Start: 2026-10-20 03:23:22 GMT [testing] Package: sortmerna Source: sortmerna (4.3.7-3) Version: 4.3.7-3+b1 Installed-Size: 1873 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), librocksdb9.11 (>= 9.11.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), python3:any Description: tool for filtering, mapping and OTU-picking NGS reads Homepage: https://github.com/sortmerna/sortmerna Description-md5: 785b2b1a824d6d755aab646a5806eba7 Section: science Priority: optional Filename: pool/main/s/sortmerna/sortmerna_4.3.7-3+b1_amd64.deb Size: 588372 MD5sum: 59b0f317f8348d3c8a8c034e2311c565 SHA256: 4061cef2ba558ab71c9ddd5eba4c135a42275088638510e88a03cabaf9b827a0 [sid] Package: sortmerna Version: 7.1.0-1 Installed-Size: 7617 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libparasail8 (>= 2.4.1), librocksdb9.11 (>= 9.11.2), libstdc++6 (>= 14), zlib1g (>= 1:1.2.3.4) Description: tool for filtering, mapping and OTU-picking NGS reads Homepage: https://github.com/sortmerna/sortmerna Commands: sortmerna Description-md5: 785b2b1a824d6d755aab646a5806eba7 Section: science Priority: optional Filename: pool/main/s/sortmerna/sortmerna_7.1.0-1_amd64.deb Size: 1158500 MD5sum: 453ce809d3a339ba13256e049753e284 SHA256: 52426ce3a27e6d3a65b1fa5530515508f3f2b944a5f5176d7337ad167da26cad Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt sortmerna=7.1.0-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202608291513~1.6.0-23-g1172a6e5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt sortmerna=7.1.0-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.12.113+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.113-1 (2026-10-15) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpj2u8h5dr 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpj2u8h5dr 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/13', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/13', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpj2u8h5dr/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'update'] 0m2.4s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [151 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6651 kB] Fetched 16.9 MB in 1s (15.6 MB/s) Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s DUMP: b86d3e78b7e094e5ba5a04a854c6568e - 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s INFO: Running scripts post_setup 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_dummy_users'] 0m4.6s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_dummy_users'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_forbid_home'] 0m4.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_forbid_home'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_minimize'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_minimize'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_zz_backports'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_setup_zz_backports'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.7s DUMP: install ok installed apt apt 3.3.3 install ok installed base-files base-files 14.2 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-4 install ok installed bsdutils bsdutils 1:2.42.4-1 install ok installed coreutils coreutils 9.10-1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.24 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.11 install ok installed findutils findutils 4.11.0-3 install ok installed gcc-16-base:amd64 gcc-16-base 16.2.0-3 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.14-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69+nmu3 install ok installed libacl1:amd64 libacl1 2.4.0-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.3.3 install ok installed libattr1:amd64 libattr1 1:2.6.0-1 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1+b2 install ok installed libblkid1:amd64 libblkid1 2.42.4-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b2 install ok installed libc-bin libc-bin 2.43-7 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.43-7 install ok installed libc6:amd64 libc6 2.43-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.2+20251210-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-11+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.283 install ok installed libgcc-s1:amd64 libgcc-s1 16.2.0-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-10 install ok installed liblzma5:amd64 liblzma5 5.8.4-1 install ok installed libmd0:amd64 libmd0 1.3.0-1 install ok installed libmount1:amd64 libmount1 2.42.4-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-8 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-8 install ok installed libpam-runtime libpam-runtime 1.7.0-8 install ok installed libpam0g:amd64 libpam0g 1.7.0-8 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.48-3.1 install ok installed libseccomp2:amd64 libseccomp2 2.6.1-1+b1 install ok installed libselinux1:amd64 libselinux1 3.11-2.1 install ok installed libsemanage-common libsemanage-common 3.11-1 install ok installed libsemanage2:amd64 libsemanage2 3.11-1+b1 install ok installed libsepol2:amd64 libsepol2 3.11-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.42.4-1 install ok installed libssl3t64:amd64 libssl3t64 3.6.5-1 install ok installed libstdc++6:amd64 libstdc++6 16.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 262-1 install ok installed libtinfo6:amd64 libtinfo6 6.6+20260608-2 install ok installed libudev1:amd64 libudev1 262-1 install ok installed libuuid1:amd64 libuuid1 2.42.4-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-4 install ok installed login login 1:4.16.0-2+really2.42.4-1 install ok installed login.defs login.defs 1:4.20.3-1 install ok installed mawk mawk 1.3.4.20260302-2 install ok installed mount mount 2.42.4-1 install ok installed ncurses-base ncurses-base 6.6+20260608-2 install ok installed ncurses-bin ncurses-bin 6.6+20260608-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.6.5-1 install ok installed passwd passwd 1:4.20.3-1 install ok installed perl-base perl-base 5.42.3-1 install ok installed sed sed 4.9-3 install ok installed sqv sqv 1.5.0-1 install ok installed sysvinit-utils sysvinit-utils 3.18-1 install ok installed tar tar 1.35+dfsg-6 install ok installed tzdata tzdata 2026e-1 install ok installed util-linux util-linux 2.42.4-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.2-3 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m5.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m5.0s INFO: Running scripts is_testable 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/is_testable_uninstallable'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/is_testable_uninstallable'] 0m5.0s INFO: Running scripts pre_test 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_test_exceptions'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_test_exceptions'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_test_root_password'] 0m5.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_test_root_password'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'show', '--no-all-versions', 'sortmerna'] 0m5.3s DUMP: Package: sortmerna Source: sortmerna (4.3.7-3) Version: 4.3.7-3+b1 Installed-Size: 1873 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), librocksdb9.11 (>= 9.11.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), python3:any Description-en: tool for filtering, mapping and OTU-picking NGS reads SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. Description-md5: 785b2b1a824d6d755aab646a5806eba7 Homepage: https://github.com/sortmerna/sortmerna Section: science Priority: optional Filename: pool/main/s/sortmerna/sortmerna_4.3.7-3+b1_amd64.deb Size: 588372 MD5sum: 59b0f317f8348d3c8a8c034e2311c565 SHA256: 4061cef2ba558ab71c9ddd5eba4c135a42275088638510e88a03cabaf9b827a0 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'show', '--no-all-versions', 'sortmerna'] 0m5.3s INFO: apt-cache knows about the following packages: sortmerna 0m5.3s INFO: Running scripts pre_install 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_database-server'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_database-server'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy'] 0m5.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy', 'sortmerna'] 0m5.4s DUMP: sortmerna: Installed: (none) Candidate: 4.3.7-3+b1 Version table: 4.3.7-3+b1 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy', 'sortmerna'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-y', 'install', 'sortmerna'] 0m10.0s DUMP: Reading package lists... Building dependency tree... Solving dependencies... The following additional packages will be installed: libexpat1 libffi8 libgflags2.2 libncursesw6 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libreadline8t64 librocksdb9.11 libsnappy1v5 libsqlite3-0 media-types netbase python3 python3-minimal python3.14 python3.14-minimal readline-common Suggested packages: python3-doc python3-tk python3-venv python3.14-venv python3.14-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates The following NEW packages will be installed: libexpat1 libffi8 libgflags2.2 libncursesw6 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libreadline8t64 librocksdb9.11 libsnappy1v5 libsqlite3-0 media-types netbase python3 python3-minimal python3.14 python3.14-minimal readline-common sortmerna 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 46.7 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.9.0-1 [133 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libpython3.14-minimal amd64 3.14.8-1 [902 kB] Get:3 http://deb.debian.org/debian forky/main amd64 python3.14-minimal amd64 3.14.8-1 [2715 kB] Get:4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.14.7-3 [25.3 kB] Get:5 http://deb.debian.org/debian forky/main amd64 media-types all 14.0.0 [30.8 kB] Get:6 http://deb.debian.org/debian forky/main amd64 netbase all 6.6 [10.3 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.8.0-2 [32.5 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libncursesw6 amd64 6.6+20260608-2 [137 kB] Get:9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-4 [74.8 kB] Get:10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Get:11 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.53.4-2 [974 kB] Get:12 http://deb.debian.org/debian forky/main amd64 libpython3.14-stdlib amd64 3.14.8-1 [2367 kB] Get:13 http://deb.debian.org/debian forky/main amd64 python3.14 amd64 3.14.8-1 [874 kB] Get:14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.14.7-3 [8252 B] Get:15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.14.7-3 [26.0 kB] Get:16 http://deb.debian.org/debian forky/main amd64 libgflags2.2 amd64 2.2.2-3 [93.2 kB] Get:17 http://deb.debian.org/debian forky/main amd64 libsnappy1v5 amd64 1.3.1-3 [32.1 kB] Get:18 http://deb.debian.org/debian forky/main amd64 librocksdb9.11 amd64 9.11.2-1 [3941 kB] Get:19 http://deb.debian.org/debian forky/main amd64 sortmerna amd64 4.3.7-3+b1 [588 kB] Fetched 13.1 MB in 0s (94.1 MB/s) Selecting previously unselected package libexpat1: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 ... 4950 files and directories currently installed.) Preparing to unpack .../libexpat1_2.9.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.9.0-1) ... Selecting previously unselected package libpython3.14-minimal:amd64. Preparing to unpack .../libpython3.14-minimal_3.14.8-1_amd64.deb ... Unpacking libpython3.14-minimal:amd64 (3.14.8-1) ... Selecting previously unselected package python3.14-minimal. Preparing to unpack .../python3.14-minimal_3.14.8-1_amd64.deb ... Unpacking python3.14-minimal (3.14.8-1) ... Setting up libpython3.14-minimal:amd64 (3.14.8-1) ... Setting up libexpat1:amd64 (2.9.0-1) ... Setting up python3.14-minimal (3.14.8-1) ... 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 ... 5306 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.14.7-3_amd64.deb ... Unpacking python3-minimal (3.14.7-3) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.6_all.deb ... Unpacking netbase (6.6) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../03-libffi8_3.8.0-2_amd64.deb ... Unpacking libffi8:amd64 (3.8.0-2) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../04-libncursesw6_6.6+20260608-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.6+20260608-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../05-readline-common_8.3-4_all.deb ... Unpacking readline-common (8.3-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../06-libreadline8t64_8.3-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../07-libsqlite3-0_3.53.4-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.53.4-2) ... Selecting previously unselected package libpython3.14-stdlib:amd64. Preparing to unpack .../08-libpython3.14-stdlib_3.14.8-1_amd64.deb ... Unpacking libpython3.14-stdlib:amd64 (3.14.8-1) ... Selecting previously unselected package python3.14. Preparing to unpack .../09-python3.14_3.14.8-1_amd64.deb ... Unpacking python3.14 (3.14.8-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../10-libpython3-stdlib_3.14.7-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.14.7-3) ... Setting up python3-minimal (3.14.7-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5836 files and directories currently installed.) Preparing to unpack .../python3_3.14.7-3_amd64.deb ... Unpacking python3 (3.14.7-3) ... Selecting previously unselected package libgflags2.2. Preparing to unpack .../libgflags2.2_2.2.2-3_amd64.deb ... Unpacking libgflags2.2 (2.2.2-3) ... Selecting previously unselected package libsnappy1v5:amd64. Preparing to unpack .../libsnappy1v5_1.3.1-3_amd64.deb ... Unpacking libsnappy1v5:amd64 (1.3.1-3) ... Selecting previously unselected package librocksdb9.11. Preparing to unpack .../librocksdb9.11_9.11.2-1_amd64.deb ... Unpacking librocksdb9.11 (9.11.2-1) ... Selecting previously unselected package sortmerna. Preparing to unpack .../sortmerna_4.3.7-3+b1_amd64.deb ... Unpacking sortmerna (4.3.7-3+b1) ... Setting up media-types (14.0.0) ... Setting up libsqlite3-0:amd64 (3.53.4-2) ... Setting up libsnappy1v5:amd64 (1.3.1-3) ... Setting up libncursesw6:amd64 (6.6+20260608-2) ... Setting up libffi8:amd64 (3.8.0-2) ... Setting up netbase (6.6) ... Setting up readline-common (8.3-4) ... Setting up libgflags2.2 (2.2.2-3) ... Setting up librocksdb9.11 (9.11.2-1) ... Setting up libreadline8t64:amd64 (8.3-4) ... Setting up libpython3.14-stdlib:amd64 (3.14.8-1) ... Setting up python3.14 (3.14.8-1) ... Setting up libpython3-stdlib:amd64 (3.14.7-3) ... Setting up python3 (3.14.7-3) ... Setting up sortmerna (4.3.7-3+b1) ... Processing triggers for libc-bin (2.43-7) ... 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-y', 'install', 'sortmerna'] 0m10.0s INFO: Running scripts post_install 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_install_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_install_exceptions'] 0m10.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m10.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m10.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpj2u8h5dr to sid 0m10.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m10.4s INFO: Running scripts pre_distupgrade 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'update'] 0m13.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [193 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.8 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7740 kB] Fetched 18.7 MB in 2s (8634 kB/s) Reading package lists... 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'update'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-yf', 'dist-upgrade'] 0m16.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libparasail8 The following packages will be upgraded: apt libapt-pkg7.0 libaudit-common libaudit1 libsystemd0 libudev1 sortmerna 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 6661 kB of archives. After this operation, 17.6 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 262.1-1 [512 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 262.1-1 [149 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.3.4 [1286 kB] Get:4 http://deb.debian.org/debian sid/main amd64 apt amd64 3.3.4 [1574 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.2.1-1 [13.3 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.2.1-1 [59.6 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libparasail8 amd64 2.6.2+dfsg-3 [1909 kB] Get:8 http://deb.debian.org/debian sid/main amd64 sortmerna amd64 7.1.0-1 [1158 kB] Fetched 6661 kB in 0s (60.8 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 ... 5901 files and directories currently installed.) Preparing to unpack .../libsystemd0_262.1-1_amd64.deb ... Unpacking libsystemd0:amd64 (262.1-1) over (262-1) ... Setting up libsystemd0:amd64 (262.1-1) ... (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 ... 5901 files and directories currently installed.) Preparing to unpack .../libudev1_262.1-1_amd64.deb ... Unpacking libudev1:amd64 (262.1-1) over (262-1) ... Setting up libudev1:amd64 (262.1-1) ... (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 ... 5901 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_3.3.4_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.3.4) over (3.3.3) ... Setting up libapt-pkg7.0:amd64 (3.3.4) ... (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 ... 5901 files and directories currently installed.) Preparing to unpack .../archives/apt_3.3.4_amd64.deb ... Unpacking apt (3.3.4) over (3.3.3) ... Setting up apt (3.3.4) ... (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 ... 5901 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.2.1-1_all.deb ... Unpacking libaudit-common (1:4.2.1-1) over (1:4.1.2-1) ... Setting up libaudit-common (1:4.2.1-1) ... (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 ... 5901 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.2.1-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.2.1-1) over (1:4.1.2-1+b2) ... Setting up libaudit1:amd64 (1:4.2.1-1) ... Selecting previously unselected package libparasail8: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 ... 5900 files and directories currently installed.) Preparing to unpack .../libparasail8_2.6.2+dfsg-3_amd64.deb ... Unpacking libparasail8:amd64 (2.6.2+dfsg-3) ... Preparing to unpack .../sortmerna_7.1.0-1_amd64.deb ... Unpacking sortmerna (7.1.0-1) over (4.3.7-3+b1) ... Setting up libparasail8:amd64 (2.6.2+dfsg-3) ... Setting up sortmerna (7.1.0-1) ... Processing triggers for libc-bin (2.43-7) ... 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-yf', 'dist-upgrade'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m17.5s DUMP: eb5dba4d0db2c7b6656363d13068317c - 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'show', '--no-all-versions', 'sortmerna'] 0m17.8s DUMP: Package: sortmerna Version: 7.1.0-1 Installed-Size: 7617 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libparasail8 (>= 2.4.1), librocksdb9.11 (>= 9.11.2), libstdc++6 (>= 14), zlib1g (>= 1:1.2.3.4) Description-en: tool for filtering, mapping and OTU-picking NGS reads SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. Description-md5: 785b2b1a824d6d755aab646a5806eba7 Homepage: https://github.com/sortmerna/sortmerna Commands: sortmerna Section: science Priority: optional Filename: pool/main/s/sortmerna/sortmerna_7.1.0-1_amd64.deb Size: 1158500 MD5sum: 453ce809d3a339ba13256e049753e284 SHA256: 52426ce3a27e6d3a65b1fa5530515508f3f2b944a5f5176d7337ad167da26cad 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'show', '--no-all-versions', 'sortmerna'] 0m17.8s INFO: apt-cache knows about the following packages: sortmerna 0m17.8s INFO: Running scripts pre_install 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_database-server'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_database-server'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_exceptions'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_exceptions'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_extras'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_extras'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy'] 0m17.9s 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: 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy', 'sortmerna'] 0m18.0s DUMP: sortmerna: Installed: 7.1.0-1 Candidate: 7.1.0-1 Version table: *** 7.1.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy', 'sortmerna'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-y', 'install', 'sortmerna'] 0m19.0s DUMP: Reading package lists... Building dependency tree... Reading state information... sortmerna is already the newest version (7.1.0-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-y', 'install', 'sortmerna'] 0m19.0s INFO: Running scripts post_install 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_install_exceptions'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_install_exceptions'] 0m19.0s INFO: Running scripts post_distupgrade 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m19.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m19.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m19.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m19.8s INFO: Running scripts pre_install 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_database-server'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_database-server'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_exceptions'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_exceptions'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_extras'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_extras'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy'] 0m19.9s 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: 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy', 'sortmerna'] 0m20.0s DUMP: sortmerna: Installed: 7.1.0-1 Candidate: 7.1.0-1 Version table: *** 7.1.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-cache', 'policy', 'sortmerna'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-y', 'install', 'sortmerna=7.1.0-1'] 0m20.9s DUMP: Reading package lists... Building dependency tree... Reading state information... sortmerna is already the newest version (7.1.0-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', '-y', 'install', 'sortmerna=7.1.0-1'] 0m20.9s INFO: Running scripts post_install 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_install_exceptions'] 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_install_exceptions'] 0m20.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m21.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m21.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', '-ac', '--ignore-obsolete'] 0m22.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', '-ac', '--ignore-obsolete'] 0m22.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.7s DUMP: 0.17.5+b5 0m22.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.7s INFO: Running adequate version 0.17.5+b5 now. 0m22.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'sortmerna'] 0m22.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'sortmerna'] 0m22.7s INFO: Running scripts pre_remove 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_exceptions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/pre_remove_exceptions'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.7s DUMP: install ok installed apt apt 3.3.4 install ok installed base-files base-files 14.2 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-4 install ok installed bsdutils bsdutils 1:2.42.4-1 install ok installed coreutils coreutils 9.10-1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.24 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.11 install ok installed findutils findutils 4.11.0-3 install ok installed gcc-16-base:amd64 gcc-16-base 16.2.0-3 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.14-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69+nmu3 install ok installed libacl1:amd64 libacl1 2.4.0-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.3.4 install ok installed libattr1:amd64 libattr1 1:2.6.0-1 install ok installed libaudit-common libaudit-common 1:4.2.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.2.1-1 install ok installed libblkid1:amd64 libblkid1 2.42.4-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b2 install ok installed libc-bin libc-bin 2.43-7 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.43-7 install ok installed libc6:amd64 libc6 2.43-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.2+20251210-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-11+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.283 install ok installed libexpat1:amd64 libexpat1 2.9.0-1 install ok installed libffi8:amd64 libffi8 3.8.0-2 install ok installed libgcc-s1:amd64 libgcc-s1 16.2.0-3 install ok installed libgflags2.2 libgflags2.2 2.2.2-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-10 install ok installed liblzma5:amd64 liblzma5 5.8.4-1 install ok installed libmd0:amd64 libmd0 1.3.0-1 install ok installed libmount1:amd64 libmount1 2.42.4-1 install ok installed libncursesw6:amd64 libncursesw6 6.6+20260608-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-8 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-8 install ok installed libpam-runtime libpam-runtime 1.7.0-8 install ok installed libpam0g:amd64 libpam0g 1.7.0-8 install ok installed libparasail8:amd64 libparasail8 2.6.2+dfsg-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.48-3.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.14.7-3 install ok installed libpython3.14-minimal:amd64 libpython3.14-minimal 3.14.8-1 install ok installed libpython3.14-stdlib:amd64 libpython3.14-stdlib 3.14.8-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.3-4 install ok installed librocksdb9.11 librocksdb9.11 9.11.2-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.1-1+b1 install ok installed libselinux1:amd64 libselinux1 3.11-2.1 install ok installed libsemanage-common libsemanage-common 3.11-1 install ok installed libsemanage2:amd64 libsemanage2 3.11-1+b1 install ok installed libsepol2:amd64 libsepol2 3.11-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.42.4-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.3.1-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.53.4-2 install ok installed libssl3t64:amd64 libssl3t64 3.6.5-1 install ok installed libstdc++6:amd64 libstdc++6 16.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 262.1-1 install ok installed libtinfo6:amd64 libtinfo6 6.6+20260608-2 install ok installed libudev1:amd64 libudev1 262.1-1 install ok installed libuuid1:amd64 libuuid1 2.42.4-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-4 install ok installed login login 1:4.16.0-2+really2.42.4-1 install ok installed login.defs login.defs 1:4.20.3-1 install ok installed mawk mawk 1.3.4.20260302-2 install ok installed media-types media-types 14.0.0 install ok installed mount mount 2.42.4-1 install ok installed ncurses-base ncurses-base 6.6+20260608-2 install ok installed ncurses-bin ncurses-bin 6.6+20260608-2 install ok installed netbase netbase 6.6 install ok installed openssl-provider-legacy openssl-provider-legacy 3.6.5-1 install ok installed passwd passwd 1:4.20.3-1 install ok installed perl-base perl-base 5.42.3-1 install ok installed python3 python3 3.14.7-3 install ok installed python3-minimal python3-minimal 3.14.7-3 install ok installed python3.14 python3.14 3.14.8-1 install ok installed python3.14-minimal python3.14-minimal 3.14.8-1 install ok installed readline-common readline-common 8.3-4 install ok installed sed sed 4.9-3 install ok installed sortmerna sortmerna 7.1.0-1 install ok installed sqv sqv 1.5.0-1 install ok installed sysvinit-utils sysvinit-utils 3.18-1 install ok installed tar tar 1.35+dfsg-6 install ok installed tzdata tzdata 2026e-1 install ok installed util-linux util-linux 2.42.4-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.2-3 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'remove', '--allow-remove-essential', 'libexpat1:amd64', 'libffi8:amd64', 'libgflags2.2', 'libncursesw6:amd64', 'libparasail8:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'librocksdb9.11', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3.14', 'python3.14-minimal', 'readline-common', 'sortmerna'] 0m25.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following packages will be REMOVED: libexpat1 libffi8 libgflags2.2 libncursesw6 libparasail8 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libreadline8t64 librocksdb9.11 libsnappy1v5 libsqlite3-0 media-types netbase python3 python3-minimal python3.14 python3.14-minimal readline-common sortmerna 0 upgraded, 0 newly installed, 20 to remove and 0 not upgraded. After this operation, 64.2 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 ... 5947 files and directories currently installed.) Removing sortmerna (7.1.0-1) ... Removing python3 (3.14.7-3) ... Removing python3.14 (3.14.8-1) ... Removing python3-minimal (3.14.7-3) ... Removing python3.14-minimal (3.14.8-1) ... Removing libexpat1:amd64 (2.9.0-1) ... Removing libpython3-stdlib:amd64 (3.14.7-3) ... Removing libpython3.14-stdlib:amd64 (3.14.8-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.8.0-2) ... Removing librocksdb9.11 (9.11.2-1) ... Removing libgflags2.2 (2.2.2-3) ... Removing libncursesw6:amd64 (6.6+20260608-2) ... Removing libparasail8:amd64 (2.6.2+dfsg-3) ... Removing libpython3.14-minimal:amd64 (3.14.8-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.3-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsnappy1v5:amd64 (1.3.1-3) ... Removing libsqlite3-0:amd64 (3.53.4-2) ... Removing media-types (14.0.0) ... Removing netbase (6.6) ... Removing readline-common (8.3-4) ... Processing triggers for libc-bin (2.43-7) ... 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'remove', '--allow-remove-essential', 'libexpat1:amd64', 'libffi8:amd64', 'libgflags2.2', 'libncursesw6:amd64', 'libparasail8:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'librocksdb9.11', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3.14', 'python3.14-minimal', 'readline-common', 'sortmerna'] 0m25.6s INFO: Running scripts post_remove 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_remove_exceptions'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_remove_exceptions'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--purge', 'libexpat1:amd64', 'libffi8:amd64', 'libgflags2.2', 'libncursesw6:amd64', 'libparasail8:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'librocksdb9.11', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3.14', 'python3.14-minimal', 'readline-common'] 0m25.7s DUMP: dpkg: warning: ignoring request to remove libexpat1 which is not installed dpkg: warning: ignoring request to remove libffi8 which is not installed dpkg: warning: ignoring request to remove libgflags2.2 which is not installed dpkg: warning: ignoring request to remove libncursesw6 which is not installed dpkg: warning: ignoring request to remove libparasail8 which is not installed dpkg: warning: ignoring request to remove libpython3-stdlib which is not installed (Reading database ... 4956 files and directories currently installed.) Purging configuration files for libpython3.14-minimal:amd64 (3.14.8-1) ... dpkg: warning: ignoring request to remove libpython3.14-stdlib which is not installed Purging configuration files for libreadline8t64:amd64 (8.3-4) ... dpkg: warning: ignoring request to remove librocksdb9.11 which is not installed dpkg: warning: ignoring request to remove libsnappy1v5 which is not installed dpkg: warning: ignoring request to remove libsqlite3-0 which is not installed Purging configuration files for media-types (14.0.0) ... Purging configuration files for netbase (6.6) ... Purging configuration files for python3 (3.14.7-3) ... dpkg: warning: ignoring request to remove python3-minimal which is not installed dpkg: warning: ignoring request to remove python3.14 which is not installed Purging configuration files for python3.14-minimal (3.14.8-1) ... Purging configuration files for readline-common (8.3-4) ... 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--purge', 'libexpat1:amd64', 'libffi8:amd64', 'libgflags2.2', 'libncursesw6:amd64', 'libparasail8:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'librocksdb9.11', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3.14', 'python3.14-minimal', 'readline-common'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--purge', 'sortmerna'] 0m25.7s DUMP: dpkg: warning: ignoring request to remove sortmerna which is not installed 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--purge', 'sortmerna'] 0m25.7s INFO: Running scripts post_purge 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_purge_exceptions'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_purge_exceptions'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--purge', '--pending'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--purge', '--pending'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--remove', '--pending'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg', '--remove', '--pending'] 0m25.7s INFO: Running scripts post_test 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_test_exceptions'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'tmp/scripts/post_test_exceptions'] 0m25.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m26.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg-divert', '--list'] 0m26.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'dpkg-divert', '--list'] 0m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'clean'] 0m26.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr', 'apt-get', 'clean'] 0m26.1s DEBUG: Recording chroot state 0m27.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/shm'] 0m27.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/shm'] 0m27.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/console'] 0m27.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/console'] 0m27.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/ptmx'] 0m27.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/ptmx'] 0m27.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/pts'] 0m27.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/dev/pts'] 0m27.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/proc'] 0m27.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr/proc'] 0m27.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m27.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpj2u8h5dr'] 0m27.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpj2u8h5dr 0m27.1s INFO: PASS: Upgrading between Debian distributions. 0m27.1s INFO: PASS: All tests. 0m27.1s INFO: piuparts run ends. ret=0 End: 2026-10-20 03:23:49 GMT