Start: 2024-03-19 13:21:04 GMT [bullseye] Package: parallel-fastq-dump Version: 0.6.6-3 Installed-Size: 22 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description: parallel fastq-dump wrapper Homepage: https://github.com/rvalieris/parallel-fastq-dump Description-md5: 11222a9a5daf56c6d715715d83ee438e Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.6-3_amd64.deb Size: 4772 MD5sum: 4c053c1ce399b215bbbdb3c1567e81b9 SHA256: fe5df57807d514fecbf9c3094c6399b22e873f9a29144f43a426fdae76c27d3f [bullseye-next] Package: parallel-fastq-dump Version: 0.6.6-3 Installed-Size: 22 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description: parallel fastq-dump wrapper Homepage: https://github.com/rvalieris/parallel-fastq-dump Description-md5: 11222a9a5daf56c6d715715d83ee438e Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.6-3_amd64.deb Size: 4772 MD5sum: 4c053c1ce399b215bbbdb3c1567e81b9 SHA256: fe5df57807d514fecbf9c3094c6399b22e873f9a29144f43a426fdae76c27d3f 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-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt parallel-fastq-dump=0.6.6-3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-g85045c69 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-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt parallel-fastq-dump=0.6.6-3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpzk0j8x6g 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpzk0j8x6g 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpzk0j8x6g/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_test_root_password'] 0m4.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_test_root_password'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m4.4s DUMP: Package: parallel-fastq-dump Version: 0.6.6-3 Installed-Size: 22 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description-en: parallel fastq-dump wrapper NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file (see the protip below). This tool speeds up the process by dividing the work into multiple threads. . This is possible because fastq-dump have options (-N and -X) to query specific ranges of the sra file, this tool works by dividing the work into the requested number of threads, running multiple fastq-dump in parallel and concatenating the results back together, as if you had just executed a plain fastq-dump call. Description-md5: 11222a9a5daf56c6d715715d83ee438e Homepage: https://github.com/rvalieris/parallel-fastq-dump Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.6-3_amd64.deb Size: 4772 MD5sum: 4c053c1ce399b215bbbdb3c1567e81b9 SHA256: fe5df57807d514fecbf9c3094c6399b22e873f9a29144f43a426fdae76c27d3f 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m4.4s INFO: apt-cache knows about the following packages: parallel-fastq-dump 0m4.4s INFO: Running scripts pre_install 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy'] 0m4.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m4.6s DUMP: parallel-fastq-dump: Installed: (none) Candidate: 0.6.6-3 Version table: 0.6.6-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m12.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libaec0 libexpat1 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncursesw6 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libsz2 libxml2 media-types python3 python3-minimal python3.9 python3.9-minimal readline-common sra-toolkit Suggested packages: fuse file libmbedtls-doc python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates med-config The following NEW packages will be installed: libaec0 libexpat1 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncursesw6 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libsz2 libxml2 media-types parallel-fastq-dump python3 python3-minimal python3.9 python3.9-minimal readline-common sra-toolkit 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 26.1 MB of archives. After this operation, 95.1 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libfuse2 amd64 2.9.9-5 [130 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get:18 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libmbedtls-dev amd64 2.16.9-0.1 [515 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 libkdf5-2 amd64 2.10.9+dfsg-2 [20.8 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libncbi-vdb2 amd64 2.10.9+dfsg-2 [1266 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libncbi-wvdb2 amd64 2.10.9+dfsg-2 [1159 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 sra-toolkit amd64 2.10.9+dfsg-2 [5178 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 parallel-fastq-dump amd64 0.6.6-3 [4772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.1 MB in 1s (48.3 MB/s) Selecting previously unselected package libpython3.9-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6674 files and directories currently installed.) Preparing to unpack .../libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6968 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.2+20201114-2+deb11u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.34.1-3_amd64.deb ... 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Preparing to unpack .../14-libncbi-vdb2_2.10.9+dfsg-2_amd64.deb ... Unpacking libncbi-vdb2 (2.10.9+dfsg-2) ... Selecting previously unselected package libncbi-wvdb2. Preparing to unpack .../15-libncbi-wvdb2_2.10.9+dfsg-2_amd64.deb ... Unpacking libncbi-wvdb2 (2.10.9+dfsg-2) ... Selecting previously unselected package sra-toolkit. Preparing to unpack .../16-sra-toolkit_2.10.9+dfsg-2_amd64.deb ... Unpacking sra-toolkit (2.10.9+dfsg-2) ... Selecting previously unselected package parallel-fastq-dump. Preparing to unpack .../17-parallel-fastq-dump_0.6.6-3_amd64.deb ... Unpacking parallel-fastq-dump (0.6.6-3) ... Setting up media-types (4.0.0) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libmagic1:amd64 (1:5.39-3+deb11u1) ... Setting up libfuse2:amd64 (2.9.9-5) ... Setting up libaec0:amd64 (1.0.4-1) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libsz2:amd64 (1.0.4-1) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libmbedtls-dev:amd64 (2.16.9-0.1) ... Setting up libncbi-vdb2 (2.10.9+dfsg-2) ... Setting up libncbi-wvdb2 (2.10.9+dfsg-2) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libkdf5-2 (2.10.9+dfsg-2) ... Setting up python3.9 (3.9.2-1) ... Setting up sra-toolkit (2.10.9+dfsg-2) ... Setting up python3 (3.9.2-3) ... Setting up parallel-fastq-dump (0.6.6-3) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m12.3s INFO: Running scripts post_install 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_install_exceptions'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_install_exceptions'] 0m12.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m12.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m12.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpzk0j8x6g to bullseye-next 0m12.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m12.9s INFO: Running scripts pre_distupgrade 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'update'] 0m14.5s DUMP: Get:1 http://security.debian.org bullseye-security InRelease [48.4 kB] Hit:2 http://deb.debian.org/debian bullseye InRelease Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:6 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:7 http://security.debian.org bullseye-security/main amd64 Packages [269 kB] Get:8 http://security.debian.org bullseye-security/main Translation-en [174 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [18.9 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [13.8 kB] Fetched 652 kB in 1s (895 kB/s) Reading package lists... 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'update'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-yf', 'dist-upgrade'] 0m15.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-yf', 'dist-upgrade'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.5s DUMP: 1c19f1dfe717069730438cc10cd7db43 - 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m15.7s DUMP: Package: parallel-fastq-dump Version: 0.6.6-3 Installed-Size: 22 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description-en: parallel fastq-dump wrapper NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file (see the protip below). This tool speeds up the process by dividing the work into multiple threads. . This is possible because fastq-dump have options (-N and -X) to query specific ranges of the sra file, this tool works by dividing the work into the requested number of threads, running multiple fastq-dump in parallel and concatenating the results back together, as if you had just executed a plain fastq-dump call. Description-md5: 11222a9a5daf56c6d715715d83ee438e Homepage: https://github.com/rvalieris/parallel-fastq-dump Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.6-3_amd64.deb Size: 4772 MD5sum: 4c053c1ce399b215bbbdb3c1567e81b9 SHA256: fe5df57807d514fecbf9c3094c6399b22e873f9a29144f43a426fdae76c27d3f 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m15.7s INFO: apt-cache knows about the following packages: parallel-fastq-dump 0m15.7s INFO: Running scripts pre_install 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_database-server'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_database-server'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_exceptions'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_exceptions'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_extras'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_extras'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy'] 0m15.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m15.9s DUMP: parallel-fastq-dump: Installed: 0.6.6-3 Candidate: 0.6.6-3 Version table: *** 0.6.6-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m16.4s DUMP: Reading package lists... Building dependency tree... Reading state information... parallel-fastq-dump is already the newest version (0.6.6-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m16.4s INFO: Running scripts post_install 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_install_exceptions'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_install_exceptions'] 0m16.4s INFO: Running scripts post_distupgrade 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m17.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m17.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m17.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m17.6s INFO: Running scripts pre_install 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_database-server'] 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_database-server'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_exceptions'] 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_exceptions'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_extras'] 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_extras'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy'] 0m17.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m17.7s DUMP: parallel-fastq-dump: Installed: 0.6.6-3 Candidate: 0.6.6-3 Version table: *** 0.6.6-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-y', 'install', 'parallel-fastq-dump=0.6.6-3'] 0m18.2s DUMP: Reading package lists... Building dependency tree... Reading state information... parallel-fastq-dump is already the newest version (0.6.6-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', '-y', 'install', 'parallel-fastq-dump=0.6.6-3'] 0m18.2s INFO: Running scripts post_install 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_install_exceptions'] 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_install_exceptions'] 0m18.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m18.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m18.9s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m19.0s INFO: /bin converted to /usr/bin by /usr merge 0m19.0s INFO: /lib converted to /usr/lib by /usr merge 0m19.0s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m19.0s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m19.0s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m19.0s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m19.0s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m19.0s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m19.0s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m19.0s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m19.0s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m19.0s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m19.0s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m19.0s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m19.0s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m19.0s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m19.0s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m19.0s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m19.0s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m19.0s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m19.0s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m19.0s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m19.0s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m19.0s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m19.0s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m19.0s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m19.0s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m19.0s INFO: /sbin converted to /usr/sbin by /usr merge 0m19.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', '-ac', '--ignore-obsolete'] 0m21.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', '-ac', '--ignore-obsolete'] 0m21.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.0s DUMP: 0.15.6 0m21.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.0s INFO: Running adequate version 0.15.6 now. 0m21.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'parallel-fastq-dump'] 0m21.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'parallel-fastq-dump'] 0m21.1s INFO: Running scripts pre_remove 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_exceptions'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/pre_remove_exceptions'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.4s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libaec0:amd64 libaec0 1.0.4-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfuse2:amd64 libfuse2 2.9.9-5 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.6+repack-4+deb11u1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkdf5-2 libkdf5-2 2.10.9+dfsg-2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmagic-mgc libmagic-mgc 1:5.39-3+deb11u1 install ok installed libmagic1:amd64 libmagic1 1:5.39-3+deb11u1 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedtls-dev:amd64 libmbedtls-dev 2.16.9-0.1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libncbi-vdb2 libncbi-vdb2 2.10.9+dfsg-2 install ok installed libncbi-wvdb2 libncbi-wvdb2 2.10.9+dfsg-2 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libsz2:amd64 libsz2 1.0.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxml2:amd64 libxml2 2.9.10+dfsg-6.7+deb11u4 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed parallel-fastq-dump parallel-fastq-dump 0.6.6-3 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed python3 python3 3.9.2-3 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.1-1 install ok installed sed sed 4.7-1 install ok installed sra-toolkit sra-toolkit 2.10.9+dfsg-2 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'remove', 'libaec0:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit', 'parallel-fastq-dump'] 0m24.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libaec0 libexpat1 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncursesw6 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libsz2 libxml2 media-types parallel-fastq-dump python3 python3-minimal python3.9 python3.9-minimal readline-common sra-toolkit 0 upgraded, 0 newly installed, 31 to remove and 0 not upgraded. After this operation, 95.1 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 ... 7761 files and directories currently installed.) Removing parallel-fastq-dump (0.6.6-3) ... Removing sra-toolkit (2.10.9+dfsg-2) ... Removing libkdf5-2 (2.10.9+dfsg-2) ... Removing libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Removing libsz2:amd64 (1.0.4-1) ... Removing libaec0:amd64 (1.0.4-1) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing libfuse2:amd64 (2.9.9-5) ... Removing libncbi-wvdb2 (2.10.9+dfsg-2) ... Removing libncbi-vdb2 (2.10.9+dfsg-2) ... Removing libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Removing libicu67:amd64 (67.1-7) ... Removing libmagic1:amd64 (1:5.39-3+deb11u1) ... Removing libmagic-mgc (1:5.39-3+deb11u1) ... Removing libmbedtls-dev:amd64 (2.16.9-0.1) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-1) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1-1) ... Removing libsqlite3-0:amd64 (3.34.1-3) ... Removing media-types (4.0.0) ... Removing readline-common (8.1-1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'remove', 'libaec0:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit', 'parallel-fastq-dump'] 0m24.6s INFO: Running scripts post_remove 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_remove_exceptions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_remove_exceptions'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--purge', 'libaec0:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit'] 0m24.7s DUMP: dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfuse2 which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libkdf5-2 which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed (Reading database ... 6684 files and directories currently installed.) Purging configuration files for libmagic1:amd64 (1:5.39-3+deb11u1) ... 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 libmpdec3 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 libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed Purging configuration files for media-types (4.0.0) ... Purging configuration files for python3 (3.9.2-3) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.1-1) ... Purging configuration files for sra-toolkit (2.10.9+dfsg-2) ... 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--purge', 'libaec0:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--purge', 'parallel-fastq-dump'] 0m24.7s DUMP: dpkg: warning: ignoring request to remove parallel-fastq-dump which isn't installed 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--purge', 'parallel-fastq-dump'] 0m24.7s INFO: Running scripts post_purge 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_purge_exceptions'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_purge_exceptions'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--purge', '--pending'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--purge', '--pending'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--remove', '--pending'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg', '--remove', '--pending'] 0m24.7s INFO: Running scripts post_test 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_test_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'tmp/scripts/post_test_exceptions'] 0m24.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m25.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg-divert', '--list'] 0m25.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'dpkg-divert', '--list'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'clean'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g', 'apt-get', 'clean'] 0m25.3s DEBUG: Recording chroot state 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/shm'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/shm'] 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/console'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/console'] 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/ptmx'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/ptmx'] 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/pts'] 0m26.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/dev/pts'] 0m26.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/proc'] 0m26.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g/proc'] 0m26.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m26.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzk0j8x6g'] 0m26.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpzk0j8x6g 0m26.9s INFO: PASS: Upgrading between Debian distributions. 0m26.9s INFO: PASS: All tests. 0m26.9s INFO: piuparts run ends. ret=0 End: 2024-03-19 13:21:31 GMT