB] Get:159 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:160 http://deb.debian.org/debian sid/main amd64 xz-utils amd64 5.4.5-0.3 [503 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-1 [1452 kB] Get:163 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-1 [751 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b1 [138 kB] Get:165 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 3.24.41-1 [45.7 kB] Get:166 http://deb.debian.org/debian sid/main amd64 adwaita-icon-theme all 46~beta-4 [614 kB] Get:167 http://deb.debian.org/debian sid/main amd64 aragorn amd64 1.2.41-2 [88.0 kB] Get:168 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.50.0-1 [163 kB] Get:169 http://deb.debian.org/debian sid/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:170 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.5.2-1 [1438 kB] Get:171 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:172 http://deb.debian.org/debian sid/main amd64 libgtk2.0-common all 2.24.33-3 [2659 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libatk1.0-0 amd64 2.50.0-1+b1 [50.1 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-13+b1 [47.1 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-13+b1 [43.3 kB] Get:177 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-13+b1 [111 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.14.10-4 [203 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libcups2 amd64 2.4.7-1+b1 [247 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [35.1 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [215 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [47.3 kB] Get:185 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1 [462 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libgtk2.0-0 amd64 2.24.33-3 [1816 kB] Get:192 http://deb.debian.org/debian sid/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:193 http://deb.debian.org/debian sid/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libvulkan1 amd64 1.3.275.0-1 [124 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libpciaccess0 amd64 0.17-3 [51.6 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libelf1 amd64 0.190-1+b1 [176 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.8-1 [125 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libllvm17 amd64 1:17.0.6-5 [23.7 MB] Get:205 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-8 [14.4 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-8+b1 [34.7 kB] Get:207 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 24.0.1-1 [8278 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 24.0.1-1 [151 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libglapi-mesa amd64 24.0.1-1 [36.1 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libgl1 amd64 1.7.0-1 [89.7 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libglx0 amd64 1.7.0-1 [34.7 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libglvnd0 amd64 1.7.0-1 [51.3 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libgif7 amd64 5.2.1-2.5+b1 [43.1 kB] Get:214 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre amd64 17.0.10+7-1 [184 kB] Get:215 http://deb.debian.org/debian sid/main amd64 java-common all 0.75 [6640 B] Get:216 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:217 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.35-1.1 [108 kB] Get:218 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.98-1 [1382 kB] Get:219 http://deb.debian.org/debian sid/main amd64 libasound2 amd64 1.2.10-3 [368 kB] Get:220 http://deb.debian.org/debian sid/main amd64 libasound2-data all 1.2.10-3 [20.7 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.0.1-1 [50.8 kB] Get:222 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre-headless amd64 17.0.10+7-1 [43.7 MB] Get:223 http://deb.debian.org/debian sid/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get:224 http://deb.debian.org/debian sid/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get:225 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-3 [36.6 kB] Get:226 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240201-3 [136 kB] Get:227 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-14 [41.2 kB] Get:228 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-5 [28.8 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get:230 http://deb.debian.org/debian sid/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:231 http://deb.debian.org/debian sid/main amd64 infernal amd64 1.1.5-2 [5914 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libabsl20220623 amd64 20220623.1-3 [393 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libcapnp-1.0.1 amd64 1.0.1-3+b1 [1460 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get:238 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:239 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-4 [215 kB] Get:240 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.6.0-3 [421 kB] Get:241 http://deb.debian.org/debian sid/main amd64 libgraphics-colorobject-perl all 0.5.0-10.1 [28.1 kB] Get:242 http://deb.debian.org/debian sid/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get:243 http://deb.debian.org/debian sid/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get:244 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19.2-1 [645 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.19+ds-1 [447 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:247 http://deb.debian.org/debian sid/main amd64 libllvm15 amd64 1:15.0.7-10 [23.2 MB] Get:248 http://deb.debian.org/debian sid/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:249 http://deb.debian.org/debian sid/main amd64 libmath-round-perl all 0.08-1 [9172 B] Get:250 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.7-1 [280 kB] Get:251 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.7-1 [130 kB] Get:252 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.7-1 [165 kB] Get:253 http://deb.debian.org/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:254 http://deb.debian.org/debian sid/main amd64 libmurmurhash2 amd64 1.6-1 [5824 B] Get:255 http://deb.debian.org/debian sid/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:256 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] Get:257 http://deb.debian.org/debian sid/main amd64 mash amd64 2.3+dfsg-6 [194 kB] Get:258 http://deb.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.5 MB] Get:259 http://deb.debian.org/debian sid/main amd64 openjdk-11-jre amd64 11.0.22+7-2 [194 kB] Get:260 http://deb.debian.org/debian sid/main amd64 openjdk-11-jre-headless amd64 11.0.22+7-2 [38.3 MB] Get:261 http://deb.debian.org/debian sid/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get:262 http://deb.debian.org/debian sid/main amd64 parallel all 20231122+ds-1 [1946 kB] Get:263 http://deb.debian.org/debian sid/main amd64 prokka all 1.14.6+dfsg-6 [15.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 282 MB in 2s (113 MB/s) (Reading database ... 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Preparing to unpack .../01-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b2_amd64.deb ... 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 Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b2) over (2.0207+dfsg+really+2.0134-1+b1) ... Preparing to unpack .../02-libparams-validate-perl_1.31-2+b1_amd64.deb ... Unpacking libparams-validate-perl:amd64 (1.31-2+b1) over (1.31-1) ... Preparing to unpack .../03-libparams-classify-perl_0.015-2+b2_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b2) over (0.015-2+b1) ... Preparing to unpack .../04-libgd-perl_2.78-1+b1_amd64.deb ... Unpacking libgd-perl (2.78-1+b1) over (2.76-4+b1) ... 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Setting up perl-base (5.38.2-3) ... (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 ... 27339 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... 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Setting up bedtools (2.31.1+dfsg-2) ... Setting up gcc-9-base:amd64 (9.5.0-5) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1) ... Setting up libavif16:amd64 (1.0.4-1) ... Setting up libxpm4:amd64 (1:3.5.17-1) ... Setting up libmbedx509-1:amd64 (2.28.7-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libmbedtls14:amd64 (2.28.7-1) ... Setting up fontconfig-config (2.15.0-1) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up libavahi-common3:amd64 (0.8-13+b1) ... Setting up e2fsprogs (1.47.0-2+b1) ... Setting up libnss3:amd64 (2:3.98-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 8 removed; done. Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Setting up shared-mime-info (2.4-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Setting up parallel (20231122+ds-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+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 libdrm2:amd64 (2.4.120-2) ... Setting up libllvm15:amd64 (1:15.0.7-10) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libharfbuzz0b:amd64 (8.3.0-2) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1) ... Setting up ca-certificates-java (20240118) ... done. Setting up libllvm17:amd64 (1:17.0.6-5) ... Setting up libavahi-client3:amd64 (0.8-13+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up gtk-update-icon-cache (3.24.41-1) ... Setting up fontconfig (2.15.0-1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up libparams-classify-perl:amd64 (0.015-2+b2) ... Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.1-1) ... Setting up libcurl3-gnutls:amd64 (8.6.0-3) ... Setting up libcairo2:amd64 (1.18.0-1+b1) ... Setting up adwaita-icon-theme (46~beta-4) ... Setting up libcups2:amd64 (2.4.7-1+b1) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... Setting up libhts3:amd64 (1.19+ds-1) ... Setting up libglx-mesa0:amd64 (24.0.1-1) ... Setting up libglx0:amd64 (1.7.0-1) ... Setting up libgtk2.0-0:amd64 (2.24.33-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-1) ... Setting up openjdk-11-jre-headless:amd64 (11.0.22+7-2) ... Setting up samtools (1.19.2-1) ... Setting up libgl1:amd64 (1.7.0-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up python3 (3.11.6-1) ... Setting up bowtie2 (2.5.2-1) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1) ... Setting up libheif1:amd64 (1.17.6-1) ... Setting up libgd3:amd64 (2.3.3-9+b1) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1) ... Setting up libgd-perl (2.78-1+b1) ... Processing triggers for debianutils (5.16) ... Processing triggers for hicolor-icon-theme (0.17-2) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for ca-certificates-java (20240118) ... done. Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.10+7-1) ... Setting up openjdk-11-jre:amd64 (11.0.22+7-2) ... Setting up default-jre (2:1.17-75) ... Setting up prokka (1.14.6+dfsg-6) ... Processing triggers for ca-certificates (20240203) ... 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. 3m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-yf', 'dist-upgrade'] 3m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m12.6s DUMP: 09b4543cfa9c08eb81dd7ad79a717b8d - 3m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 3m12.8s 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 3m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'show', '--no-all-versions', 'plasmidid'] 3m12.8s INFO: apt-cache knows about the following packages: plasmidid 3m12.8s INFO: Running scripts pre_install 3m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 3m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 3m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 3m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 3m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 3m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 3m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 3m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 3m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 3m12.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 3m12.9s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid'] 3m13.4s DUMP: Reading package lists... Building dependency tree... Reading state information... plasmidid is already the newest version (1.6.5+dfsg-2). The following packages were automatically installed and are no longer required: gcc-12-base libcapnp-0.7.0 libcapnp-0.9.2 libdav1d6 libicu67 libldap-2.4-2 libllvm11 libllvm15 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libnuma1 libperl5.32 libperl5.36 libprocps8 libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 libx265-199 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 perl-modules-5.36 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid'] 3m13.4s INFO: Running scripts post_install 3m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 3m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 3m13.4s INFO: Running scripts post_distupgrade 3m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_exceptions'] 3m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_exceptions'] 3m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_zz_backports'] 3m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_distupgrade_zz_backports'] 3m13.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m14.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m14.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m16.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m16.0s INFO: Running scripts pre_install 3m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 3m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_database-server'] 3m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 3m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_exceptions'] 3m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 3m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_extras'] 3m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 3m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture'] 3m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 3m16.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 3m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy'] 3m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 3m16.1s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 3m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-cache', 'policy', 'plasmidid'] 3m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid=1.6.5+dfsg-2'] 3m16.5s DUMP: Reading package lists... Building dependency tree... Reading state information... plasmidid is already the newest version (1.6.5+dfsg-2). The following packages were automatically installed and are no longer required: gcc-12-base libcapnp-0.7.0 libcapnp-0.9.2 libdav1d6 libicu67 libldap-2.4-2 libllvm11 libllvm15 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libnuma1 libperl5.32 libperl5.36 libprocps8 libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 libx265-199 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 perl-modules-5.36 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', '-y', 'install', 'plasmidid=1.6.5+dfsg-2'] 3m16.5s INFO: Running scripts post_install 3m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 3m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_install_exceptions'] 3m16.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m17.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m17.8s INFO: /bin converted to /usr/bin by /usr merge 3m17.8s INFO: /lib converted to /usr/lib by /usr merge 3m17.8s INFO: /lib/init converted to /usr/lib/init by /usr merge 3m17.8s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 3m17.8s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 3m17.8s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 3m17.8s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 3m17.8s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 3m17.8s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 3m17.8s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 3m17.8s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 3m17.8s INFO: /lib64 converted to /usr/lib64 by /usr merge 3m17.8s INFO: /sbin converted to /usr/sbin by /usr merge 3m20.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', '-ac', '--ignore-obsolete'] 3m25.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', '-ac', '--ignore-obsolete'] 3m25.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 3m25.9s DUMP: 0.15.6 3m25.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 3m25.9s INFO: Running adequate version 0.15.6 now. 3m25.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'plasmidid'] 3m26.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'plasmidid'] 3m26.1s INFO: Running scripts pre_remove 3m26.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 3m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 3m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 3m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 3m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 3m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 3m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 3m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 3m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 3m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 3m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_exceptions'] 3m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/pre_remove_exceptions'] 3m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 3m35.8s DUMP: install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 46~beta-4 install ok installed apt apt 2.7.12 install ok installed aragorn aragorn 1.2.41-2 install ok installed at-spi2-common at-spi2-common 2.50.0-1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bedtools bedtools 2.31.1+dfsg-2 install ok installed bowtie2 bowtie2 2.5.2-1 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed ca-certificates ca-certificates 20240203 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 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed default-jre default-jre 2:1.17-75 install ok installed default-jre-headless default-jre-headless 2:1.17-75 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.4 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1 install ok installed fontconfig-config fontconfig-config 2.15.0-1 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-10-base:amd64 gcc-10-base 10.5.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-14 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240201-3 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-5 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.41-1 install ok installed gzip gzip 1.12-1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.17-2 install ok installed hmmer hmmer 3.4+dfsg-2 install ok installed hostname hostname 3.23+nmu2 install ok installed infernal infernal 1.1.5-2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed java-common java-common 0.75 install ok installed less less 590-2 install ok installed libabsl20220623:amd64 libabsl20220623 20220623.1-3 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libaom3:amd64 libaom3 3.8.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.12 install ok installed libasound2:amd64 libasound2 1.2.10-3 install ok installed libasound2-data libasound2-data 1.2.10-3 install ok installed libatk1.0-0:amd64 libatk1.0-0 2.50.0-1+b1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b1 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b1 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b1 install ok installed libavif16:amd64 libavif16 1.0.4-1 install ok installed libb-hooks-op-check-perl:amd64 libb-hooks-op-check-perl 0.22-2+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 2.39.3-6 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.11.8-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 install ok installed libcairo2:amd64 libcairo2 1.18.0-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcapnp-0.7.0:amd64 libcapnp-0.7.0 0.7.0-7 install ok installed libcapnp-0.9.2:amd64 libcapnp-0.9.2 0.9.2-2 install ok installed libcapnp-1.0.1:amd64 libcapnp-1.0.1 1.0.1-3+b1 install ok installed libcarp-always-perl libcarp-always-perl 0.16-1 install ok installed libclone-perl:amd64 libclone-perl 0.46-1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libconfig-general-perl libconfig-general-perl 2.65-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcups2:amd64 libcups2 2.4.7-1+b1 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.6.0-3 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 install ok installed libdav1d6:amd64 libdav1d6 1.0.0-2 install ok installed libdav1d7:amd64 libdav1d7 1.4.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-4 install ok installed libde265-0:amd64 libde265-0 1.0.15-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libdevel-callchecker-perl:amd64 libdevel-callchecker-perl 0.008-2+b1 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-6 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.120-2 install ok installed libdrm-common libdrm-common 2.4.120-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.120-2 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.120-2 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.120-2 install ok installed libdrm2:amd64 libdrm2 2.4.120-2 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.003-3 install ok installed libedit2:amd64 libedit2 3.1-20230828-1 install ok installed libelf1:amd64 libelf1 0.190-1+b1 install ok installed libexpat1:amd64 libexpat1 2.6.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-basedir-perl libfile-basedir-perl 0.09-2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfont-ttf-perl libfont-ttf-perl 1.06-2 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgav1-1:amd64 libgav1-1 0.18.0-1+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240201-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgd-perl libgd-perl 2.78-1+b1 install ok installed libgd3:amd64 libgd3 2.3.3-9+b1 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5+b1 install ok installed libgdbm6:amd64 libgdbm6 1.23-5+b1 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.10+dfsg-3+b1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.10+dfsg-3 install ok installed libgetopt-simple-perl libgetopt-simple-perl 1.52-7 install ok installed libgif7:amd64 libgif7 5.2.1-2.5+b1 install ok installed libgl1:amd64 libgl1 1.7.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.0.1-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.0.1-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-1 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.0.1-1 install ok installed libglx0:amd64 libglx0 1.7.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgomp1:amd64 libgomp1 14-20240201-3 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphics-colornames-perl libgraphics-colornames-perl 3.5.0-3 install ok installed libgraphics-colorobject-perl libgraphics-colorobject-perl 0.5.0-10.1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgsl27:amd64 libgsl27 2.7.1+dfsg-6+b1 install ok installed libgslcblas0:amd64 libgslcblas0 2.7.1+dfsg-6+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5+b1 install ok installed libgtk2.0-0:amd64 libgtk2.0-0 2.24.33-3 install ok installed libgtk2.0-common libgtk2.0-common 2.24.33-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 install ok installed libheif-plugin-dav1d:amd64 libheif-plugin-dav1d 1.17.6-1 install ok installed libheif-plugin-libde265:amd64 libheif-plugin-libde265 1.17.6-1 install ok installed libheif1:amd64 libheif1 1.17.6-1 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhts3:amd64 libhts3 1.19+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 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+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5+b1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5+b3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 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 libllvm11:amd64 libllvm11 1:11.0.1-2 install ok installed libllvm15:amd64 libllvm15 1:15.0.7-10 install ok installed libllvm17:amd64 libllvm17 1:17.0.6-5 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 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 libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.7-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.7-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.7-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-2 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libmurmurhash2:amd64 libmurmurhash2 1.6-1 install ok installed libncbi6:amd64 libncbi6 6.1.20170106+dfsg1-10 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1 install ok installed libnss3:amd64 libnss3 2:3.98-1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libnumber-format-perl libnumber-format-perl 1.76-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.51.0+ds-4 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.51.0+ds-4 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.51.0+ds-4 install ok installed libparams-classify-perl:amd64 libparams-classify-perl 0.015-2+b2 install ok installed libparams-validate-perl:amd64 libparams-validate-perl 1.31-2+b1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libpcsclite1:amd64 libpcsclite1 2.0.1-1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.42-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-4 install ok installed libprocps8:amd64 libprocps8 2:3.3.17-5 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-1 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed librav1e0:amd64 librav1e0 0.7.1-2 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed libreadonly-perl libreadonly-perl 2.050-3 install ok installed libregexp-common-perl libregexp-common-perl 2017060201-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsensors-config libsensors-config 1:3.6.0-8 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-8+b1 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libset-intspan-perl libset-intspan-perl 1.19-3 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libspiffy-perl libspiffy-perl 0.46-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-4 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3:amd64 libssl3 3.1.5-1 install ok installed libstatistics-basic-perl libstatistics-basic-perl 1.6611-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240201-3 install ok installed libsvg-perl libsvg-perl 2.87-1 install ok installed libsvtav1enc1d1:amd64 libsvtav1enc1d1 1.7.0+dfsg-2+b1 install ok installed libswiss-perl libswiss-perl 1.80-1 install ok installed libsystemd0:amd64 libsystemd0 255.3-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtbb2:amd64 libtbb2 2020.3-1 install ok installed libtext-format-perl libtext-format-perl 0.62-1 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.31-2 install ok installed libudev1:amd64 libudev1 255.3-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libvulkan1:amd64 libvulkan1 1.3.275.0-1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.7-1 install ok installed libx265-199:amd64 libx265-199 3.5-2+b1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.15-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.15-1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.15-1 install ok installed libxcb-present0:amd64 libxcb-present0 1.15-1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.15-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.15-1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.5-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.1-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2 install ok installed libxi6:amd64 libxi6 2:1.8.1-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 install ok installed libxml-libxml-perl libxml-libxml-perl 2.0207+dfsg+really+2.0134-1+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-3 install ok installed libxml-simple-perl libxml-simple-perl 2.25-2 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxpm4:amd64 libxpm4 1:3.5.17-1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.2-2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyuv0:amd64 libyuv0 0.0~git202401110.af6ac82-1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2+b1 install ok installed lsb-base lsb-base 11.6 install ok installed mash mash 2.3+dfsg-6 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-6 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-4 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-10 install ok installed ncbi-tools-bin ncbi-tools-bin 6.1.20170106+dfsg1-10 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed openjdk-11-jre:amd64 openjdk-11-jre 11.0.22+7-2 install ok installed openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.22+7-2 install ok installed openjdk-17-jre:amd64 openjdk-17-jre 17.0.10+7-1 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.10+7-1 install ok installed openssl openssl 3.1.5-1 install ok installed parallel parallel 20231122+ds-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed plasmidid plasmidid 1.6.5+dfsg-2 install ok installed procps procps 2:4.0.4-4 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 3.11.6-1 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3.11 python3.11 3.11.8-1 install ok installed python3.11-minimal python3.11-minimal 3.11.8-1 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.2-3 install ok installed samtools samtools 1.19.2-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed shared-mime-info shared-mime-info 2.4-1 install ok installed sysstat sysstat 12.7.5-2 install ok installed sysvinit-utils sysvinit-utils 3.08-6 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed util-linux-extra util-linux-extra 2.39.3-6 install ok installed x11-common x11-common 1:7.7+23 install ok installed xz-utils xz-utils 5.4.5-0.3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 3m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 3m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'remove', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', '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', 'libabsl20220623:amd64', 'libaom3:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0: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', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d6:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libnumber-format-perl', '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', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'librav1e0:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc1d1:amd64', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libx265-199:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', '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', 'ncbi-blast+-', 'ncbi-data', 'ncbi-tools-bin', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parallel', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'ucf', 'x11-common', 'xz-utils', 'plasmidid'] 3m40.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: gcc-12-base libperl5.36 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: adwaita-icon-theme aragorn at-spi2-common bedtools bowtie2 ca-certificates ca-certificates-java cd-hit circos 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 libabsl20220623 libaom3 libasound2 libasound2-data libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libavif16 libb-hooks-op-check-perl libbio-perl-perl libbio-searchio-hmmer-perl libbrotli1 libbsd0 libcairo2 libcapnp-0.7.0 libcapnp-0.9.2 libcapnp-1.0.1 libcarp-always-perl libclone-perl libconfig-general-perl libcups2 libcurl3-gnutls libdata-dumper-simple-perl libdata-stag-perl libdatrie1 libdav1d6 libdav1d7 libdbus-1-3 libde265-0 libdeflate0 libdevel-callchecker-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdynaloader-functions-perl libedit2 libelf1 libexpat1 libfile-basedir-perl libfont-ttf-perl libfontconfig1 libfreetype6 libfribidi0 libgav1-1 libgd-perl libgd3 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-simple-perl libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphics-colornames-perl libgraphics-colorobject-perl libgraphite2-3 libgsl27 libgslcblas0 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhts3 libhtscodecs2 libicu67 libicu72 libio-all-perl libio-string-perl libipc-system-simple-perl libjbig0 libjpeg62-turbo liblcms2-2 libldap-2.4-2 libldap-2.5-0 liblerc4 liblist-allutils-perl liblist-someutils-perl liblist-utilsby-perl libllvm11 libllvm15 libllvm17 liblmdb0 libmath-bezier-perl libmath-round-perl libmath-vec-perl libmath-vecstat-perl libmbedcrypto3 libmbedcrypto7 libmbedtls12 libmbedtls14 libmbedx509-0 libmbedx509-1 libmodule-implementation-perl libmodule-runtime-perl libmpdec3 libmurmurhash2 libncbi6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libnuma1 libnumber-format-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libparams-classify-perl libparams-validate-perl libpciaccess0 libpcsclite1 libperl5.32 libpixman-1-0 libpng16-16 libproc2-0 libprocps8 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib librav1e0 libreadline8 libreadonly-perl libregexp-common-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libset-intspan-perl libsharpyuv0 libspiffy-perl libsqlite3-0 libssh2-1 libstatistics-basic-perl libsvg-perl libsvtav1enc1d1 libswiss-perl libtbb2 libtext-format-perl libthai-data libthai0 libtiff5 libtiff6 libtry-tiny-perl libvulkan1 libwebp6 libwebp7 libx11-6 libx11-data libx11-xcb1 libx265-199 libxau6 libxcb-dri2-0 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 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 ncbi-blast+ ncbi-data ncbi-tools-bin netbase openjdk-11-jre openjdk-11-jre-headless openjdk-17-jre openjdk-17-jre-headless openssl parallel perl-modules-5.32 plasmidid procps prodigal prokka python3 python3-minimal python3.11 python3.11-minimal python3.9 python3.9-minimal readline-common samtools sensible-utils shared-mime-info sysstat ucf x11-common xz-utils 0 upgraded, 0 newly installed, 253 to remove and 0 not upgraded. After this operation, 1486 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 ... 21838 files and directories currently installed.) Removing plasmidid (1.6.5+dfsg-2) ... Removing prokka (1.14.6+dfsg-6) ... Removing default-jre (2:1.17-75) ... Removing openjdk-17-jre:amd64 (17.0.10+7-1) ... Removing libgtk2.0-0:amd64 (2.24.33-3) ... Removing adwaita-icon-theme (46~beta-4) ... Removing aragorn (1.2.41-2) ... Removing libatk1.0-0:amd64 (2.50.0-1+b1) ... Removing at-spi2-common (2.50.0-1) ... Removing bedtools (2.31.1+dfsg-2) ... Removing bowtie2 (2.5.2-1) ... Removing openjdk-11-jre:amd64 (11.0.22+7-2) ... Removing openjdk-11-jre-headless:amd64 (11.0.22+7-2) ... Removing default-jre-headless (2:1.17-75) ... Removing openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cd-hit (4.8.1-4) ... Removing circos (0.69.9+dfsg-2) ... Removing libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... Removing libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... Removing libpango-1.0-0:amd64 (1.51.0+ds-4) ... Removing fontconfig (2.15.0-1) ... Removing libgd-perl (2.78-1+b1) ... Removing libgd3:amd64 (2.3.3-9+b1) ... Removing fonts-circos-symbols (0.69.9+dfsg-2) ... Removing fonts-cmu (0.7.0-5) ... Removing gtk-update-icon-cache (3.24.41-1) ... Removing hicolor-icon-theme (0.17-2) ... Removing hmmer (3.4+dfsg-2) ... Removing infernal (1.1.5-2) ... Removing java-common (0.75) ... Removing less (590-2) ... Removing libavif16:amd64 (1.0.4-1) ... Removing libgav1-1:amd64 (0.18.0-1+b1) ... Removing libabsl20220623:amd64 (20220623.1-3) ... Removing libaom3:amd64 (3.8.1-1) ... Removing libasound2:amd64 (1.2.10-3) ... Removing libasound2-data (1.2.10-3) ... Removing libcups2:amd64 (2.4.7-1+b1) ... Removing libavahi-client3:amd64 (0.8-13+b1) ... Removing libavahi-common3:amd64 (0.8-13+b1) ... Removing libavahi-common-data:amd64 (0.8-13+b1) ... Removing libparams-validate-perl:amd64 (1.31-2+b1) ... 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 (0.016-2) ... Removing libparams-classify-perl:amd64 (0.015-2+b2) ... Removing libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Removing libb-hooks-op-check-perl:amd64 (0.22-2+b2) ... Removing libbio-searchio-hmmer-perl (1.7.3-2) ... Removing libbio-perl-perl (1.7.8-1) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libcairo2:amd64 (1.18.0-1+b1) ... Removing samtools (1.19.2-1) ... Removing libhts3:amd64 (1.19+ds-1) ... Removing libcurl3-gnutls:amd64 (8.6.0-3) ... Removing libgl1:amd64 (1.7.0-1) ... Removing libglx0:amd64 (1.7.0-1) ... Removing libglx-mesa0:amd64 (24.0.1-1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libllvm11:amd64 (1:11.0.1-2) ... Removing libcapnp-0.7.0:amd64 (0.7.0-7) ... Removing libcapnp-0.9.2:amd64 (0.9.2-2) ... Removing mash (2.3+dfsg-6) ... Removing libcapnp-1.0.1:amd64 (1.0.1-3+b1) ... Removing libcarp-always-perl (0.16-1) ... Removing libclone-perl:amd64 (0.46-1+b1) ... Removing libconfig-general-perl (2.65-2) ... Removing libdata-dumper-simple-perl (0.11-7) ... Removing libdata-stag-perl (0.14-3) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libdav1d6:amd64 (1.0.0-2) ... Removing libdbus-1-3:amd64 (1.14.10-4) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Removing libdivsufsort3:amd64 (2.0.1-6) ... Removing libgl1-mesa-dri:amd64 (24.0.1-1) ... Removing libdrm-amdgpu1:amd64 (2.4.120-2) ... Removing libdrm-radeon1:amd64 (2.4.120-2) ... Removing libdrm-nouveau2:amd64 (2.4.120-2) ... Removing libdrm-intel1:amd64 (2.4.120-2) ... Removing libdynaloader-functions-perl (0.003-3) ... Removing libelf1:amd64 (0.190-1+b1) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing ncbi-blast+ (2.12.0+ds-4) ... Removing python3 (3.11.6-1) ... Removing python3.11 (3.11.8-1) ... Removing libfile-basedir-perl (0.09-2) ... Removing libfont-ttf-perl (1.06-2) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Removing libgetopt-simple-perl (1.52-7) ... Removing libgif7:amd64 (5.2.1-2.5+b1) ... Removing libglapi-mesa:amd64 (24.0.1-1) ... Removing shared-mime-info (2.4-1) ... Removing libglib2.0-0:amd64 (2.78.4-1) ... Removing libglvnd0:amd64 (1.7.0-1) ... Removing libgomp1:amd64 (14-20240201-3) ... Removing libgraphics-colorobject-perl (0.5.0-10.1) ... Removing libgraphics-colornames-perl (3.5.0-3) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Removing libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Removing libgtk2.0-common (2.24.33-3) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libicu67:amd64 (67.1-7) ... Removing libllvm17:amd64 (1:17.0.6-5) ... Removing libllvm15:amd64 (1:15.0.7-10) ... Removing libio-all-perl (0.87-2) ... Removing libio-string-perl (1.08-4) ... Removing libipc-system-simple-perl (1.30-2) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libyuv0:amd64 (0.0~git202401110.af6ac82-1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing liblist-utilsby-perl (0.12-2) ... Removing liblmdb0:amd64 (0.9.31-1+b1) ... 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 libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libmbedtls14:amd64 (2.28.7-1) ... Removing libmbedx509-1:amd64 (2.28.7-1) ... Removing libmbedcrypto7:amd64 (2.28.7-1) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-2) ... Removing libmurmurhash2:amd64 (1.6-1) ... Removing ncbi-tools-bin (6.1.20170106+dfsg1-10) ... Removing libncbi6:amd64 (6.1.20170106+dfsg1-10) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-1) ... find: '/usr/lib/python3': No such file or directory Removing parallel (20231122+ds-1) ... Removing 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Removing 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Removing procps (2:4.0.4-4) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libnghttp2-14:amd64 (1.59.0-1) ... Removing libnss3:amd64 (2:3.98-1) ... Removing libnspr4:amd64 (2:4.35-1.1) ... Removing libx265-199:amd64 (3.5-2+b1) ... Removing libnuma1:amd64 (2.0.18-1) ... Removing libstatistics-basic-perl (1.6611-3) ... Removing libnumber-format-perl (1.76-1) ... Removing libpciaccess0:amd64 (0.17-3) ... Removing libpcsclite1:amd64 (2.0.1-1) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libproc2-0:amd64 (2:4.0.4-4) ... Removing libprocps8:amd64 (2:3.3.17-5) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing python3-minimal (3.11.6-1) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing librav1e0:amd64 (0.7.1-2) ... Removing libreadline8:amd64 (8.2-3) ... Removing libreadonly-perl (2.050-3) ... Removing libregexp-common-perl (2017060201-3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Removing sysstat (12.7.5-2) ... Removing libsensors5:amd64 (1:3.6.0-8+b1) ... Removing libsensors-config (1:3.6.0-8) ... Removing libset-intspan-perl (1.19-3) ... Removing libwebp7:amd64 (1.3.2-0.4) ... Removing libspiffy-perl (0.46-1) ... Removing libsqlite3-0:amd64 (3.45.1-1) ... Removing libssh2-1:amd64 (1.11.0-4) ... Removing libsvg-perl (2.87-1) ... Removing libsvtav1enc1d1:amd64 (1.7.0+dfsg-2+b1) ... Removing libswiss-perl (1.80-1) ... Removing libtbb2:amd64 (2020.3-1) ... Removing libtext-format-perl (0.62-1) ... Removing libthai-data (0.1.29-2) ... Removing libtry-tiny-perl (0.31-2) ... Removing libvulkan1:amd64 (1.3.275.0-1) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libx11-xcb1:amd64 (2:1.8.7-1) ... Removing libxcb-dri2-0:amd64 (1.15-1) ... Removing libxcb-dri3-0:amd64 (1.15-1) ... Removing libxcb-glx0:amd64 (1.15-1) ... Removing libxcb-present0:amd64 (1.15-1) ... Removing libxcb-randr0:amd64 (1.15-1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxcb-sync1:amd64 (1.15-1) ... Removing libxcb-xfixes0:amd64 (1.15-1) ... Removing libxcomposite1:amd64 (1:0.4.5-1) ... Removing libxcursor1:amd64 (1:1.2.1-1) ... Removing libxdamage1:amd64 (1:1.1.6-1) ... Removing libxtst6:amd64 (2:1.2.3-1.1) ... Removing libxrandr2:amd64 (2:1.5.2-2+b1) ... Removing libxfixes3:amd64 (1:6.0.0-2) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxinerama1:amd64 (2:1.1.4-3) ... Removing libxml-simple-perl (2.25-2) ... Removing libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+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 libxml-sax-perl (1.02+dfsg-3) ... 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 libxpm4:amd64 (1:3.5.17-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libz3-4:amd64 (4.8.12-3.1+b2) ... Removing media-types (10.1.0) ... Removing ncbi-data (6.1.20170106+dfsg1-10) ... Removing netbase (6.4) ... Removing openssl (3.1.5-1) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing prodigal (1:2.6.3-6) ... Removing readline-common (8.2-3) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xz-utils (5.4.5-0.3) ... Removing libfontconfig1:amd64 (2.15.0-1) ... Removing fontconfig-config (2.15.0-1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libedit2:amd64 (3.1-20230828-1) ... Removing libdrm2:amd64 (2.4.120-2) ... Removing libdrm-common (2.4.120-2) ... Removing python3.11-minimal (3.11.8-1) ... Removing libexpat1:amd64 (2.6.0-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libpng16-16:amd64 (1.6.42-1) ... Removing libpython3.11-minimal:amd64 (3.11.8-1) ... find: '/usr/lib/python3': No such file or directory Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.8-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libheif1:amd64 (1.17.6-1) ... Removing libheif-plugin-libde265:amd64 (1.17.6-1) ... Removing libde265-0:amd64 (1.0.15-1) ... Removing libsharpyuv0:amd64 (1.3.2-0.4) ... Removing libheif-plugin-dav1d:amd64 (1.17.6-1) ... Removing libdav1d7:amd64 (1.4.0-1) ... Processing triggers for libc-bin (2.37-15) ... 3m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'remove', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', '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', 'libabsl20220623:amd64', 'libaom3:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0: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', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d6:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libnumber-format-perl', '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', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'librav1e0:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc1d1:amd64', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libx265-199:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', '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', 'ncbi-blast+-', 'ncbi-data', 'ncbi-tools-bin', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parallel', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'ucf', 'x11-common', 'xz-utils', 'plasmidid'] 3m40.4s INFO: Running scripts post_remove 3m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_remove_exceptions'] 3m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_remove_exceptions'] 3m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--purge', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', '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', 'libabsl20220623:amd64', 'libaom3:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0: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', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d6:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libnumber-format-perl', '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', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'librav1e0:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc1d1:amd64', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libx265-199:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', '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', 'ncbi-blast+', 'ncbi-data', 'ncbi-tools-bin', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parallel', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'ucf', 'x11-common', 'xz-utils'] 3m41.4s DUMP: (Reading database ... 9616 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (46~beta-4) ... 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 (20240203) ... 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) ... 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 (2.15.0-1) ... Purging configuration files for fontconfig-config (2.15.0-1) ... 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 (0.75) ... dpkg: warning: ignoring request to remove less which isn't installed dpkg: warning: ignoring request to remove libabsl20220623 which isn't installed dpkg: warning: ignoring request to remove libaom3 which isn't installed dpkg: warning: ignoring request to remove libasound2 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0 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 libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcapnp-0.7.0 which isn't installed dpkg: warning: ignoring request to remove libcapnp-0.9.2 which isn't installed dpkg: warning: ignoring request to remove libcapnp-1.0.1 which isn't installed dpkg: warning: ignoring request to remove libcarp-always-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libconfig-general-perl which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdata-dumper-simple-perl which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdav1d6 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 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 libdrm-nouveau2 which isn't installed dpkg: warning: ignoring request to remove libdrm-radeon1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libdynaloader-functions-perl which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfile-basedir-perl which isn't installed dpkg: warning: ignoring request to remove libfont-ttf-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgav1-1 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 Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... 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 (24.0.1-1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.78.4-1) ... 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 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 libgsl27 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed Purging configuration files for libgtk2.0-0:amd64 (2.24.33-3) ... Purging configuration files for libgtk2.0-common (2.24.33-3) ... 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 libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-all-perl which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libipc-system-simple-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 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 libllvm11 which isn't installed dpkg: warning: ignoring request to remove libllvm15 which isn't installed dpkg: warning: ignoring request to remove libllvm17 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmath-bezier-perl which isn't installed dpkg: warning: ignoring request to remove libmath-round-perl which isn't installed dpkg: warning: ignoring request to remove libmath-vec-perl which isn't installed dpkg: warning: ignoring request to remove libmath-vecstat-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmodule-implementation-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libmurmurhash2 which isn't installed dpkg: warning: ignoring request to remove libncbi6 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libnumber-format-perl 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 libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libprocps8 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-1) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove librav1e0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libreadonly-perl which isn't installed dpkg: warning: ignoring request to remove libregexp-common-perl which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-8) ... 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 libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libstatistics-basic-perl which isn't installed dpkg: warning: ignoring request to remove libsvg-perl which isn't installed dpkg: warning: ignoring request to remove libsvtav1enc1d1 which isn't installed dpkg: warning: ignoring request to remove libswiss-perl which isn't installed dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libtext-format-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 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 libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwebp6 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 libx265-199 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri2-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri3-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-glx0 which isn't installed dpkg: warning: ignoring request to remove libxcb-present0 which isn't installed dpkg: warning: ignoring request to remove libxcb-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 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-3) ... 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 (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-10) ... dpkg: warning: ignoring request to remove ncbi-tools-bin which isn't installed Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove openjdk-11-jre which isn't installed Purging configuration files for openjdk-11-jre-headless:amd64 (11.0.22+7-2) ... dpkg: warning: ignoring request to remove openjdk-17-jre which isn't installed Purging configuration files for openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... Purging configuration files for openssl (3.1.5-1) ... Purging configuration files for parallel (20231122+ds-1) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for procps (2:4.0.4-4) ... 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 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-1) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.2-3) ... 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 (2.4-1) ... Purging configuration files for sysstat (12.7.5-2) ... Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xz-utils which isn't installed 3m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--purge', 'adwaita-icon-theme', 'aragorn', 'at-spi2-common', 'bedtools', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'circos', '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', 'libabsl20220623:amd64', 'libaom3:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0: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', 'libbsd0:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcarp-always-perl', 'libclone-perl:amd64', 'libconfig-general-perl', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdata-dumper-simple-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdav1d6:amd64', 'libdav1d7:amd64', 'libdbus-1-3:amd64', 'libde265-0:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libdynaloader-functions-perl', 'libedit2:amd64', 'libelf1:amd64', 'libexpat1:amd64', 'libfile-basedir-perl', 'libfont-ttf-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgav1-1:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-simple-perl', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphics-colornames-perl', 'libgraphics-colorobject-perl', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libheif-plugin-dav1d:amd64', 'libheif-plugin-libde265:amd64', 'libheif1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-all-perl', 'libio-string-perl', 'libipc-system-simple-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblist-allutils-perl', 'liblist-someutils-perl', 'liblist-utilsby-perl', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17:amd64', 'liblmdb0:amd64', 'libmath-bezier-perl', 'libmath-round-perl', 'libmath-vec-perl', 'libmath-vecstat-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-perl', 'libmpdec3:amd64', 'libmurmurhash2:amd64', 'libncbi6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libnumber-format-perl', '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', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'librav1e0:amd64', 'libreadline8: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', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstatistics-basic-perl', 'libsvg-perl', 'libsvtav1enc1d1:amd64', 'libswiss-perl', 'libtbb2:amd64', 'libtext-format-perl', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtry-tiny-perl', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libx265-199:amd64', 'libxau6:amd64', 'libxcb-dri2-0: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', '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', 'ncbi-blast+', 'ncbi-data', 'ncbi-tools-bin', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parallel', 'perl-modules-5.32', 'procps', 'prodigal', 'prokka', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'shared-mime-info', 'sysstat', 'ucf', 'x11-common', 'xz-utils'] 3m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--purge', 'plasmidid'] 3m41.5s DUMP: (Reading database ... 9420 files and directories currently installed.) Purging configuration files for plasmidid (1.6.5+dfsg-2) ... 3m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--purge', 'plasmidid'] 3m41.5s INFO: Running scripts post_purge 3m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_purge_exceptions'] 3m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_purge_exceptions'] 3m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--purge', '--pending'] 3m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--purge', '--pending'] 3m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--remove', '--pending'] 3m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg', '--remove', '--pending'] 3m41.5s INFO: Running scripts post_test 3m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_test_exceptions'] 3m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'tmp/scripts/post_test_exceptions'] 3m41.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m42.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg-divert', '--list'] 3m42.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 3m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'dpkg-divert', '--list'] 3m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'clean'] 3m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqduirf4p', 'apt-get', 'clean'] 3m42.3s DEBUG: Recording chroot state 3m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/shm'] 3m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/shm'] 3m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/console'] 3m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/console'] 3m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/ptmx'] 3m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/ptmx'] 3m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/pts'] 3m43.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/dev/pts'] 3m43.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/proc'] 3m44.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqduirf4p/proc'] 3m44.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m44.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqduirf4p'] 3m44.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpqduirf4p 3m44.2s INFO: PASS: Upgrading between Debian distributions. 3m44.2s INFO: PASS: All tests. 3m44.2s INFO: piuparts run ends. ret=0 End: 2024-02-22 11:14:01 GMT