Start: 2023-10-12 05:32:44 GMT [buster] Package: seqsero Version: 1.0.1+dfsg-1 Installed-Size: 3497 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description: Salmonella serotyping from genome sequencing data Homepage: https://github.com/denglab/SeqSero Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-1_all.deb Size: 357736 MD5sum: bde4f7eef3f44d26a3ac660bfa7fddf0 SHA256: 8dd2870bcbe679b79221918eb8965b3c0130d0a1f3cde0a63333c49432828309 [buster-next] Package: seqsero Version: 1.0.1+dfsg-1 Installed-Size: 3497 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description: Salmonella serotyping from genome sequencing data Homepage: https://github.com/denglab/SeqSero Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-1_all.deb Size: 357736 MD5sum: bde4f7eef3f44d26a3ac660bfa7fddf0 SHA256: 8dd2870bcbe679b79221918eb8965b3c0130d0a1f3cde0a63333c49432828309 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt seqsero=1.0.1+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt seqsero=1.0.1+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-26-amd64 #1 SMP Debian 5.10.197-1 (2023-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpmkou2d3v 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpmkou2d3v 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpmkou2d3v/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'update'] 0m3.4s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s INFO: Running scripts post_setup 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_dummy_users'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_dummy_users'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_forbid_home'] 0m5.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_forbid_home'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.1s 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' 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.2s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat 0m5.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m5.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m5.7s INFO: Running scripts is_testable 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/is_testable_uninstallable'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/is_testable_uninstallable'] 0m5.7s INFO: Running scripts pre_test 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_test_exceptions'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_test_exceptions'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_test_root_password'] 0m5.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_test_root_password'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m5.9s DUMP: Package: seqsero Version: 1.0.1+dfsg-1 Installed-Size: 3497 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description-en: Salmonella serotyping from genome sequencing data SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. . SeqSero is a novel tool for determining Salmonella serotypes using high- throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing 1. raw reads from genomes of 308 Salmonella isolates of known serotype 2. raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and 3. 354 other publicly available draft or complete Salmonella genomes. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization. Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Homepage: https://github.com/denglab/SeqSero Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-1_all.deb Size: 357736 MD5sum: bde4f7eef3f44d26a3ac660bfa7fddf0 SHA256: 8dd2870bcbe679b79221918eb8965b3c0130d0a1f3cde0a63333c49432828309 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m5.9s INFO: apt-cache knows about the following packages: seqsero 0m5.9s INFO: Running scripts pre_install 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy'] 0m6.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy', 'seqsero'] 0m6.1s DUMP: seqsero: Installed: (none) Candidate: 1.0.1+dfsg-1 Version table: 1.0.1+dfsg-1 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy', 'seqsero'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-y', 'install', 'seqsero'] 0m18.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bwa libaec0 libblas3 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libfuse2 libgfortran5 libgssapi-krb5-2 libhdf5-103 libhts2 libicu63 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkdf5-2 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libncbi-vdb2 libncbi-wvdb2 libncurses6 libnghttp2-14 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 libxml2 mime-support python python-biopython python-minimal python-numpy python-pil python-pkg-resources python-reportlab python-reportlab-accel python2 python2-minimal python2.7 python2.7-minimal readline-common samtools sra-toolkit Suggested packages: fuse krb5-doc krb5-user liblcms2-utils file libmbedtls-doc python-doc python-tk clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python-mysqldb python-matplotlib python-rdflib python-renderpm python-psycopg2 python-scipy raxml t-coffee wise w3-dtd-mathml gcc gfortran python-dev python-pytest python-numpy-dbg python-numpy-doc python-pil-doc python-pil-dbg python-setuptools pdf-viewer python-egenix-mxtexttools python-reportlab-doc python2-doc python2.7-doc binutils binfmt-support readline-doc ispcr Recommended packages: ca-certificates krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils python-biopython-doc ncbi-blast+ python-olefile python-renderpm cwltool med-config The following NEW packages will be installed: bwa libaec0 libblas3 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libfuse2 libgfortran5 libgssapi-krb5-2 libhdf5-103 libhts2 libicu63 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkdf5-2 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libncbi-vdb2 libncbi-wvdb2 libncurses6 libnghttp2-14 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 libxml2 mime-support python python-biopython python-minimal python-numpy python-pil python-pkg-resources python-reportlab python-reportlab-accel python2 python2-minimal python2.7 python2.7-minimal readline-common samtools seqsero sra-toolkit 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 38.2 MB of archives. After this operation, 142 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:2 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:3 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:4 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:6 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:7 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:8 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:12 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:15 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:16 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:17 http://deb.debian.org/debian buster/main amd64 bwa amd64 0.7.17-3 [195 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:33 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:37 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:38 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:39 http://deb.debian.org/debian buster/main amd64 libfuse2 amd64 2.9.9-1+deb10u1 [128 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get:41 http://deb.debian.org/debian buster/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u3 [8293 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libmbedtls-dev amd64 2.16.0-1 [488 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libkdf5-2 amd64 2.9.3+dfsg-2 [17.0 kB] Get:52 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:53 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u4 [689 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libncbi-vdb2 amd64 2.9.3+dfsg-2 [1132 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libncbi-wvdb2 amd64 2.9.3+dfsg-2 [1028 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get:64 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get:65 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get:66 http://deb.debian.org/debian buster/main amd64 python-pil amd64 5.4.1-2+deb10u3 [395 kB] Get:67 http://deb.debian.org/debian buster/main amd64 python-reportlab-accel amd64 3.5.13-1+deb10u1 [39.8 kB] Get:68 http://deb.debian.org/debian buster/main amd64 python-reportlab all 3.5.13-1+deb10u1 [545 kB] Get:69 http://deb.debian.org/debian buster/main amd64 python-biopython amd64 1.73+dfsg-1 [1334 kB] Get:70 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get:71 http://deb.debian.org/debian buster/main amd64 sra-toolkit amd64 2.9.3+dfsg-1+b1 [4932 kB] Get:72 http://deb.debian.org/debian buster/main amd64 seqsero all 1.0.1+dfsg-1 [358 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.2 MB in 1s (46.7 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. 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Unpacking libpython-stdlib:amd64 (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 7299 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... 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Unpacking libk5crypto3:amd64 (1.17-3+deb10u4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../09-libkrb5-3_1.17-3+deb10u4_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u4) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../10-libgssapi-krb5-2_1.17-3+deb10u4_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../11-libsasl2-modules-db_2.1.27+dfsg-1+deb10u2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../12-libsasl2-2_2.1.27+dfsg-1+deb10u2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Selecting previously unselected package libldap-common. Preparing to unpack .../13-libldap-common_2.4.47+dfsg-3+deb10u7_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u7) ... 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Preparing to unpack .../19-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../20-libdeflate0_1.2-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.2-1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../21-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../22-libfreetype6_2.9.1-3+deb10u3_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3+deb10u3) ... Selecting previously unselected package libfuse2:amd64. Preparing to unpack .../23-libfuse2_2.9.9-1+deb10u1_amd64.deb ... Unpacking libfuse2:amd64 (2.9.9-1+deb10u1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../24-libsz2_1.0.2-1_amd64.deb ... Unpacking libsz2:amd64 (1.0.2-1) ... Selecting previously unselected package libhdf5-103:amd64. Preparing to unpack .../25-libhdf5-103_1.10.4+repack-10_amd64.deb ... Unpacking libhdf5-103:amd64 (1.10.4+repack-10) ... Selecting previously unselected package libhts2:amd64. Preparing to unpack .../26-libhts2_1.9-12~deb10u1_amd64.deb ... Unpacking libhts2:amd64 (1.9-12~deb10u1) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../27-libicu63_63.1-6+deb10u3_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u3) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../28-libimagequant0_2.12.2-1.1_amd64.deb ... Unpacking libimagequant0:amd64 (2.12.2-1.1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../29-libjbig0_2.1-3.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../30-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package libmbedcrypto3:amd64. Preparing to unpack .../31-libmbedcrypto3_2.16.0-1_amd64.deb ... Unpacking libmbedcrypto3:amd64 (2.16.0-1) ... Selecting previously unselected package libmbedx509-0:amd64. Preparing to unpack .../32-libmbedx509-0_2.16.0-1_amd64.deb ... Unpacking libmbedx509-0:amd64 (2.16.0-1) ... Selecting previously unselected package libmbedtls12:amd64. Preparing to unpack .../33-libmbedtls12_2.16.0-1_amd64.deb ... Unpacking libmbedtls12:amd64 (2.16.0-1) ... Selecting previously unselected package libmbedtls-dev:amd64. Preparing to unpack .../34-libmbedtls-dev_2.16.0-1_amd64.deb ... Unpacking libmbedtls-dev:amd64 (2.16.0-1) ... Selecting previously unselected package libkdf5-2. Preparing to unpack .../35-libkdf5-2_2.9.3+dfsg-2_amd64.deb ... Unpacking libkdf5-2 (2.9.3+dfsg-2) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../36-liblapack3_3.8.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.8.0-2) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../37-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../38-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../39-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../40-libxml2_2.9.4+dfsg1-7+deb10u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u4) ... Selecting previously unselected package libncbi-vdb2. Preparing to unpack .../41-libncbi-vdb2_2.9.3+dfsg-2_amd64.deb ... Unpacking libncbi-vdb2 (2.9.3+dfsg-2) ... Selecting previously unselected package libncbi-wvdb2. Preparing to unpack .../42-libncbi-wvdb2_2.9.3+dfsg-2_amd64.deb ... Unpacking libncbi-wvdb2 (2.9.3+dfsg-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../43-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libwebp6:amd64. Preparing to unpack .../44-libwebp6_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package libtiff5:amd64. Preparing to unpack .../45-libtiff5_4.1.0+git191117-2~deb10u4_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../46-libwebpdemux2_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../47-libwebpmux3_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../48-python-pkg-resources_40.8.0-1_all.deb ... Unpacking python-pkg-resources (40.8.0-1) ... Selecting previously unselected package python-numpy. Preparing to unpack .../49-python-numpy_1%3a1.16.2-1_amd64.deb ... Unpacking python-numpy (1:1.16.2-1) ... Selecting previously unselected package python-pil:amd64. Preparing to unpack .../50-python-pil_5.4.1-2+deb10u3_amd64.deb ... Unpacking python-pil:amd64 (5.4.1-2+deb10u3) ... Selecting previously unselected package python-reportlab-accel:amd64. Preparing to unpack .../51-python-reportlab-accel_3.5.13-1+deb10u1_amd64.deb ... Unpacking python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Selecting previously unselected package python-reportlab. Preparing to unpack .../52-python-reportlab_3.5.13-1+deb10u1_all.deb ... Unpacking python-reportlab (3.5.13-1+deb10u1) ... Selecting previously unselected package python-biopython. Preparing to unpack .../53-python-biopython_1.73+dfsg-1_amd64.deb ... Unpacking python-biopython (1.73+dfsg-1) ... Selecting previously unselected package samtools. Preparing to unpack .../54-samtools_1.9-4_amd64.deb ... Unpacking samtools (1.9-4) ... Selecting previously unselected package sra-toolkit. Preparing to unpack .../55-sra-toolkit_2.9.3+dfsg-1+b1_amd64.deb ... Unpacking sra-toolkit (2.9.3+dfsg-1+b1) ... Selecting previously unselected package seqsero. Preparing to unpack .../56-seqsero_1.0.1+dfsg-1_all.deb ... Unpacking seqsero (1.0.1+dfsg-1) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u4) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up bwa (0.7.17-3) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libfuse2:amd64 (2.9.9-1+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libaec0:amd64 (1.0.2-1) ... Setting up libicu63:amd64 (63.1-6+deb10u3) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up libmbedcrypto3:amd64 (2.16.0-1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u4) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libmbedx509-0:amd64 (2.16.0-1) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libmbedtls12:amd64 (2.16.0-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libmbedtls-dev:amd64 (2.16.0-1) ... Setting up libncbi-vdb2 (2.9.3+dfsg-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libblas3:amd64 (3.8.0-2) ... 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 libfreetype6:amd64 (2.9.1-3+deb10u3) ... Setting up libncbi-wvdb2 (2.9.3+dfsg-2) ... Setting up libhdf5-103:amd64 (1.10.4+repack-10) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up liblapack3:amd64 (3.8.0-2) ... 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 python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up libkdf5-2 (2.9.3+dfsg-2) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up sra-toolkit (2.9.3+dfsg-1+b1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up python-pil:amd64 (5.4.1-2+deb10u3) ... Setting up samtools (1.9-4) ... Setting up python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up python-numpy (1:1.16.2-1) ... Setting up python-reportlab (3.5.13-1+deb10u1) ... Setting up python-biopython (1.73+dfsg-1) ... Setting up seqsero (1.0.1+dfsg-1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-y', 'install', 'seqsero'] 0m18.6s INFO: Running scripts post_install 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_install_exceptions'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_install_exceptions'] 0m18.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m19.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m19.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpmkou2d3v to buster-next 0m19.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main deb http://security.debian.org buster/updates main deb http://deb.debian.org/debian/ buster-updates main deb http://deb.debian.org/debian/ buster-proposed-updates main 0m19.3s INFO: Running scripts pre_distupgrade 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_exceptions'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_exceptions'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'update'] 0m21.1s DUMP: Get:1 http://security.debian.org buster/updates InRelease [34.8 kB] Hit:2 http://deb.debian.org/debian buster InRelease Get:3 http://deb.debian.org/debian buster-updates InRelease [56.6 kB] Get:4 http://deb.debian.org/debian buster-proposed-updates InRelease [59.2 kB] Get:5 http://deb.debian.org/debian buster-updates/main amd64 Packages [8788 B] Get:6 http://deb.debian.org/debian buster-updates/main Translation-en [6915 B] Get:7 http://security.debian.org buster/updates/main amd64 Packages [550 kB] Get:8 http://security.debian.org buster/updates/main Translation-en [299 kB] Get:9 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages [736 B] Get:10 http://deb.debian.org/debian buster-proposed-updates/main Translation-en [859 B] Fetched 1017 kB in 1s (1462 kB/s) Reading package lists... 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'update'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-yf', 'dist-upgrade'] 0m29.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debian-archive-keyring libbz2-1.0 libc-bin libc6 libcurl3-gnutls libexpat1 libgnutls30 libgssapi-krb5-2 libhdf5-103 libk5crypto3 libkrb5-3 libkrb5support0 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libncurses6 libncursesw6 libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssh2-1 libssl1.1 libsystemd0 libtasn1-6 libtiff5 libtinfo6 libudev1 libwebp6 libwebpdemux2 libwebpmux3 libxml2 ncurses-base ncurses-bin python-reportlab python-reportlab-accel python2.7 python2.7-minimal tzdata zlib1g 40 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 18.8 MB of archives. After this operation, 319 kB of additional disk space will be used. Get:1 http://security.debian.org buster/updates/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u4 [407 kB] Get:2 http://security.debian.org buster/updates/main amd64 libc6 amd64 2.28-10+deb10u2 [2869 kB] Get:3 http://security.debian.org buster/updates/main amd64 libc-bin amd64 2.28-10+deb10u2 [793 kB] Get:4 http://security.debian.org buster/updates/main amd64 ncurses-base all 6.1+20181013-2+deb10u4 [259 kB] Get:5 http://security.debian.org buster/updates/main amd64 libsystemd0 amd64 241-7~deb10u10 [332 kB] Get:6 http://security.debian.org buster/updates/main amd64 python2.7 amd64 2.7.16-2+deb10u3 [306 kB] Get:7 http://security.debian.org buster/updates/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u6 [1552 kB] Get:8 http://security.debian.org buster/updates/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u2 [45.4 kB] Get:9 http://security.debian.org buster/updates/main amd64 libexpat1 amd64 2.2.6-2+deb10u6 [108 kB] Get:10 http://security.debian.org buster/updates/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u4 [102 kB] Get:11 http://security.debian.org buster/updates/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u4 [326 kB] Get:12 http://security.debian.org buster/updates/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u4 [131 kB] Get:13 http://security.debian.org buster/updates/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u2 [641 kB] Get:14 http://security.debian.org buster/updates/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u3 [1910 kB] Get:15 http://security.debian.org buster/updates/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u3 [1362 kB] Get:16 http://security.debian.org buster/updates/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u3 [397 kB] Get:17 http://security.debian.org buster/updates/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u2 [90.9 kB] Get:18 http://security.debian.org buster/updates/main amd64 debian-archive-keyring all 2019.1+deb10u2 [110 kB] Get:19 http://security.debian.org buster/updates/main amd64 libudev1 amd64 241-7~deb10u10 [151 kB] Get:20 http://security.debian.org buster/updates/main amd64 libtasn1-6 amd64 4.13-3+deb10u1 [52.0 kB] Get:21 http://security.debian.org buster/updates/main amd64 libgnutls30 amd64 3.6.7-4+deb10u10 [1126 kB] Get:22 http://security.debian.org buster/updates/main amd64 tzdata all 2021a-0+deb10u11 [267 kB] Get:23 http://security.debian.org buster/updates/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u5 [159 kB] Get:24 http://security.debian.org buster/updates/main amd64 libkrb5-3 amd64 1.17-3+deb10u5 [369 kB] Get:25 http://security.debian.org buster/updates/main amd64 libkrb5support0 amd64 1.17-3+deb10u5 [66.0 kB] Get:26 http://security.debian.org buster/updates/main amd64 libk5crypto3 amd64 1.17-3+deb10u5 [122 kB] Get:27 http://security.debian.org buster/updates/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u6 [690 kB] Get:28 http://security.debian.org buster/updates/main amd64 libssh2-1 amd64 1.8.0-2.1+deb10u1 [141 kB] Get:29 http://security.debian.org buster/updates/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u7 [333 kB] Get:30 http://security.debian.org buster/updates/main amd64 libhdf5-103 amd64 1.10.4+repack-10+deb10u1 [1327 kB] Get:31 http://security.debian.org buster/updates/main amd64 libmbedtls-dev amd64 2.16.9-0~deb10u1 [514 kB] Get:32 http://security.debian.org buster/updates/main amd64 libmbedx509-0 amd64 2.16.9-0~deb10u1 [109 kB] Get:33 http://security.debian.org buster/updates/main amd64 libmbedtls12 amd64 2.16.9-0~deb10u1 [140 kB] Get:34 http://security.debian.org buster/updates/main amd64 libmbedcrypto3 amd64 2.16.9-0~deb10u1 [220 kB] Get:35 http://security.debian.org buster/updates/main amd64 libwebp6 amd64 0.6.1-2+deb10u3 [263 kB] Get:36 http://security.debian.org buster/updates/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u8 [273 kB] Get:37 http://security.debian.org buster/updates/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u3 [87.9 kB] Get:38 http://security.debian.org buster/updates/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u3 [98.1 kB] Get:39 http://security.debian.org buster/updates/main amd64 python-reportlab-accel amd64 3.5.13-1+deb10u2 [40.1 kB] Get:40 http://security.debian.org buster/updates/main amd64 python-reportlab all 3.5.13-1+deb10u2 [545 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.8 MB in 0s (66.8 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9461 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20181013-2+deb10u4_amd64.deb ... Unpacking ncurses-bin (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-bin (6.1+20181013-2+deb10u4) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9461 files and directories currently installed.) Preparing to unpack .../libc-bin_2.28-10+deb10u2_amd64.deb ... Unpacking libc-bin (2.28-10+deb10u2) over (2.28-10+deb10u1) ... Setting up libc-bin (2.28-10+deb10u2) ... (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 ... 9461 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2+deb10u4_all.deb ... Unpacking ncurses-base (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-base (6.1+20181013-2+deb10u4) ... (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 ... 9461 files and directories currently installed.) Preparing to unpack .../libsystemd0_241-7~deb10u10_amd64.deb ... Unpacking libsystemd0:amd64 (241-7~deb10u10) over (241-7~deb10u8) ... Setting up libsystemd0:amd64 (241-7~deb10u10) ... (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 ... 9461 files and directories currently installed.) Preparing to unpack .../python2.7_2.7.16-2+deb10u3_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../libssl1.1_1.1.1n-0+deb10u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u6) over (1.1.1n-0+deb10u3) ... Preparing to unpack .../libbz2-1.0_1.0.6-9.2~deb10u2_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.6-9.2~deb10u2) over (1.0.6-9.2~deb10u1) ... Setting up libbz2-1.0:amd64 (1.0.6-9.2~deb10u2) ... (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 ... 9461 files and directories currently installed.) Preparing to unpack .../libexpat1_2.2.6-2+deb10u6_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u6) over (2.2.6-2+deb10u4) ... Preparing to unpack .../libncurses6_6.1+20181013-2+deb10u4_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u4_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+deb10u4) ... (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 ... 9461 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u4_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u4) over (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u4) ... (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 ... 9461 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.27.2-3+deb10u2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.27.2-3+deb10u2) over (3.27.2-3+deb10u1) ... Preparing to unpack .../libpython2.7-stdlib_2.7.16-2+deb10u3_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../python2.7-minimal_2.7.16-2+deb10u3_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../libpython2.7-minimal_2.7.16-2+deb10u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) over (2.7.16-2+deb10u1) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-1+deb10u2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-1+deb10u2) over (1:1.2.11.dfsg-1+deb10u1) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-1+deb10u2) ... (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 ... 9461 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2019.1+deb10u2_all.deb ... Unpacking debian-archive-keyring (2019.1+deb10u2) over (2019.1+deb10u1) ... Setting up debian-archive-keyring (2019.1+deb10u2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9467 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.13-3+deb10u1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.13-3+deb10u1) over (4.13-3) ... Setting up libtasn1-6:amd64 (4.13-3+deb10u1) ... (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 ... 9467 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.7-4+deb10u10_amd64.deb ... Unpacking libgnutls30:amd64 (3.6.7-4+deb10u10) over (3.6.7-4+deb10u8) ... Setting up libgnutls30:amd64 (3.6.7-4+deb10u10) ... (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 ... 9467 files and directories currently installed.) Preparing to unpack .../00-tzdata_2021a-0+deb10u11_all.deb ... Unpacking tzdata (2021a-0+deb10u11) over (2021a-0+deb10u6) ... Preparing to unpack .../01-libgssapi-krb5-2_1.17-3+deb10u5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../02-libkrb5-3_1.17-3+deb10u5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../03-libkrb5support0_1.17-3+deb10u5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../04-libk5crypto3_1.17-3+deb10u5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u5) over (1.17-3+deb10u4) ... Preparing to unpack .../05-libxml2_2.9.4+dfsg1-7+deb10u6_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u6) over (2.9.4+dfsg1-7+deb10u4) ... Preparing to unpack .../06-libssh2-1_1.8.0-2.1+deb10u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1+deb10u1) over (1.8.0-2.1) ... Preparing to unpack .../07-libcurl3-gnutls_7.64.0-4+deb10u7_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u7) over (7.64.0-4+deb10u2) ... Preparing to unpack .../08-libhdf5-103_1.10.4+repack-10+deb10u1_amd64.deb ... Unpacking libhdf5-103:amd64 (1.10.4+repack-10+deb10u1) over (1.10.4+repack-10) ... Preparing to unpack .../09-libmbedtls-dev_2.16.9-0~deb10u1_amd64.deb ... Unpacking libmbedtls-dev:amd64 (2.16.9-0~deb10u1) over (2.16.0-1) ... Preparing to unpack .../10-libmbedx509-0_2.16.9-0~deb10u1_amd64.deb ... Unpacking libmbedx509-0:amd64 (2.16.9-0~deb10u1) over (2.16.0-1) ... Preparing to unpack .../11-libmbedtls12_2.16.9-0~deb10u1_amd64.deb ... Unpacking libmbedtls12:amd64 (2.16.9-0~deb10u1) over (2.16.0-1) ... Preparing to unpack .../12-libmbedcrypto3_2.16.9-0~deb10u1_amd64.deb ... Unpacking libmbedcrypto3:amd64 (2.16.9-0~deb10u1) over (2.16.0-1) ... Preparing to unpack .../13-libwebp6_0.6.1-2+deb10u3_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2+deb10u3) over (0.6.1-2+deb10u1) ... Preparing to unpack .../14-libtiff5_4.1.0+git191117-2~deb10u8_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2~deb10u8) over (4.1.0+git191117-2~deb10u4) ... Preparing to unpack .../15-libwebpdemux2_0.6.1-2+deb10u3_amd64.deb ... Unpacking libwebpdemux2:amd64 (0.6.1-2+deb10u3) over (0.6.1-2+deb10u1) ... Preparing to unpack .../16-libwebpmux3_0.6.1-2+deb10u3_amd64.deb ... Unpacking libwebpmux3:amd64 (0.6.1-2+deb10u3) over (0.6.1-2+deb10u1) ... Preparing to unpack .../17-python-reportlab-accel_3.5.13-1+deb10u2_amd64.deb ... Unpacking python-reportlab-accel:amd64 (3.5.13-1+deb10u2) over (3.5.13-1+deb10u1) ... Preparing to unpack .../18-python-reportlab_3.5.13-1+deb10u2_all.deb ... Unpacking python-reportlab (3.5.13-1+deb10u2) over (3.5.13-1+deb10u1) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u6) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u6) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u5) ... Setting up tzdata (2021a-0+deb10u11) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Oct 12 05:33:12 UTC 2023. Universal Time is now: Thu Oct 12 05:33:12 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) ... Setting up python2.7-minimal (2.7.16-2+deb10u3) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u4) ... Setting up libhdf5-103:amd64 (1.10.4+repack-10+deb10u1) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u3) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u5) ... Setting up libmbedcrypto3:amd64 (2.16.9-0~deb10u1) ... Setting up libssh2-1:amd64 (1.8.0-2.1+deb10u1) ... Setting up python-reportlab-accel:amd64 (3.5.13-1+deb10u2) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u5) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u8) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u6) ... Setting up libmbedx509-0:amd64 (2.16.9-0~deb10u1) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u3) ... Setting up libmbedtls12:amd64 (2.16.9-0~deb10u1) ... Setting up libmbedtls-dev:amd64 (2.16.9-0~deb10u1) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u3) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Setting up python-reportlab (3.5.13-1+deb10u2) ... Setting up python2.7 (2.7.16-2+deb10u3) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u7) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... Processing triggers for mime-support (3.62) ... 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-yf', 'dist-upgrade'] 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m29.5s DUMP: fda2740789a1b3843c326ecef1409b4b - 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m29.8s DUMP: Package: seqsero Version: 1.0.1+dfsg-1 Installed-Size: 3497 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description-en: Salmonella serotyping from genome sequencing data SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. . SeqSero is a novel tool for determining Salmonella serotypes using high- throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing 1. raw reads from genomes of 308 Salmonella isolates of known serotype 2. raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and 3. 354 other publicly available draft or complete Salmonella genomes. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization. Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Homepage: https://github.com/denglab/SeqSero Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-1_all.deb Size: 357736 MD5sum: bde4f7eef3f44d26a3ac660bfa7fddf0 SHA256: 8dd2870bcbe679b79221918eb8965b3c0130d0a1f3cde0a63333c49432828309 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m29.8s INFO: apt-cache knows about the following packages: seqsero 0m29.8s INFO: Running scripts pre_install 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_database-server'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_database-server'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_exceptions'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_exceptions'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_extras'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_extras'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy'] 0m29.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy', 'seqsero'] 0m29.9s DUMP: seqsero: Installed: 1.0.1+dfsg-1 Candidate: 1.0.1+dfsg-1 Version table: *** 1.0.1+dfsg-1 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy', 'seqsero'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-y', 'install', 'seqsero'] 0m30.4s DUMP: Reading package lists... Building dependency tree... Reading state information... seqsero is already the newest version (1.0.1+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-y', 'install', 'seqsero'] 0m30.4s INFO: Running scripts post_install 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_install_exceptions'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_install_exceptions'] 0m30.4s INFO: Running scripts post_distupgrade 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_exceptions'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_exceptions'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_zz_backports'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_distupgrade_zz_backports'] 0m30.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m31.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m31.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m31.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m31.9s INFO: Running scripts pre_install 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_database-server'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_database-server'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_exceptions'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_exceptions'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_extras'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_extras'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy'] 0m32.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy'] 0m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy', 'seqsero'] 0m32.0s DUMP: seqsero: Installed: 1.0.1+dfsg-1 Candidate: 1.0.1+dfsg-1 Version table: *** 1.0.1+dfsg-1 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-cache', 'policy', 'seqsero'] 0m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-1'] 0m32.5s DUMP: Reading package lists... Building dependency tree... Reading state information... seqsero is already the newest version (1.0.1+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-1'] 0m32.5s INFO: Running scripts post_install 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_install_exceptions'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_install_exceptions'] 0m32.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m33.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m34.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', '-ac', '--ignore-obsolete'] 0m35.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', '-ac', '--ignore-obsolete'] 0m35.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m35.7s DUMP: 0.15.6 0m35.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m35.7s INFO: Running adequate version 0.15.6 now. 0m35.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'seqsero'] 0m35.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'seqsero'] 0m35.8s INFO: Running scripts pre_remove 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_exceptions'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/pre_remove_exceptions'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.9s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed bwa bwa 0.7.17-3 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u2 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libaec0:amd64 libaec0 1.0.2-1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblas3:amd64 libblas3 3.8.0-2 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u2 install ok installed libc-bin libc-bin 2.28-10+deb10u2 install ok installed libc6:amd64 libc6 2.28-10+deb10u2 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u7 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libexpat1:amd64 libexpat1 2.2.6-2+deb10u6 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libfreetype6:amd64 libfreetype6 2.9.1-3+deb10u3 install ok installed libfuse2:amd64 libfuse2 2.9.9-1+deb10u1 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u10 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u5 install ok installed libhdf5-103:amd64 libhdf5-103 1.10.4+repack-10+deb10u1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libicu63:amd64 libicu63 63.1-6+deb10u3 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed libimagequant0:amd64 libimagequant0 2.12.2-1.1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.2-2+deb10u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u5 install ok installed libkdf5-2 libkdf5-2 2.9.3+dfsg-2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u5 install ok installed liblapack3:amd64 liblapack3 3.8.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.9-3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.47+dfsg-3+deb10u7 install ok installed libldap-common libldap-common 2.4.47+dfsg-3+deb10u7 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmagic-mgc libmagic-mgc 1:5.35-4+deb10u2 install ok installed libmagic1:amd64 libmagic1 1:5.35-4+deb10u2 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0~deb10u1 install ok installed libmbedtls-dev:amd64 libmbedtls-dev 2.16.9-0~deb10u1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0~deb10u1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0~deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncbi-vdb2 libncbi-vdb2 2.9.3+dfsg-2 install ok installed libncbi-wvdb2 libncbi-wvdb2 2.9.3+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.1+20181013-2+deb10u4 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u4 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.36.0-2+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libpng16-16:amd64 libpng16-16 1.6.36-6 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2+deb10u3 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u3 install ok installed libquadmath0:amd64 libquadmath0 8.3.0-6 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1+deb10u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1+deb10u2 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u2 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1+deb10u1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u6 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u10 install ok installed libsz2:amd64 libsz2 1.0.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3+deb10u1 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u8 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u4 install ok installed libudev1:amd64 libudev1 241-7~deb10u10 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u3 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+deb10u3 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+deb10u3 install ok installed libxml2:amd64 libxml2 2.9.4+dfsg1-7+deb10u6 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u4 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u4 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed python python 2.7.16-1 install ok installed python-biopython python-biopython 1.73+dfsg-1 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python-numpy python-numpy 1:1.16.2-1 install ok installed python-pil:amd64 python-pil 5.4.1-2+deb10u3 install ok installed python-pkg-resources python-pkg-resources 40.8.0-1 install ok installed python-reportlab python-reportlab 3.5.13-1+deb10u2 install ok installed python-reportlab-accel:amd64 python-reportlab-accel 3.5.13-1+deb10u2 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u3 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u3 install ok installed readline-common readline-common 7.0-5 install ok installed samtools samtools 1.9-4 install ok installed sed sed 4.7-1 install ok installed seqsero seqsero 1.0.1+dfsg-1 install ok installed sra-toolkit sra-toolkit 2.9.3+dfsg-1+b1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u11 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u2 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'remove', 'bwa', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxml2:amd64', 'mime-support', 'python', 'python-biopython', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'sra-toolkit', 'seqsero'] 0m39.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bwa libaec0 libblas3 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libfuse2 libgfortran5 libgssapi-krb5-2 libhdf5-103 libhts2 libicu63 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkdf5-2 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libncbi-vdb2 libncbi-wvdb2 libncurses6 libnghttp2-14 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 libxml2 mime-support python python-biopython python-minimal python-numpy python-pil python-pkg-resources python-reportlab python-reportlab-accel python2 python2-minimal python2.7 python2.7-minimal readline-common samtools seqsero sra-toolkit 0 upgraded, 0 newly installed, 72 to remove and 0 not upgraded. After this operation, 143 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 ... 9470 files and directories currently installed.) Removing seqsero (1.0.1+dfsg-1) ... Removing bwa (0.7.17-3) ... Removing sra-toolkit (2.9.3+dfsg-1+b1) ... Removing libkdf5-2 (2.9.3+dfsg-2) ... Removing libhdf5-103:amd64 (1.10.4+repack-10+deb10u1) ... Removing libsz2:amd64 (1.0.2-1) ... Removing libaec0:amd64 (1.0.2-1) ... Removing python-biopython (1.73+dfsg-1) ... Removing python-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing samtools (1.9-4) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u7) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python-reportlab (3.5.13-1+deb10u2) ... Removing python-reportlab-accel:amd64 (3.5.13-1+deb10u2) ... Removing python-pkg-resources (40.8.0-1) ... Removing python-pil:amd64 (5.4.1-2+deb10u3) ... Removing python (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u3) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing libfuse2:amd64 (2.9.9-1+deb10u1) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Removing libncbi-wvdb2 (2.9.3+dfsg-2) ... Removing libncbi-vdb2 (2.9.3+dfsg-2) ... Removing libxml2:amd64 (2.9.4+dfsg1-7+deb10u6) ... Removing libicu63:amd64 (63.1-6+deb10u3) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u8) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing libkrb5-3:amd64 (1.17-3+deb10u5) ... Removing libk5crypto3:amd64 (1.17-3+deb10u5) ... Removing libkrb5support0:amd64 (1.17-3+deb10u5) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing liblcms2-2:amd64 (2.9-3) ... Removing libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Removing libldap-common (2.4.47+dfsg-3+deb10u7) ... Removing libmagic1:amd64 (1:5.35-4+deb10u2) ... Removing libmagic-mgc (1:5.35-4+deb10u2) ... Removing libmbedtls-dev:amd64 (2.16.9-0~deb10u1) ... Removing libmbedtls12:amd64 (2.16.9-0~deb10u1) ... Removing libmbedx509-0:amd64 (2.16.9-0~deb10u1) ... Removing libmbedcrypto3:amd64 (2.16.9-0~deb10u1) ... Removing libncurses6:amd64 (6.1+20181013-2+deb10u4) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libpng16-16:amd64 (1.6.36-6) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... Removing python2-minimal (2.7.16-1) ... Removing python2.7-minimal (2.7.16-2+deb10u3) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libssh2-1:amd64 (1.8.0-2.1+deb10u1) ... Removing libwebpmux3:amd64 (0.6.1-2+deb10u3) ... Removing libwebpdemux2:amd64 (0.6.1-2+deb10u3) ... Removing libwebp6:amd64 (0.6.1-2+deb10u3) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u3) ... Removing libexpat1:amd64 (2.2.6-2+deb10u6) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) ... find: '/usr/lib/python2.7': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Removing libssl1.1:amd64 (1.1.1n-0+deb10u6) ... Removing mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'remove', 'bwa', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxml2:amd64', 'mime-support', 'python', 'python-biopython', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'sra-toolkit', 'seqsero'] 0m39.5s INFO: Running scripts post_remove 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_remove_exceptions'] 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_remove_exceptions'] 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--purge', 'bwa', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxml2:amd64', 'mime-support', 'python', 'python-biopython', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'sra-toolkit'] 0m39.7s DUMP: dpkg: warning: ignoring request to remove bwa which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls 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 libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfuse2 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed (Reading database ... 6483 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... dpkg: warning: ignoring request to remove libhdf5-103 which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libicu63 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkdf5-2 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-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.47+dfsg-3+deb10u7) ... dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1:amd64 (1:5.35-4+deb10u2) ... dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedtls-dev which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb2 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb2 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 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 libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.16-2+deb10u3) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 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 libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1n-0+deb10u6) ... dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed Purging configuration files for mime-support (3.62) ... Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-biopython which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove python-pil which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-reportlab which isn't installed dpkg: warning: ignoring request to remove python-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.16-2+deb10u3) ... Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sra-toolkit (2.9.3+dfsg-1+b1) ... 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--purge', 'bwa', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts2:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxml2:amd64', 'mime-support', 'python', 'python-biopython', 'python-minimal', 'python-numpy', 'python-pil:amd64', 'python-pkg-resources', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'sra-toolkit'] 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--purge', 'seqsero'] 0m39.7s DUMP: dpkg: warning: ignoring request to remove seqsero which isn't installed 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--purge', 'seqsero'] 0m39.7s INFO: Running scripts post_purge 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_purge_exceptions'] 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_purge_exceptions'] 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--purge', '--pending'] 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--purge', '--pending'] 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--remove', '--pending'] 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg', '--remove', '--pending'] 0m39.7s INFO: Running scripts post_test 0m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_test_exceptions'] 0m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'tmp/scripts/post_test_exceptions'] 0m39.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m40.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg-divert', '--list'] 0m40.3s 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 0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'dpkg-divert', '--list'] 0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'clean'] 0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v', 'apt-get', 'clean'] 0m40.3s DEBUG: Recording chroot state 0m41.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/shm'] 0m41.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/shm'] 0m41.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/console'] 0m41.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/console'] 0m41.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/ptmx'] 0m41.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/ptmx'] 0m41.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/pts'] 0m41.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/dev/pts'] 0m41.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/proc'] 0m41.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v/proc'] 0m41.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m41.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmkou2d3v'] 0m41.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpmkou2d3v 0m41.8s INFO: PASS: Upgrading between Debian distributions. 0m41.8s INFO: PASS: All tests. 0m41.8s INFO: piuparts run ends. ret=0 End: 2023-10-12 05:33:26 GMT