Start: 2024-11-05 05:31:43 GMT [bullseye] Package: augustus Version: 3.4.0+dfsg2-2 Installed-Size: 10146 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.29), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.0), libgsl25 (>= 2.6), libhts3 (>= 1.10), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 9), augustus-data Recommends: samtools Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython Description: gene prediction in eukaryotic genomes Homepage: https://bioinf.uni-greifswald.de/augustus/ Description-md5: ab0f2f2c476597fc454d6e64ee4cdcaf Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, science::calculation, scope::utility, uitoolkit::ncurses, use::analysing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/a/augustus/augustus_3.4.0+dfsg2-2_amd64.deb Size: 1951832 MD5sum: 45fa8e170a70e81af2141d3636de237a SHA256: c4b0aa58735caf3f3a4bc4a4bf26e5225b93bb437061d7c709e1be90703ef91a [bullseye-next] Package: augustus Version: 3.4.0+dfsg2-2 Installed-Size: 10146 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.29), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.0), libgsl25 (>= 2.6), libhts3 (>= 1.10), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 9), augustus-data Recommends: samtools Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython Description: gene prediction in eukaryotic genomes Homepage: https://bioinf.uni-greifswald.de/augustus/ Description-md5: ab0f2f2c476597fc454d6e64ee4cdcaf Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, science::calculation, scope::utility, uitoolkit::ncurses, use::analysing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/a/augustus/augustus_3.4.0+dfsg2-2_amd64.deb Size: 1951832 MD5sum: 45fa8e170a70e81af2141d3636de237a SHA256: c4b0aa58735caf3f3a4bc4a4bf26e5225b93bb437061d7c709e1be90703ef91a 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 augustus=3.4.0+dfsg2-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 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 augustus=3.4.0+dfsg2-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmplfzyt6d4 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmplfzyt6d4 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmplfzyt6d4/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'update'] 0m0.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'update'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-yf', 'dist-upgrade'] 0m0.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-yf', 'dist-upgrade'] 0m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.0s DUMP: f58ca9ba0b3223edf5b7797c101a5448 - 0m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.0s INFO: Running scripts post_setup 0m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_dummy_users'] 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_dummy_users'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s 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' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_zz_backports'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_setup_zz_backports'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.5s 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+deb11u11 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+deb11u2 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+deb11u2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u11 install ok installed libc6:amd64 libc6 2.31-13+deb11u11 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+deb11u5 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+deb11u5 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+deb11u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u5 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+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 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+deb11u2 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+deb11u5 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+deb11u5 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 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+deb11u2 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+deb11u2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m1.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m1.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m1.7s INFO: Running scripts is_testable 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/is_testable_uninstallable'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/is_testable_uninstallable'] 0m1.7s INFO: Running scripts pre_test 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_test_exceptions'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_test_exceptions'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_test_root_password'] 0m1.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_test_root_password'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'show', '--no-all-versions', 'augustus'] 0m1.8s DUMP: Package: augustus Version: 3.4.0+dfsg2-2 Installed-Size: 10146 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.29), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.0), libgsl25 (>= 2.6), libhts3 (>= 1.10), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 9), augustus-data Recommends: samtools Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython Description-en: gene prediction in eukaryotic genomes AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes. Description-md5: ab0f2f2c476597fc454d6e64ee4cdcaf Homepage: https://bioinf.uni-greifswald.de/augustus/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, science::calculation, scope::utility, uitoolkit::ncurses, use::analysing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/a/augustus/augustus_3.4.0+dfsg2-2_amd64.deb Size: 1951832 MD5sum: 45fa8e170a70e81af2141d3636de237a SHA256: c4b0aa58735caf3f3a4bc4a4bf26e5225b93bb437061d7c709e1be90703ef91a 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'show', '--no-all-versions', 'augustus'] 0m1.8s INFO: apt-cache knows about the following packages: augustus 0m1.8s INFO: Running scripts pre_install 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_database-server'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_database-server'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy'] 0m1.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy', 'augustus'] 0m1.9s DUMP: augustus: Installed: (none) Candidate: 3.4.0+dfsg2-2 Version table: 3.4.0+dfsg2-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy', 'augustus'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-y', 'install', 'augustus'] 0m7.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: augustus-data libbamtools2.5.1 libboost-iostreams1.74.0 libbrotli1 libcolamd2 libcurl3-gnutls libdeflate0 libgsl25 libgslcblas0 libhts3 libldap-2.4-2 libmariadb3 libmysql++3v5 libnghttp2-14 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsuitesparseconfig5 mariadb-common mysql-common Suggested packages: cdbfasta diamond-aligner libfile-which-perl libparallel-forkmanager-perl libyaml-perl libdbd-mysql-perl python3-biopython gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html Recommended packages: samtools ca-certificates libldap-common publicsuffix libsasl2-modules The following NEW packages will be installed: augustus augustus-data libbamtools2.5.1 libboost-iostreams1.74.0 libbrotli1 libcolamd2 libcurl3-gnutls libdeflate0 libgsl25 libgslcblas0 libhts3 libldap-2.4-2 libmariadb3 libmysql++3v5 libnghttp2-14 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsuitesparseconfig5 mariadb-common mysql-common 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. Need to get 24.4 MB of archives. After this operation, 151 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-9 [158 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams1.74.0 amd64 1.74.0-9 [264 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libsuitesparseconfig5 amd64 1:5.8.1+dfsg-2 [23.0 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libcolamd2 amd64 1:5.8.1+dfsg-2 [32.1 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2+deb11u1 [156 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u13 [344 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 mysql-common all 5.8+1.0.7 [7464 B] Get:19 http://deb.debian.org/debian bullseye/main amd64 mariadb-common all 1:10.5.23-0+deb11u1 [37.2 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libmariadb3 amd64 1:10.5.23-0+deb11u1 [176 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libmysql++3v5 amd64 3.2.5-2 [159 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 augustus-data all 3.4.0+dfsg2-2 [18.0 MB] Get:24 http://deb.debian.org/debian bullseye/main amd64 augustus amd64 3.4.0+dfsg2-2 [1952 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.4 MB in 3s (7473 kB/s) Selecting previously unselected package libbamtools2.5.1: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 .../00-libbamtools2.5.1_2.5.1+dfsg-9_amd64.deb ... Unpacking libbamtools2.5.1:amd64 (2.5.1+dfsg-9) ... Selecting previously unselected package libboost-iostreams1.74.0:amd64. Preparing to unpack .../01-libboost-iostreams1.74.0_1.74.0-9_amd64.deb ... Unpacking libboost-iostreams1.74.0:amd64 (1.74.0-9) ... Selecting previously unselected package libsuitesparseconfig5:amd64. Preparing to unpack .../02-libsuitesparseconfig5_1%3a5.8.1+dfsg-2_amd64.deb ... Unpacking libsuitesparseconfig5:amd64 (1:5.8.1+dfsg-2) ... Selecting previously unselected package libcolamd2:amd64. Preparing to unpack .../03-libcolamd2_1%3a5.8.1+dfsg-2_amd64.deb ... Unpacking libcolamd2:amd64 (1:5.8.1+dfsg-2) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../04-libgslcblas0_2.6+dfsg-2_amd64.deb ... Unpacking libgslcblas0:amd64 (2.6+dfsg-2) ... Selecting previously unselected package libgsl25:amd64. Preparing to unpack .../05-libgsl25_2.6+dfsg-2_amd64.deb ... Unpacking libgsl25:amd64 (2.6+dfsg-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../06-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. 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Unpacking augustus (3.4.0+dfsg2-2) ... Setting up mysql-common (5.8+1.0.7) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libgslcblas0:amd64 (2.6+dfsg-2) ... Setting up libgsl25:amd64 (2.6+dfsg-2) ... Setting up libboost-iostreams1.74.0:amd64 (1.74.0-9) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up augustus-data (3.4.0+dfsg2-2) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up mariadb-common (1:10.5.23-0+deb11u1) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-9) ... Setting up libmariadb3:amd64 (1:10.5.23-0+deb11u1) ... Setting up libmysql++3v5:amd64 (3.2.5-2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libssh2-1:amd64 (1.9.0-2+deb11u1) ... Setting up libsuitesparseconfig5:amd64 (1:5.8.1+dfsg-2) ... Setting up libcolamd2:amd64 (1:5.8.1+dfsg-2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u13) ... Setting up libhts3:amd64 (1.11-4) ... Setting up augustus (3.4.0+dfsg2-2) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-y', 'install', 'augustus'] 0m7.3s INFO: Running scripts post_install 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_install_exceptions'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_install_exceptions'] 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m7.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m7.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmplfzyt6d4 to bullseye-next 0m7.6s 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 0m7.6s INFO: Running scripts pre_distupgrade 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'update'] 0m8.3s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Get:2 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:3 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:4 http://security.debian.org bullseye-security InRelease [27.2 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 [307 kB] Get:8 http://security.debian.org bullseye-security/main Translation-en [198 kB] Fetched 660 kB in 0s (1803 kB/s) Reading package lists... 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'update'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-yf', 'dist-upgrade'] 0m9.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: e2fsprogs libcom-err2 libext2fs2 libgnutls30 libmariadb3 libnghttp2-14 libsepol1 libsqlite3-0 libss2 libssl1.1 libsystemd0 libudev1 logsave mariadb-common perl-base 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7535 kB of archives. After this operation, 14.3 kB of additional disk space will be used. Get:1 http://security.debian.org bullseye-security/main amd64 perl-base amd64 5.32.1-4+deb11u4 [1629 kB] Get:2 http://security.debian.org bullseye-security/main amd64 libsystemd0 amd64 247.3-7+deb11u6 [377 kB] Get:3 http://security.debian.org bullseye-security/main amd64 logsave amd64 1.46.2-2+deb11u1 [75.0 kB] Get:4 http://security.debian.org bullseye-security/main amd64 libext2fs2 amd64 1.46.2-2+deb11u1 [257 kB] Get:5 http://security.debian.org bullseye-security/main amd64 e2fsprogs amd64 1.46.2-2+deb11u1 [614 kB] Get:6 http://security.debian.org bullseye-security/main amd64 libcom-err2 amd64 1.46.2-2+deb11u1 [74.3 kB] Get:7 http://security.debian.org bullseye-security/main amd64 libgnutls30 amd64 3.7.1-5+deb11u6 [1340 kB] Get:8 http://security.debian.org bullseye-security/main amd64 libsepol1 amd64 3.1-1+deb11u1 [269 kB] Get:9 http://security.debian.org bullseye-security/main amd64 libssl1.1 amd64 1.1.1w-0+deb11u2 [1565 kB] Get:10 http://security.debian.org bullseye-security/main amd64 libudev1 amd64 247.3-7+deb11u6 [169 kB] Get:11 http://security.debian.org bullseye-security/main amd64 mariadb-common all 1:10.5.26-0+deb11u2 [37.5 kB] Get:12 http://security.debian.org bullseye-security/main amd64 libmariadb3 amd64 1:10.5.26-0+deb11u2 [177 kB] Get:13 http://security.debian.org bullseye-security/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u2 [77.0 kB] Get:14 http://security.debian.org bullseye-security/main amd64 libsqlite3-0 amd64 3.34.1-3+deb11u1 [797 kB] Get:15 http://security.debian.org bullseye-security/main amd64 libss2 amd64 1.46.2-2+deb11u1 [78.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7535 kB in 0s (65.1 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8321 files and directories currently installed.) Preparing to unpack .../perl-base_5.32.1-4+deb11u4_amd64.deb ... Unpacking perl-base (5.32.1-4+deb11u4) over (5.32.1-4+deb11u3) ... Setting up perl-base (5.32.1-4+deb11u4) ... (Reading database ... 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Unpacking libnghttp2-14:amd64 (1.43.0-1+deb11u2) over (1.43.0-1+deb11u1) ... Preparing to unpack .../libsqlite3-0_3.34.1-3+deb11u1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.34.1-3+deb11u1) over (3.34.1-3) ... Preparing to unpack .../libss2_1.46.2-2+deb11u1_amd64.deb ... Unpacking libss2:amd64 (1.46.2-2+deb11u1) over (1.46.2-2) ... Setting up libsqlite3-0:amd64 (3.34.1-3+deb11u1) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u2) ... Setting up mariadb-common (1:10.5.26-0+deb11u2) ... Setting up libss2:amd64 (1.46.2-2+deb11u1) ... Setting up libmariadb3:amd64 (1:10.5.26-0+deb11u2) ... Setting up logsave (1.46.2-2+deb11u1) ... Setting up e2fsprogs (1.46.2-2+deb11u1) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-yf', 'dist-upgrade'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.8s DUMP: 3612e6f7a7521a0b0f91985607de31fa - 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'show', '--no-all-versions', 'augustus'] 0m9.9s DUMP: Package: augustus Version: 3.4.0+dfsg2-2 Installed-Size: 10146 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.29), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.0), libgsl25 (>= 2.6), libhts3 (>= 1.10), libmariadb3 (>= 3.0.0), libmysql++3v5 (>= 3.2.5-1~), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 9), augustus-data Recommends: samtools Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython Description-en: gene prediction in eukaryotic genomes AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes. Description-md5: ab0f2f2c476597fc454d6e64ee4cdcaf Homepage: https://bioinf.uni-greifswald.de/augustus/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, science::calculation, scope::utility, uitoolkit::ncurses, use::analysing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/a/augustus/augustus_3.4.0+dfsg2-2_amd64.deb Size: 1951832 MD5sum: 45fa8e170a70e81af2141d3636de237a SHA256: c4b0aa58735caf3f3a4bc4a4bf26e5225b93bb437061d7c709e1be90703ef91a 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'show', '--no-all-versions', 'augustus'] 0m9.9s INFO: apt-cache knows about the following packages: augustus 0m9.9s INFO: Running scripts pre_install 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_database-server'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_database-server'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_exceptions'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_exceptions'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_extras'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_extras'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy'] 0m9.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 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=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy', 'augustus'] 0m9.9s DUMP: augustus: Installed: 3.4.0+dfsg2-2 Candidate: 3.4.0+dfsg2-2 Version table: *** 3.4.0+dfsg2-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy', 'augustus'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-y', 'install', 'augustus'] 0m10.1s DUMP: Reading package lists... Building dependency tree... Reading state information... augustus is already the newest version (3.4.0+dfsg2-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-y', 'install', 'augustus'] 0m10.1s INFO: Running scripts post_install 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_install_exceptions'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_install_exceptions'] 0m10.1s INFO: Running scripts post_distupgrade 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_exceptions'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_exceptions'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m10.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m10.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m10.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m10.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m10.6s INFO: Running scripts pre_install 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_database-server'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_database-server'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_exceptions'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_exceptions'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_extras'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_extras'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy'] 0m10.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 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=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy', 'augustus'] 0m10.7s DUMP: augustus: Installed: 3.4.0+dfsg2-2 Candidate: 3.4.0+dfsg2-2 Version table: *** 3.4.0+dfsg2-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-cache', 'policy', 'augustus'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-y', 'install', 'augustus=3.4.0+dfsg2-2'] 0m10.9s DUMP: Reading package lists... Building dependency tree... Reading state information... augustus is already the newest version (3.4.0+dfsg2-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', '-y', 'install', 'augustus=3.4.0+dfsg2-2'] 0m10.9s INFO: Running scripts post_install 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_install_exceptions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_install_exceptions'] 0m10.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m11.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m11.2s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m11.2s INFO: /bin converted to /usr/bin by /usr merge 0m11.2s INFO: /lib converted to /usr/lib by /usr merge 0m11.2s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m11.2s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m11.2s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m11.2s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m11.2s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m11.2s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m11.2s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m11.2s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m11.2s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m11.2s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m11.2s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m11.2s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m11.2s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m11.2s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m11.2s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m11.2s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m11.2s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m11.2s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m11.2s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m11.2s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m11.2s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m11.2s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m11.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m11.2s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m11.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m11.2s INFO: /sbin converted to /usr/sbin by /usr merge 0m11.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', '-ac', '--ignore-obsolete'] 0m12.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', '-ac', '--ignore-obsolete'] 0m12.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.1s DUMP: 0.15.6 0m12.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.1s INFO: Running adequate version 0.15.6 now. 0m12.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'augustus'] 0m12.3s DUMP: augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/augustify.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/bamToWig.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/extractAnno.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/fix_in_frame_stop_codon_genes.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py 0m12.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'augustus'] 0m12.3s ERROR: WARN: Inadequate results from running adequate! augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/augustify.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/bamToWig.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/extractAnno.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/fix_in_frame_stop_codon_genes.py augustus: py-file-not-bytecompiled /usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py 0m12.3s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 0m12.3s INFO: Running scripts pre_remove 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_exceptions'] 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/pre_remove_exceptions'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.2s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed augustus augustus 3.4.0+dfsg2-2 install ok installed augustus-data augustus-data 3.4.0+dfsg2-2 install ok installed base-files base-files 11.1+deb11u11 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+deb11u2 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+deb11u1 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 libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-9 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u2 install ok installed libboost-iostreams1.74.0:amd64 libboost-iostreams1.74.0 1.74.0-9 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u11 install ok installed libc6:amd64 libc6 2.31-13+deb11u11 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcolamd2:amd64 libcolamd2 1:5.8.1+dfsg-2 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2+deb11u1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.74.0-1.3+deb11u13 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 libdeflate0:amd64 libdeflate0 1.7-1 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2+deb11u1 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+deb11u6 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgsl25:amd64 libgsl25 2.6+dfsg-2 install ok installed libgslcblas0:amd64 libgslcblas0 2.6+dfsg-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u5 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhts3:amd64 libhts3 1.11-4 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u5 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 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 libmariadb3:amd64 libmariadb3 1:10.5.26-0+deb11u2 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u2 install ok installed libmysql++3v5:amd64 libmysql++3v5 3.2.5-2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1+deb11u2 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 libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1+deb11u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1+deb11u1 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+deb11u1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2+deb11u1 install ok installed libssh2-1:amd64 libssh2-1 1.9.0-2+deb11u1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u2 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsuitesparseconfig5:amd64 libsuitesparseconfig5 1:5.8.1+dfsg-2 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u6 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+deb11u6 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 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+deb11u1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mariadb-common mariadb-common 1:10.5.26-0+deb11u2 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u2 install ok installed mysql-common mysql-common 5.8+1.0.7 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+deb11u4 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+deb11u2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'remove', 'augustus-data', 'libbamtools2.5.1:amd64', 'libboost-iostreams1.74.0:amd64', 'libbrotli1:amd64', 'libcolamd2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libhts3:amd64', 'libldap-2.4-2:amd64', 'libmariadb3:amd64', 'libmysql++3v5:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsuitesparseconfig5:amd64', 'mariadb-common', 'mysql-common', 'augustus'] 0m13.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: augustus augustus-data libbamtools2.5.1 libboost-iostreams1.74.0 libbrotli1 libcolamd2 libcurl3-gnutls libdeflate0 libgsl25 libgslcblas0 libhts3 libldap-2.4-2 libmariadb3 libmysql++3v5 libnghttp2-14 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsuitesparseconfig5 mariadb-common mysql-common 0 upgraded, 0 newly installed, 24 to remove and 0 not upgraded. After this operation, 151 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 ... 8321 files and directories currently installed.) Removing augustus (3.4.0+dfsg2-2) ... Removing augustus-data (3.4.0+dfsg2-2) ... Removing libbamtools2.5.1:amd64 (2.5.1+dfsg-9) ... Removing libboost-iostreams1.74.0:amd64 (1.74.0-9) ... Removing libhts3:amd64 (1.11-4) ... Removing libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u13) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Removing libcolamd2:amd64 (1:5.8.1+dfsg-2) ... Removing libdeflate0:amd64 (1.7-1) ... Removing libgsl25:amd64 (2.6+dfsg-2) ... Removing libgslcblas0:amd64 (2.6+dfsg-2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libmysql++3v5:amd64 (3.2.5-2) ... Removing libmariadb3:amd64 (1:10.5.26-0+deb11u2) ... Removing libnghttp2-14:amd64 (1.43.0-1+deb11u2) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsqlite3-0:amd64 (3.34.1-3+deb11u1) ... Removing libssh2-1:amd64 (1.9.0-2+deb11u1) ... Removing libsuitesparseconfig5:amd64 (1:5.8.1+dfsg-2) ... Removing mariadb-common (1:10.5.26-0+deb11u2) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Removing mysql-common (5.8+1.0.7) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'remove', 'augustus-data', 'libbamtools2.5.1:amd64', 'libboost-iostreams1.74.0:amd64', 'libbrotli1:amd64', 'libcolamd2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libhts3:amd64', 'libldap-2.4-2:amd64', 'libmariadb3:amd64', 'libmysql++3v5:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsuitesparseconfig5:amd64', 'mariadb-common', 'mysql-common', 'augustus'] 0m13.6s INFO: Running scripts post_remove 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_remove_exceptions'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_remove_exceptions'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--purge', 'augustus-data', 'libbamtools2.5.1:amd64', 'libboost-iostreams1.74.0:amd64', 'libbrotli1:amd64', 'libcolamd2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libhts3:amd64', 'libldap-2.4-2:amd64', 'libmariadb3:amd64', 'libmysql++3v5:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsuitesparseconfig5:amd64', 'mariadb-common', 'mysql-common'] 0m13.7s DUMP: dpkg: warning: ignoring request to remove augustus-data which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.1 which isn't installed dpkg: warning: ignoring request to remove libboost-iostreams1.74.0 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcolamd2 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 libgsl25 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libmariadb3 which isn't installed dpkg: warning: ignoring request to remove libmysql++3v5 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpsl5 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 dpkg: warning: ignoring request to remove libsuitesparseconfig5 which isn't installed (Reading database ... 6680 files and directories currently installed.) Purging configuration files for mariadb-common (1:10.5.26-0+deb11u2) ... Purging configuration files for mysql-common (5.8+1.0.7) ... 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--purge', 'augustus-data', 'libbamtools2.5.1:amd64', 'libboost-iostreams1.74.0:amd64', 'libbrotli1:amd64', 'libcolamd2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgsl25:amd64', 'libgslcblas0:amd64', 'libhts3:amd64', 'libldap-2.4-2:amd64', 'libmariadb3:amd64', 'libmysql++3v5:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsuitesparseconfig5:amd64', 'mariadb-common', 'mysql-common'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--purge', 'augustus'] 0m13.7s DUMP: dpkg: warning: ignoring request to remove augustus which isn't installed 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--purge', 'augustus'] 0m13.7s INFO: Running scripts post_purge 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_purge_exceptions'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_purge_exceptions'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--purge', '--pending'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--purge', '--pending'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--remove', '--pending'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg', '--remove', '--pending'] 0m13.7s INFO: Running scripts post_test 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_test_exceptions'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'tmp/scripts/post_test_exceptions'] 0m13.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m13.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg-divert', '--list'] 0m13.9s 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 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'dpkg-divert', '--list'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'clean'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4', 'apt-get', 'clean'] 0m14.0s DEBUG: Recording chroot state 0m14.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/shm'] 0m14.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/shm'] 0m14.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/console'] 0m14.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/console'] 0m14.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/ptmx'] 0m14.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/ptmx'] 0m14.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/pts'] 0m14.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/dev/pts'] 0m14.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/proc'] 0m14.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4/proc'] 0m14.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m14.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmplfzyt6d4'] 0m14.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmplfzyt6d4 0m14.7s INFO: PASS: Upgrading between Debian distributions. 0m14.7s INFO: PASS: All tests. 0m14.7s INFO: piuparts run ends. ret=0 End: 2024-11-05 05:31:58 GMT