Start: 2022-12-02 21:40:14 GMT [testing] Package: iva Version: 1.0.11+ds-2 Installed-Size: 8770 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-2_amd64.deb Size: 8581940 MD5sum: 52e98efc7d844e90838060445ac15bef SHA256: c7123cafc046fdce796b902cf194fb4513f4abef2dbd2f4834820556c0e1fb66 [sid] Package: iva Version: 1.0.11+ds-3 Installed-Size: 8769 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-3_amd64.deb Size: 8581420 MD5sum: 864abd579df5ba10cf15608cb6a94d23 SHA256: 4fee119ffb251dc1467267c3f31f14d7d68777dc40cd3a3c3a64a3781bd0ba26 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/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt iva=1.0.11+ds-3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 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/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt iva=1.0.11+ds-3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp9bab9c6g 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp9bab9c6g 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m3.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m3.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/proc'] 0m3.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/proc'] 0m3.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/pts'] 0m3.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/pts'] 0m3.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/ptmx'] 0m3.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/ptmx'] 0m3.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/console'] 0m3.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/console'] 0m3.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/shm'] 0m3.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/shm'] 0m3.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m3.1s DEBUG: Created policy-rc.d and chmodded it. 0m3.1s DEBUG: Created resolv.conf. 0m3.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp9bab9c6g/tmp/scripts/ 0m3.1s INFO: Running scripts post_chroot_unpack 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'update'] 0m6.2s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [164 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8773 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5927 kB] Fetched 14.9 MB in 2s (6375 kB/s) Reading package lists... 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'update'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-yf', 'dist-upgrade'] 0m7.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libsystemd0 libudev1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 435 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.2-1 [329 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.2-1 [106 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 435 kB in 0s (8778 kB/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 ... 8594 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.2-1_amd64.deb ... Unpacking libsystemd0:amd64 (252.2-1) over (252.1-1) ... Setting up libsystemd0:amd64 (252.2-1) ... (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 ... 8594 files and directories currently installed.) Preparing to unpack .../libudev1_252.2-1_amd64.deb ... Unpacking libudev1:amd64 (252.2-1) over (252.1-1) ... Setting up libudev1:amd64 (252.2-1) ... Processing triggers for libc-bin (2.36-5) ... 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-yf', 'dist-upgrade'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.5s DUMP: 7c165ec85c4e96a8252075c95acb3fa1 - 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.5s INFO: Running scripts post_setup 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_dummy_users'] 0m8.6s 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 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_dummy_users'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_forbid_home'] 0m8.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_forbid_home'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.7s 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' 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_minimize'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_minimize'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_zz_backports'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_setup_zz_backports'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.7s DUMP: install ok installed apt apt 2.5.4 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-2+b1 install ok installed bsdutils bsdutils 1:2.38.1-4 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9+b1 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-9 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.8-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.4 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b2 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-5 install ok installed libc6:amd64 libc6 2.36-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b2 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.265 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.8-0.0 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-5 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-5 install ok installed libpam-runtime libpam-runtime 1.5.2-5 install ok installed libpam0g:amd64 libpam0g 1.5.2-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-2 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b2 install ok installed libselinux1:amd64 libselinux1 3.4-1+b3 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b3 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 252.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 252.2-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-4 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-7 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022f-1 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m8.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m9.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m9.3s INFO: Running scripts is_testable 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/is_testable_uninstallable'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/is_testable_uninstallable'] 0m9.3s INFO: Running scripts pre_test 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_test_exceptions'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_test_exceptions'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_test_root_password'] 0m9.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_test_root_password'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m9.6s DUMP: Package: iva Version: 1.0.11+ds-2 Installed-Size: 8770 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-2_amd64.deb Size: 8581940 MD5sum: 52e98efc7d844e90838060445ac15bef SHA256: c7123cafc046fdce796b902cf194fb4513f4abef2dbd2f4834820556c0e1fb66 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m9.6s INFO: apt-cache knows about the following packages: iva 0m9.6s INFO: Running scripts pre_install 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_database-server'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_database-server'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_exceptions'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_extras'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_extras'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy'] 0m9.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy', 'iva'] 0m9.9s DUMP: iva: Installed: (none) Candidate: 1.0.11+ds-2 Version table: 1.0.11+ds-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy', 'iva'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-y', 'install', 'iva'] 0m42.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates ca-certificates-java default-jre-headless fastaq fontconfig-config fonts-dejavu-core gawk java-common kmc libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libbrotli1 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libnspr4 libnss3 libpcsclite1 libpng16-16 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl3 libtirpc-common libtirpc3 media-types mummer openjdk-17-jre-headless openssl python3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pyparsing python3-pysam python3.10 python3.10-minimal python3.11 python3.11-minimal readline-common samtools sensible-utils smalt ucf Suggested packages: default-jre gawk-doc libasound2-plugins alsa-utils cups-common low-memory-monitor krb5-doc krb5-user liblcms2-utils pcscd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic python3-doc python3-tk python3-venv python-networkx-doc gcc gfortran python-numpy-doc python3-dev python3-pytest python3-setuptools python-pyparsing-doc python3.10-venv python3.10-doc binutils binfmt-support python3.11-venv python3.11-doc readline-doc cwltool Recommended packages: r-base-core bioperl trimmomatic alsa-ucm-conf alsa-topology-conf dbus libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-yaml The following NEW packages will be installed: ca-certificates ca-certificates-java default-jre-headless fastaq fontconfig-config fonts-dejavu-core gawk iva java-common kmc libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libbrotli1 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libnspr4 libnss3 libpcsclite1 libpng16-16 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl3 libtirpc-common libtirpc3 media-types mummer openjdk-17-jre-headless openssl python3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pyparsing python3-pysam python3.10 python3.10-minimal python3.11 python3.11-minimal readline-common samtools sensible-utils smalt ucf 0 upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 94.1 MB of archives. After this operation, 351 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.1.0-3 [2012 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.2 [68.5 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.2 [165 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 gawk amd64 1:5.1.0-1 [605 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.7-1 [2008 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.10-minimal amd64 3.10.8-3 [784 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.10-minimal amd64 3.10.8-3 [1951 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.10.6-1 [38.7 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 8.0.0 [33.4 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.3+20220423-2 [133 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-1 [32.2 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-1 [78.6 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-1 [15.7 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-1 [331 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-1 [134 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.0-1 [838 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libpython3.10-stdlib amd64 3.10.8-3 [1685 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 python3.10 amd64 3.10.8-3 [506 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.10.6-1 [21.7 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.10.6-1 [38.2 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.0-3 [812 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.0-3 [2064 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.7-1 [1400 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20211016 [156 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043 [74.0 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20220719 [16.1 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.73 [6268 B] Get:35 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-6+b1 [106 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-6+b1 [41.1 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.4-1 [235 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-6+b1 [44.9 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-1+b2 [243 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.13.1-1+b1 [153 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.2-1+b1 [169 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b5 [279 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.38-2 [290 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-3 [420 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.13.1-4.5 [281 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.13.1-4.5 [351 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.85-1 [1333 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1 [362 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.1-2 [1393 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 5.2.0-2+b1 [1886 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-1 [60.8 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.5+8-2 [43.6 MB] Get:57 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-73 [2812 B] Get:58 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 65.5.0-1 [278 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-2+b1 [183 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.50.0-1+b1 [73.1 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.86.0-2 [359 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.3+20220423-2 [102 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 fastaq all 3.17.0-5 [48.2 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.6.3-1 [943 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.7-3 [136 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 21.3-1.1 [34.2 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.17.0+ds-2+b2 [1618 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 kmc amd64 3.2.1+dfsg-1 [1007 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 mummer amd64 3.23+dfsg-7 [664 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libbambamc0 amd64 0.0.50-6+b1 [39.1 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 smalt amd64 0.7.6-12 [115 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.0-3 [1712 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.0-3 [559 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.10.1-2 [156 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-9 [145 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-9 [792 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.10.1-2 [2202 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.21.5-2 [3845 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 iva amd64 1.0.11+ds-2 [8582 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 94.1 MB in 5s (20.0 MB/s) Selecting previously unselected package libmpfr6: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 ... 8596 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.1.0-3_amd64.deb ... Unpacking libmpfr6:amd64 (4.1.0-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-1.2_all.deb ... Unpacking readline-common (8.2-1.2) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../libreadline8_8.2-1.2_amd64.deb ... 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Setting up libglib2.0-0:amd64 (2.74.1-2) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b5) ... Setting up libsqlite3-0:amd64 (3.40.0-1) ... Setting up libnghttp2-14:amd64 (1.50.0-1+b1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libkrb5support0:amd64 (1.20.1-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libasound2-data (1.2.8-1) ... Setting up libblas3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.2-1+b1) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:amd64 (0.8-6+b1) ... Setting up libncurses6:amd64 (6.3+20220423-2) ... Setting up libdbus-1-3:amd64 (1.14.4-1) ... Setting up libquadmath0:amd64 (12.2.0-9) ... Setting up libbambamc0:amd64 (0.0.50-6+b1) ... Setting up libpng16-16:amd64 (1.6.38-2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libpcsclite1:amd64 (1.9.9-1) ... Setting up libncursesw6:amd64 (6.3+20220423-2) ... Setting up libk5crypto3:amd64 (1.20.1-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-9) ... Setting up sensible-utils (0.0.17) ... Setting up libasound2:amd64 (1.2.8-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up mummer (3.23+dfsg-7) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-1) ... Setting up libpython3.11-minimal:amd64 (3.11.0-3) ... Setting up openssl (3.0.7-1) ... Setting up kmc (3.2.1+dfsg-1) ... Setting up python3.11-minimal (3.11.0-3) ... Setting up smalt (0.7.6-12) ... Setting up liblapack3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libavahi-common3:amd64 (0.8-6+b1) ... Setting up libnss3:amd64 (2:3.85-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-2+b1) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 127 added, 0 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-1) ... Setting up ucf (3.0043) ... Setting up libharfbuzz0b:amd64 (5.2.0-2+b1) ... Setting up ca-certificates-java (20220719) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:EC-ACC.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem done. Setting up libavahi-client3:amd64 (0.8-6+b1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up fontconfig-config (2.13.1-4.5) ... Setting up libcurl3-gnutls:amd64 (7.86.0-2) ... Setting up libcups2:amd64 (2.4.2-1+b2) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libfontconfig1:amd64 (2.13.1-4.5) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.0-3) ... Setting up samtools (1.16.1-1) ... Setting up libpython3.10-stdlib:amd64 (3.10.8-3) ... Setting up openjdk-17-jre-headless:amd64 (17.0.5+8-2) ... 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 libpython3-stdlib:amd64 (3.10.6-1) ... Setting up python3.11 (3.11.0-3) ... Setting up python3.10 (3.10.8-3) ... Setting up default-jre-headless (2:1.17-73) ... Setting up python3 (3.10.6-1) ... Setting up python3-pyparsing (3.0.7-3) ... Setting up python3-pkg-resources (65.5.0-1) ... Setting up python3-pysam (0.17.0+ds-2+b2) ... Setting up fastaq (3.17.0-5) ... Setting up python3-networkx (2.6.3-1) ... Setting up python3-packaging (21.3-1.1) ... Setting up python3-numpy (1:1.21.5-2) ... Setting up iva (1.0.11+ds-2) ... Processing triggers for libc-bin (2.36-5) ... Processing triggers for ca-certificates (20211016) ... 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 (20220719) ... done. 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-y', 'install', 'iva'] 0m42.6s INFO: Running scripts post_install 0m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_install_exceptions'] 0m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_install_exceptions'] 0m42.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m43.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m43.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp9bab9c6g to sid 0m43.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m43.2s INFO: Running scripts pre_distupgrade 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_exceptions'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_exceptions'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'update'] 0m47.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [161 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9395 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6947 kB] Fetched 16.5 MB in 4s (4469 kB/s) Reading package lists... 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'update'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-yf', 'dist-upgrade'] 0m54.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libmd0 The following packages will be upgraded: debconf dpkg iva libblas3 libc-bin libc6 libglib2.0-0 liblapack3 libpcre2-8-0 libpng16-16 libpython3-stdlib python3 python3-minimal python3-pysam tar zlib1g 16 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 21.5 MB of archives. After this operation, 387 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.36-6 [2745 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:3 http://deb.debian.org/debian sid/main amd64 tar amd64 1.34+dfsg-1.1 [836 kB] Get:4 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.21.10 [2402 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.36-6 [604 kB] Get:6 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.10.6-3 [25.5 kB] Get:7 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.10.6-3 [25.2 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.10.6-3 [8588 B] Get:9 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.80 [121 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.40-3 [260 kB] Get:11 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:12 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.20.0+ds-1 [1678 kB] Get:13 http://deb.debian.org/debian sid/main amd64 iva amd64 1.0.11+ds-3 [8581 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.74.2-1 [1394 kB] Get:16 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.5 MB in 2s (14.1 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 ... 13747 files and directories currently installed.) Preparing to unpack .../libc6_2.36-6_amd64.deb ... Unpacking libc6:amd64 (2.36-6) over (2.36-5) ... Setting up libc6:amd64 (2.36-6) ... Selecting previously unselected package libmd0: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 ... 13747 files and directories currently installed.) Preparing to unpack .../libmd0_1.0.4-2_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-2) ... Setting up libmd0:amd64 (1.0.4-2) ... (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 ... 13753 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1.1_amd64.deb ... Unpacking tar (1.34+dfsg-1.1) over (1.34+dfsg-1) ... Setting up tar (1.34+dfsg-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 ... 13753 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.10_amd64.deb ... Unpacking dpkg (1.21.10) over (1.21.9+b1) ... Setting up dpkg (1.21.10) ... (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 ... 13751 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-6_amd64.deb ... Unpacking libc-bin (2.36-6) over (2.36-5) ... Setting up libc-bin (2.36-6) ... (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 ... 13751 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.10.6-3_amd64.deb ... Unpacking python3-minimal (3.10.6-3) over (3.10.6-1) ... Setting up python3-minimal (3.10.6-3) ... (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 ... 13751 files and directories currently installed.) Preparing to unpack .../python3_3.10.6-3_amd64.deb ... Unpacking python3 (3.10.6-3) over (3.10.6-1) ... Preparing to unpack .../libpython3-stdlib_3.10.6-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.10.6-3) over (3.10.6-1) ... Preparing to unpack .../debconf_1.5.80_all.deb ... Unpacking debconf (1.5.80) over (1.5.79) ... Setting up debconf (1.5.80) ... (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 ... 13751 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.40-3_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.40-3) over (10.40-2) ... Setting up libpcre2-8-0:amd64 (10.40-3) ... (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 ... 13751 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.13.dfsg-1) over (1:1.2.11.dfsg-4.1) ... Setting up zlib1g:amd64 (1:1.2.13.dfsg-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 ... 13751 files and directories currently installed.) Preparing to unpack .../0-python3-pysam_0.20.0+ds-1_amd64.deb ... Unpacking python3-pysam (0.20.0+ds-1) over (0.17.0+ds-2+b2) ... Preparing to unpack .../1-iva_1.0.11+ds-3_amd64.deb ... Unpacking iva (1.0.11+ds-3) over (1.0.11+ds-2) ... Preparing to unpack .../2-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) over (3.10.1-2) ... Preparing to unpack .../3-libglib2.0-0_2.74.2-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.2-1) over (2.74.1-2) ... Preparing to unpack .../4-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) over (3.10.1-2) ... Preparing to unpack .../5-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) over (1.6.38-2) ... Setting up libglib2.0-0:amd64 (2.74.2-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.11.0-2) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libpython3-stdlib:amd64 (3.10.6-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... Setting up python3 (3.10.6-3) ... Setting up python3-pysam (0.20.0+ds-1) ... Setting up iva (1.0.11+ds-3) ... Processing triggers for libc-bin (2.36-6) ... 0m54.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-yf', 'dist-upgrade'] 0m54.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m55.0s DUMP: f3f64f31f28bec138b90a95559badc70 - 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m55.3s DUMP: Package: iva Version: 1.0.11+ds-3 Installed-Size: 8769 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-3_amd64.deb Size: 8581420 MD5sum: 864abd579df5ba10cf15608cb6a94d23 SHA256: 4fee119ffb251dc1467267c3f31f14d7d68777dc40cd3a3c3a64a3781bd0ba26 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m55.3s INFO: apt-cache knows about the following packages: iva 0m55.3s INFO: Running scripts pre_install 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_database-server'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_database-server'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_exceptions'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_exceptions'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_extras'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_extras'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy'] 0m55.4s 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: 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy', 'iva'] 0m55.5s DUMP: iva: Installed: 1.0.11+ds-3 Candidate: 1.0.11+ds-3 Version table: *** 1.0.11+ds-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy', 'iva'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-y', 'install', 'iva'] 0m56.0s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m56.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-y', 'install', 'iva'] 0m56.0s INFO: Running scripts post_install 0m56.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_install_exceptions'] 0m56.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_install_exceptions'] 0m56.0s INFO: Running scripts post_distupgrade 0m56.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m56.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m56.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_exceptions'] 0m56.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_exceptions'] 0m56.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m56.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m56.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m56.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m56.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_zz_backports'] 0m56.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_distupgrade_zz_backports'] 0m56.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m56.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m56.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m57.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m57.1s INFO: Running scripts pre_install 0m57.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_database-server'] 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_database-server'] 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_exceptions'] 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_exceptions'] 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_extras'] 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_extras'] 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy'] 0m57.3s 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: 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy', 'iva'] 0m57.3s DUMP: iva: Installed: 1.0.11+ds-3 Candidate: 1.0.11+ds-3 Version table: *** 1.0.11+ds-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-cache', 'policy', 'iva'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-3'] 0m57.8s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m57.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-3'] 0m57.8s INFO: Running scripts post_install 0m57.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_install_exceptions'] 0m57.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_install_exceptions'] 0m57.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m58.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 0m59.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', '-ac', '--ignore-obsolete'] 1m0.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', '-ac', '--ignore-obsolete'] 1m0.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m0.9s DUMP: 0.15.6 1m0.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m0.9s INFO: Running adequate version 0.15.6 now. 1m0.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'iva'] 1m1.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'iva'] 1m1.2s INFO: Running scripts pre_remove 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_exceptions'] 1m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/pre_remove_exceptions'] 1m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m3.6s DUMP: install ok installed apt apt 2.5.4 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-2+b1 install ok installed bsdutils bsdutils 1:2.38.1-4 install ok installed ca-certificates ca-certificates 20211016 install ok installed ca-certificates-java ca-certificates-java 20220719 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.80 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed default-jre-headless default-jre-headless 2:1.17-73 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.10 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed fastaq fastaq 3.17.0-5 install ok installed findutils findutils 4.9.0-3 install ok installed fontconfig-config fontconfig-config 2.13.1-4.5 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-2 install ok installed gawk gawk 1:5.1.0-1 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-9 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.8-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed iva iva 1.0.11+ds-3 install ok installed java-common java-common 0.73 install ok installed kmc kmc 3.2.1+dfsg-1 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.4 install ok installed libasound2:amd64 libasound2 1.2.8-1 install ok installed libasound2-data libasound2-data 1.2.8-1 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-6+b1 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-6+b1 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-6+b1 install ok installed libbambamc0:amd64 libbambamc0 0.0.50-6+b1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b5 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-6 install ok installed libc6:amd64 libc6 2.36-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b2 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-1 install ok installed libcups2:amd64 libcups2 2.4.2-1+b2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.86.0-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.4-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.265 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-4.5 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-9 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.2-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 5.2.0-2+b1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhts3:amd64 libhts3 1.16+ds-3 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.3.0-4 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.2-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-1 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-1 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.13.1-1+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.8-0.0 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libmpfr6:amd64 libmpfr6 4.1.0-3 install ok installed libncurses6:amd64 libncurses6 6.3+20220423-2 install ok installed libncursesw6:amd64 libncursesw6 6.3+20220423-2 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.50.0-1+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.35-1 install ok installed libnss3:amd64 libnss3 2:3.85-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-5 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-5 install ok installed libpam-runtime libpam-runtime 1.5.2-5 install ok installed libpam0g:amd64 libpam0g 1.5.2-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-3 install ok installed libpcsclite1:amd64 libpcsclite1 1.9.9-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.10.6-3 install ok installed libpython3.10-minimal:amd64 libpython3.10-minimal 3.10.8-3 install ok installed libpython3.10-stdlib:amd64 libpython3.10-stdlib 3.10.8-3 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.0-3 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.0-3 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-9 install ok installed libreadline8:amd64 libreadline8 8.2-1.2 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-10 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-10 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b2 install ok installed libselinux1:amd64 libselinux1 3.4-1+b3 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b3 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.0-1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.7-1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 252.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 252.2-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 8.0.0 install ok installed mount mount 2.38.1-4 install ok installed mummer mummer 3.23+dfsg-7 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.5+8-2 install ok installed openssl openssl 3.0.7-1 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 install ok installed python3 python3 3.10.6-3 install ok installed python3-minimal python3-minimal 3.10.6-3 install ok installed python3-networkx python3-networkx 2.6.3-1 install ok installed python3-numpy python3-numpy 1:1.21.5-2 install ok installed python3-packaging python3-packaging 21.3-1.1 install ok installed python3-pkg-resources python3-pkg-resources 65.5.0-1 install ok installed python3-pyparsing python3-pyparsing 3.0.7-3 install ok installed python3-pysam python3-pysam 0.20.0+ds-1 install ok installed python3.10 python3.10 3.10.8-3 install ok installed python3.10-minimal python3.10-minimal 3.10.8-3 install ok installed python3.11 python3.11 3.11.0-3 install ok installed python3.11-minimal python3.11-minimal 3.11.0-3 install ok installed readline-common readline-common 8.2-1.2 install ok installed samtools samtools 1.16.1-1 install ok installed sed sed 4.8-1 install ok installed sensible-utils sensible-utils 0.0.17 install ok installed smalt smalt 0.7.6-12 install ok installed sysvinit-utils sysvinit-utils 3.05-7 install ok installed tar tar 1.34+dfsg-1.1 install ok installed tzdata tzdata 2022f-1 install ok installed ucf ucf 3.0043 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 1m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'mummer', 'openjdk-17-jre-headless:amd64', 'openssl', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.10', 'python3.10-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf', 'iva'] 1m7.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates ca-certificates-java default-jre-headless fastaq fontconfig-config fonts-dejavu-core gawk iva java-common kmc libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libbrotli1 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libnspr4 libnss3 libpcsclite1 libpng16-16 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl3 libtirpc-common libtirpc3 media-types mummer openjdk-17-jre-headless openssl python3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pyparsing python3-pysam python3.10 python3.10-minimal python3.11 python3.11-minimal readline-common samtools sensible-utils smalt ucf 0 upgraded, 0 newly installed, 88 to remove and 0 not upgraded. After this operation, 351 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 ... 13765 files and directories currently installed.) Removing iva (1.0.11+ds-3) ... Removing default-jre-headless (2:1.17-73) ... Removing openjdk-17-jre-headless:amd64 (17.0.5+8-2) ... Removing ca-certificates-java (20220719) ... Removing ca-certificates (20211016) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing fastaq (3.17.0-5) ... Removing libfontconfig1:amd64 (2.13.1-4.5) ... Removing fontconfig-config (2.13.1-4.5) ... Removing fonts-dejavu-core (2.37-2) ... Removing mummer (3.23+dfsg-7) ... Removing gawk (1:5.1.0-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing java-common (0.73) ... Removing kmc (3.2.1+dfsg-1) ... Removing libasound2:amd64 (1.2.8-1) ... Removing libasound2-data (1.2.8-1) ... Removing libcups2:amd64 (2.4.2-1+b2) ... Removing libavahi-client3:amd64 (0.8-6+b1) ... Removing libavahi-common3:amd64 (0.8-6+b1) ... Removing libavahi-common-data:amd64 (0.8-6+b1) ... Removing smalt (0.7.6-12) ... Removing libbambamc0:amd64 (0.0.50-6+b1) ... Removing python3-numpy (1:1.21.5-2) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libharfbuzz0b:amd64 (5.2.0-2+b1) ... Removing libfreetype6:amd64 (2.12.1+dfsg-3) ... Removing samtools (1.16.1-1) ... Removing libdbus-1-3:amd64 (1.14.4-1) ... Removing python3.11 (3.11.0-3) ... Removing python3.11-minimal (3.11.0-3) ... Removing python3-pysam (0.20.0+ds-1) ... Removing python3-networkx (2.6.3-1) ... Removing python3-pkg-resources (65.5.0-1) ... Removing libgfortran5:amd64 (12.2.0-9) ... Removing libglib2.0-0:amd64 (2.74.2-1) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libpython3.11-stdlib:amd64 (3.11.0-3) ... Removing libjpeg62-turbo:amd64 (1:2.1.2-1+b1) ... Removing liblcms2-2:amd64 (2.13.1-1+b1) ... Removing libmpfr6:amd64 (4.1.0-3) ... Removing libncurses6:amd64 (6.3+20220423-2) ... Removing libnss3:amd64 (2:3.85-1) ... Removing libnspr4:amd64 (2:4.35-1) ... Removing libpcsclite1:amd64 (1.9.9-1) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libpython3.11-minimal:amd64 (3.11.0-3) ... Removing libquadmath0:amd64 (12.2.0-9) ... Removing libsigsegv2:amd64 (2.14-1) ... Removing openssl (3.0.7-1) ... Removing python3-packaging (21.3-1.1) ... Removing python3-pyparsing (3.0.7-3) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.17) ... Removing libhts3:amd64 (1.16+ds-3) ... Removing libcurl3-gnutls:amd64 (7.86.0-2) ... Removing libbrotli1:amd64 (1.0.9-2+b5) ... Removing libdeflate0:amd64 (1.14-1) ... Removing python3 (3.10.6-3) ... Removing python3.10 (3.10.8-3) ... Removing libpython3-stdlib:amd64 (3.10.6-3) ... Removing libpython3.10-stdlib:amd64 (3.10.8-3) ... find: '/usr/lib/python3': No such file or directory Removing libhtscodecs2:amd64 (1.3.0-4) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-2+b1) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libncursesw6:amd64 (6.3+20220423-2) ... Removing libnghttp2-14:amd64 (1.50.0-1+b1) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing python3-minimal (3.10.6-3) ... Removing libreadline8:amd64 (8.2-1.2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-10) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Removing libsqlite3-0:amd64 (3.40.0-1) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing media-types (8.0.0) ... Removing readline-common (8.2-1.2) ... Removing python3.10-minimal (3.10.8-3) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-1) ... Removing libkrb5-3:amd64 (1.20.1-1) ... Removing libk5crypto3:amd64 (1.20.1-1) ... Removing libkeyutils1:amd64 (1.6.3-1) ... Removing libkrb5support0:amd64 (1.20.1-1) ... Removing libpython3.10-minimal:amd64 (3.10.8-3) ... find: '/usr/lib/python3': No such file or directory Removing libssl3:amd64 (3.0.7-1) ... Removing libtirpc-common (1.3.3+ds-1) ... Processing triggers for libc-bin (2.36-6) ... 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'mummer', 'openjdk-17-jre-headless:amd64', 'openssl', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.10', 'python3.10-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf', 'iva'] 1m7.7s INFO: Running scripts post_remove 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_remove_exceptions'] 1m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_remove_exceptions'] 1m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'mummer', 'openjdk-17-jre-headless:amd64', 'openssl', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.10', 'python3.10-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf'] 1m8.6s DUMP: (Reading database ... 8666 files and directories currently installed.) Purging configuration files for ca-certificates (20211016) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20220719) ... dpkg: warning: ignoring request to remove default-jre-headless which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't installed Purging configuration files for fontconfig-config (2.13.1-4.5) ... Purging configuration files for fonts-dejavu-core (2.37-2) ... Purging configuration files for gawk (1:5.1.0-1) ... Purging configuration files for java-common (0.73) ... dpkg: warning: ignoring request to remove kmc which isn't installed dpkg: warning: ignoring request to remove libasound2 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libbambamc0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 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 libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 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 libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.2-1) ... dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-1) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 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 libnsl2 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 libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 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 libpython3.10-minimal:amd64 (3.10.8-3) ... dpkg: warning: ignoring request to remove libpython3.10-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.0-3) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 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 dpkg: warning: ignoring request to remove libsigsegv2 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 libssl3 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed Purging configuration files for media-types (8.0.0) ... dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for openjdk-17-jre-headless:amd64 (17.0.5+8-2) ... Purging configuration files for openssl (3.0.7-1) ... Purging configuration files for python3 (3.10.6-3) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3.10 which isn't installed Purging configuration files for python3.10-minimal (3.10.8-3) ... dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.0-3) ... Purging configuration files for readline-common (8.2-1.2) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove smalt which isn't installed Purging configuration files for ucf (3.0043) ... 1m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'mummer', 'openjdk-17-jre-headless:amd64', 'openssl', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.10', 'python3.10-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf'] 1m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--purge', 'iva'] 1m8.6s DUMP: dpkg: warning: ignoring request to remove iva which isn't installed 1m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--purge', 'iva'] 1m8.6s INFO: Running scripts post_purge 1m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_purge_exceptions'] 1m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_purge_exceptions'] 1m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--purge', '--pending'] 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--purge', '--pending'] 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--remove', '--pending'] 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg', '--remove', '--pending'] 1m8.7s INFO: Running scripts post_test 1m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_test_exceptions'] 1m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'tmp/scripts/post_test_exceptions'] 1m8.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 1m9.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 1m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg-divert', '--list'] 1m9.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'dpkg-divert', '--list'] 1m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'clean'] 1m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g', 'apt-get', 'clean'] 1m9.3s DEBUG: Recording chroot state 1m10.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/shm'] 1m10.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/shm'] 1m10.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/console'] 1m10.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/console'] 1m10.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/ptmx'] 1m10.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/ptmx'] 1m10.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/pts'] 1m10.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/dev/pts'] 1m10.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/proc'] 1m10.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g/proc'] 1m10.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 1m10.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9bab9c6g'] 1m10.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp9bab9c6g 1m10.4s INFO: PASS: Upgrading between Debian distributions. 1m10.4s INFO: PASS: All tests. 1m10.4s INFO: piuparts run ends. ret=0 End: 2022-12-02 21:41:25 GMT