Start: 2022-12-31 10:15:56 GMT [stretch] Package: spades Version: 3.9.1+dfsg-1 Installed-Size: 17258 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libjemalloc1 (>= 2.1.1), libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description: genome assembler for single-cell and isolates data sets Homepage: http://bioinf.spbau.ru/en/spades Description-md5: a8af60ccfdd2e159193efb52065bef14 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.9.1+dfsg-1_amd64.deb Size: 3449736 MD5sum: 7babab4f83d9622eb2503fb257104b32 SHA256: b2212137f2175a8d7e623d9a5d4b94c14c3f88046a91a53e2d34b095d6e3d92f [buster] Package: spades Version: 3.13.0+dfsg2-2 Installed-Size: 23056 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 6), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description: genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ Description-md5: a8af60ccfdd2e159193efb52065bef14 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.13.0+dfsg2-2_amd64.deb Size: 4755188 MD5sum: 4f03853de5a2b271302b8ecaded12e52 SHA256: a38a37cd56b239a55562331a5ed9ddd15170e0584b00adf3f3c59ca4038236d2 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2buster/reference-chroot-metadata.dat --apt spades=3.13.0+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 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2buster/reference-chroot-metadata.dat --apt spades=3.13.0+dfsg2-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpnccxs99d 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpnccxs99d 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/pts'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.3s DEBUG: Created policy-rc.d and chmodded it. 0m1.3s DEBUG: Created resolv.conf. 0m1.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpnccxs99d/tmp/scripts/ 0m1.3s INFO: Running scripts post_chroot_unpack 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'update'] 0m2.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'update'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s INFO: Running scripts post_setup 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_dummy_users'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_dummy_users'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_forbid_home'] 0m3.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_forbid_home'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_minimize'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_minimize'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2buster/reference-chroot-metadata.dat 0m4.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m4.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m4.3s INFO: Running scripts is_testable 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s INFO: Running scripts pre_test 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_test_root_password'] 0m4.4s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_test_root_password'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m4.6s DUMP: Package: spades Version: 3.9.1+dfsg-1 Installed-Size: 17258 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libjemalloc1 (>= 2.1.1), libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description-en: genome assembler for single-cell and isolates data sets The SPAdes ?? St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads. Description-md5: a8af60ccfdd2e159193efb52065bef14 Homepage: http://bioinf.spbau.ru/en/spades Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.9.1+dfsg-1_amd64.deb Size: 3449736 MD5sum: 7babab4f83d9622eb2503fb257104b32 SHA256: b2212137f2175a8d7e623d9a5d4b94c14c3f88046a91a53e2d34b095d6e3d92f 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m4.6s INFO: apt-cache knows about the following packages: spades 0m4.6s INFO: Running scripts pre_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy'] 0m4.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy', 'spades'] 0m4.8s DUMP: spades: Installed: (none) Candidate: 3.9.1+dfsg-1 Version table: 3.9.1+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy', 'spades'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-y', 'install', 'spades'] 0m9.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bamtools bwa libbamtools2.4.0 libcurl3-gnutls libexpat1 libffi6 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhat-trie0 libhogweed4 libhts1 libidn11 libidn2-0 libjemalloc1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libnlopt0 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libssw0 libtasn1-6 libunistring0 libyaml-0-2 mime-support python python-joblib python-minimal python-yaml python2.7 python2.7-minimal readline-common samtools Suggested packages: gnutls-bin krb5-doc krb5-user python-doc python-tk python2.7-doc binutils binfmt-support readline-doc Recommended packages: ca-certificates krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils python-numpy python-pytest python-simplejson The following NEW packages will be installed: bamtools bwa libbamtools2.4.0 libcurl3-gnutls libexpat1 libffi6 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhat-trie0 libhogweed4 libhts1 libidn11 libidn2-0 libjemalloc1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libncurses5 libnettle6 libnghttp2-14 libnlopt0 libp11-kit0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libssw0 libtasn1-6 libunistring0 libyaml-0-2 mime-support python python-joblib python-minimal python-yaml python2.7 python2.7-minimal readline-common samtools spades 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 15.7 MB of archives. After this operation, 56.2 MB of additional disk space will be used. 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libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:22 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amd64 2.4.1+dfsg-1 [190 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 bamtools amd64 2.4.1+dfsg-1 [214 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 bwa amd64 0.7.15-2+deb9u1 [194 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libhat-trie0 amd64 0.0~git25f9e946-2 [10.7 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libnlopt0 amd64 2.4.2+dfsg-2+b2 [162 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libssw0 amd64 1.1-1+b1 [16.5 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libyaml-0-2 amd64 0.1.7-2 [47.6 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 python-joblib all 0.10.3+git55-g660fe5d-1 [115 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 python-yaml amd64 3.12-1 [119 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 samtools amd64 1.3.1-3 [254 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 libjemalloc1 amd64 3.6.0-9.1 [89.8 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 spades amd64 3.9.1+dfsg-1 [3450 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.7 MB in 0s (41.1 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. 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Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libhat-trie0:amd64 (0.0~git25f9e946-2) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up bamtools (2.4.1+dfsg-1) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up python (2.7.13-2) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up python-yaml (3.12-1) ... Setting up python-joblib (0.10.3+git55-g660fe5d-1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up samtools (1.3.1-3) ... Setting up spades (3.9.1+dfsg-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-y', 'install', 'spades'] 0m9.7s INFO: Running scripts post_install 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_install_exceptions'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_install_exceptions'] 0m9.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m10.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m10.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpnccxs99d to buster 0m10.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m10.2s INFO: Running scripts pre_distupgrade 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'update'] 0m13.9s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7909 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5969 kB] Fetched 14.0 MB in 2s (4922 kB/s) Reading package lists... 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'update'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-yf', 'dist-upgrade'] 0m26.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libbamtools2.4.0 libhts1 libidn11 libjemalloc1 libunistring0 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: fdisk gcc-8-base libbamtools2.5.1 libcom-err2 libdeflate0 libext2fs2 libhts2 libncurses6 libncursesw6 libprocps7 libpython2-stdlib libseccomp2 libtinfo6 libunistring2 libzstd1 lsb-base procps python2 python2-minimal The following packages will be upgraded: adduser apt bamtools base-files base-passwd bash bsdutils bwa coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fslibs e2fsprogs findutils gpgv grep gzip hostname init-system-helpers libacl1 libapt-pkg5.0 libattr1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcomerr2 libcurl3-gnutls libdb5.3 libdebconfclient0 libexpat1 libfdisk1 libffi6 libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhat-trie0 libhogweed4 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblz4-1 liblzma5 libmount1 libncurses5 libncursesw5 libnettle6 libnghttp2-14 libnlopt0 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libssl1.1 libssw0 libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libudev1 libuuid1 libyaml-0-2 login mime-support mount multiarch-support ncurses-base ncurses-bin passwd perl-base python python-joblib python-minimal python-yaml python2.7 python2.7-minimal readline-common samtools sed sensible-utils spades sysvinit-utils tar util-linux zlib1g 119 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 48.4 MB of archives. After this operation, 22.1 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u13 [69.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libc6 amd64 2.28-10+deb10u1 [2863 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libc-bin amd64 2.28-10+deb10u1 [795 kB] Get:4 http://deb.debian.org/debian buster/main amd64 gcc-8-base amd64 8.3.0-6 [191 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u2 [325 kB] Get:7 http://deb.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:8 http://deb.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:9 http://deb.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:10 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3+deb10u2 [237 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1+deb10u1 [76.7 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2+deb10u1 [316 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u8 [1126 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:22 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1+deb10u1 [93.5 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:26 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:36 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:37 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:38 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:39 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5+deb10u1 [556 kB] Get:40 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u1 [90.8 kB] Get:41 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2.3 [967 kB] Get:44 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2.3 [1418 kB] Get:45 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1+deb10u1 [53.3 kB] Get:46 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1+deb10u1 [153 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:49 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:50 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.8 [2210 kB] Get:51 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:52 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:56 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:57 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:58 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:59 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:60 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3+deb10u1 [128 kB] Get:61 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:68 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:69 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:70 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:71 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:72 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:73 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:74 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:76 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:77 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libncurses5 amd64 6.1+20181013-2+deb10u2 [96.2 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:81 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:82 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:84 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:85 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:86 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:87 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:88 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:89 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:90 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:92 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:93 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:94 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:95 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:96 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:97 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:98 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:99 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:100 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:101 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:102 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:103 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:104 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:105 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get:106 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get:107 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get:108 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get:109 http://deb.debian.org/debian buster/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get:110 http://deb.debian.org/debian buster/main amd64 bamtools amd64 2.5.1+dfsg-3 [171 kB] Get:111 http://deb.debian.org/debian buster/main amd64 bwa amd64 0.7.17-3 [195 kB] Get:112 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:113 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:114 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:115 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:116 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:117 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:118 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:119 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:120 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:121 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:122 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:123 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:124 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:125 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:126 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:127 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:128 http://deb.debian.org/debian buster/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get:129 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:130 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:131 http://deb.debian.org/debian buster/main amd64 libnlopt0 amd64 2.4.2+dfsg-8+b1 [165 kB] Get:132 http://deb.debian.org/debian buster/main amd64 libssw0 amd64 1.1-2 [16.5 kB] Get:133 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:134 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:135 http://deb.debian.org/debian buster/main amd64 python-joblib all 0.13.0-2 [190 kB] Get:136 http://deb.debian.org/debian buster/main amd64 python-yaml amd64 3.13-2 [127 kB] Get:137 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get:138 http://deb.debian.org/debian buster/main amd64 spades amd64 3.13.0+dfsg2-2 [4755 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 48.4 MB in 0s (110 MB/s) (Reading database ... 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Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-stable.gpg ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5935 files and directories currently installed.) Preparing to unpack .../libselinux1_2.8-1+b1_amd64.deb ... Unpacking libselinux1:amd64 (2.8-1+b1) over (2.6-3+b3) ... Setting up libselinux1:amd64 (2.8-1+b1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5933 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.8-2_all.deb ... Unpacking libsemanage-common (2.8-2) over (2.6-2) ... Setting up libsemanage-common (2.8-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5932 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.8-2_amd64.deb ... Unpacking libsemanage1:amd64 (2.8-2) over (2.6-2) ... Setting up libsemanage1:amd64 (2.8-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5931 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.3.1-5_amd64.deb ... Unpacking libpam-modules:amd64 (1.3.1-5) over (1.1.8-3.6) ... Setting up libpam-modules:amd64 (1.3.1-5) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/limits.conf ... (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 ... 5932 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.5-1.1_amd64.deb ... Unpacking passwd (1:4.5-1.1) over (1:4.4-4.1) ... Setting up passwd (1:4.5-1.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5913 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-1+deb10u1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-1+deb10u1) over (1:1.2.8.dfsg-5) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-1+deb10u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5913 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.12-1+deb10u2_amd64.deb ... Unpacking gpgv (2.2.12-1+deb10u2) over (2.1.18-8~deb9u4) ... Setting up gpgv (2.2.12-1+deb10u2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5913 files and directories currently installed.) Preparing to unpack .../libstdc++6_8.3.0-6_amd64.deb ... Unpacking libstdc++6:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Setting up libstdc++6:amd64 (8.3.0-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5913 files and directories currently installed.) Preparing to unpack .../archives/apt_1.8.2.3_amd64.deb ... Unpacking apt (1.8.2.3) over (1.4.10) ... Preparing to unpack .../libapt-pkg5.0_1.8.2.3_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.8.2.3) over (1.4.10) ... Setting up libapt-pkg5.0:amd64 (1.8.2.3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5942 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.8.3-1+deb10u1_amd64.deb ... Unpacking liblz4-1:amd64 (1.8.3-1+deb10u1) over (0.0~r131-2+b1) ... Setting up liblz4-1:amd64 (1.8.3-1+deb10u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5941 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1+deb10u1_amd64.deb ... Unpacking liblzma5:amd64 (5.2.4-1+deb10u1) over (5.2.2-1.2+b1) ... Setting up liblzma5:amd64 (5.2.4-1+deb10u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5940 files and directories currently installed.) Preparing to unpack .../libsystemd0_241-7~deb10u8_amd64.deb ... Unpacking libsystemd0:amd64 (241-7~deb10u8) over (232-25+deb9u12) ... Setting up libsystemd0:amd64 (241-7~deb10u8) ... (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 ... 5940 files and directories currently installed.) Preparing to unpack .../libudev1_241-7~deb10u8_amd64.deb ... Unpacking libudev1:amd64 (241-7~deb10u8) over (232-25+deb9u12) ... Setting up libudev1:amd64 (241-7~deb10u8) ... (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 ... 5940 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-6_amd64.deb ... Unpacking tar (1.30+dfsg-6) over (1.29b-1.1) ... Setting up tar (1.30+dfsg-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5938 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.19.8_amd64.deb ... Unpacking dpkg (1.19.8) over (1.18.25) ... Setting up dpkg (1.19.8) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (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 ... 5936 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-5_amd64.deb ... Unpacking dash (0.5.10.2-5) over (0.5.8-2.4) ... Setting up dash (0.5.10.2-5) ... (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 ... 5937 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.7-3_amd64.deb ... Unpacking diffutils (1:3.7-3) over (1:3.5-3) ... Setting up diffutils (1:3.7-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5939 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libcomerr2:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../libcom-err2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libcom-err2:amd64 (1.44.5-1+deb10u3) ... Setting up libcom-err2:amd64 (1.44.5-1+deb10u3) ... (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 ... 5942 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.44.5-1+deb10u3_amd64.deb ... Unpacking e2fslibs:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Selecting previously unselected package libext2fs2:amd64. Preparing to unpack .../libext2fs2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libext2fs2:amd64 (1.44.5-1+deb10u3) ... Setting up libext2fs2:amd64 (1.44.5-1+deb10u3) ... (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 ... 5945 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.5-1+deb10u3_amd64.deb ... Unpacking e2fsprogs (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Setting up e2fsprogs (1.44.5-1+deb10u3) ... Installing new version of config file /etc/mke2fs.conf ... (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 ... 5928 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20190209-2_amd64.deb ... Unpacking findutils (4.6.0+git+20190209-2) over (4.6.0+git+20161106-2) ... Setting up findutils (4.6.0+git+20190209-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5930 files and directories currently installed.) Preparing to unpack .../archives/grep_3.3-1_amd64.deb ... Unpacking grep (3.3-1) over (2.27-2) ... Setting up grep (3.3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5930 files and directories currently installed.) Preparing to unpack .../gzip_1.9-3+deb10u1_amd64.deb ... Unpacking gzip (1.9-3+deb10u1) over (1.6-5+b1) ... Setting up gzip (1.9-3+deb10u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5929 files and directories currently installed.) Preparing to unpack .../hostname_3.21_amd64.deb ... Unpacking hostname (3.21) over (3.18+b1) ... Setting up hostname (3.21) ... (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 ... 5928 files and directories currently installed.) Preparing to unpack .../libuuid1_2.33.1-0.1_amd64.deb ... Unpacking libuuid1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libuuid1:amd64 (2.33.1-0.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5928 files and directories currently installed.) Preparing to unpack .../libblkid1_2.33.1-0.1_amd64.deb ... Unpacking libblkid1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libblkid1:amd64 (2.33.1-0.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5928 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.33.1-0.1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libsmartcols1:amd64 (2.33.1-0.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5928 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.33.1-0.1_amd64.deb ... Unpacking libfdisk1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libfdisk1:amd64 (2.33.1-0.1) ... Selecting previously unselected package libncursesw6: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 ... 5928 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5937 files and directories currently installed.) Preparing to unpack .../libmount1_2.33.1-0.1_amd64.deb ... Unpacking libmount1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libmount1:amd64 (2.33.1-0.1) ... (Reading database ... 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Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up bwa (0.7.17-3) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libnlopt0:amd64 (2.4.2+dfsg-8+b1) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up libncurses5:amd64 (6.1+20181013-2+deb10u2) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libhat-trie0:amd64 (0.1.2-2) ... Setting up multiarch-support (2.28-10+deb10u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up mount (2.33.1-0.1) ... Setting up libcomerr2:amd64 (1.44.5-1+deb10u3) ... Setting up bamtools (2.5.1+dfsg-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libssw0:amd64 (1.1-2) ... Setting up readline-common (7.0-5) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up samtools (1.9-4) ... Setting up python-joblib (0.13.0-2) ... Setting up python-yaml (3.13-2) ... Setting up spades (3.13.0+dfsg2-2) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-yf', 'dist-upgrade'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m27.1s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m27.3s DUMP: Package: spades Version: 3.13.0+dfsg2-2 Installed-Size: 23056 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc1 (>= 1:4.0), libgomp1 (>= 4.9), libhat-trie0, libnlopt0 (>= 2.2.4), libssw0, libstdc++6 (>= 6), zlib1g (>= 1:1.2.3.3), python, python-joblib, python-yaml, bwa, bamtools, samtools Description-en: genome assembler for single-cell and isolates data sets The SPAdes ?? St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads. Description-md5: a8af60ccfdd2e159193efb52065bef14 Homepage: http://cab.spbu.ru/software/spades/ Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, implemented-in::python, interface::commandline, role::program, scope::utility, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/s/spades/spades_3.13.0+dfsg2-2_amd64.deb Size: 4755188 MD5sum: 4f03853de5a2b271302b8ecaded12e52 SHA256: a38a37cd56b239a55562331a5ed9ddd15170e0584b00adf3f3c59ca4038236d2 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'show', '--no-all-versions', 'spades'] 0m27.3s INFO: apt-cache knows about the following packages: spades 0m27.3s INFO: Running scripts pre_install 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_database-server'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_database-server'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_exceptions'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_exceptions'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_extras'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_extras'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy'] 0m27.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy', 'spades'] 0m27.3s DUMP: spades: Installed: 3.13.0+dfsg2-2 Candidate: 3.13.0+dfsg2-2 Version table: *** 3.13.0+dfsg2-2 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy', 'spades'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-y', 'install', 'spades'] 0m27.7s DUMP: Reading package lists... Building dependency tree... Reading state information... spades is already the newest version (3.13.0+dfsg2-2). The following packages were automatically installed and are no longer required: libbamtools2.4.0 libhts1 libidn11 libjemalloc1 libncurses5 libunistring0 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-y', 'install', 'spades'] 0m27.7s INFO: Running scripts post_install 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_install_exceptions'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_install_exceptions'] 0m27.7s INFO: Running scripts post_distupgrade 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_exceptions'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_exceptions'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_zz_backports'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_distupgrade_zz_backports'] 0m27.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m28.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m28.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m28.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m28.3s INFO: Running scripts pre_install 0m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_database-server'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_database-server'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_exceptions'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_exceptions'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_extras'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_extras'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy'] 0m28.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy', 'spades'] 0m28.5s DUMP: spades: Installed: 3.13.0+dfsg2-2 Candidate: 3.13.0+dfsg2-2 Version table: *** 3.13.0+dfsg2-2 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-cache', 'policy', 'spades'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-y', 'install', 'spades=3.13.0+dfsg2-2'] 0m28.8s DUMP: Reading package lists... Building dependency tree... Reading state information... spades is already the newest version (3.13.0+dfsg2-2). The following packages were automatically installed and are no longer required: libbamtools2.4.0 libhts1 libidn11 libjemalloc1 libncurses5 libunistring0 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', '-y', 'install', 'spades=3.13.0+dfsg2-2'] 0m28.8s INFO: Running scripts post_install 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_install_exceptions'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_install_exceptions'] 0m28.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m29.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m29.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', '-ac', '--ignore-obsolete'] 0m30.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', '-ac', '--ignore-obsolete'] 0m30.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.0s DUMP: 0.15.6 0m30.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.0s INFO: Running adequate version 0.15.6 now. 0m30.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'spades'] 0m30.1s DUMP: spades: py-file-not-bytecompiled /usr/lib/spades/bin/spades_init.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/SeqIO.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/__init__.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/alignment.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/parallel_launcher.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/sam_parser.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/corrector_logic.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/hammer_logic.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/lucigen_nxmate.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/options_storage.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/process_cfg.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/spades_logic.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/support.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/barcode_extraction.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/break_by_coverage.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/generate_quality.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/id_generation.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/launch_options.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/reference_construction.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/string_dist_utils.py 0m30.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'spades'] 0m30.1s ERROR: WARN: Inadequate results from running adequate! spades: py-file-not-bytecompiled /usr/lib/spades/bin/spades_init.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/SeqIO.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/__init__.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/alignment.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/parallel_launcher.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/common/sam_parser.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/corrector_logic.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/hammer_logic.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/lucigen_nxmate.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/options_storage.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/process_cfg.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/spades_logic.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/support.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/barcode_extraction.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/break_by_coverage.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/generate_quality.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/id_generation.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/launch_options.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/reference_construction.py spades: py-file-not-bytecompiled /usr/share/spades/spades_pipeline/truspades/string_dist_utils.py 0m30.1s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 0m30.1s INFO: Running scripts pre_remove 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_exceptions'] 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/pre_remove_exceptions'] 0m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m31.7s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed bamtools bamtools 2.5.1+dfsg-3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed bwa bwa 0.7.17-3 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fslibs:amd64 e2fslibs 1.44.5-1+deb10u3 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libbamtools2.4.0 libbamtools2.4.0 2.4.1+dfsg-1 install ok installed libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcomerr2:amd64 libcomerr2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libexpat1:amd64 libexpat1 2.2.6-2+deb10u4 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u4 install ok installed libhat-trie0:amd64 libhat-trie0 0.1.2-2 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libidn11:amd64 libidn11 1.33-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed libjemalloc1 libjemalloc1 3.6.0-9.1 install ok installed libjsoncpp1:amd64 libjsoncpp1 1.7.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u4 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.47+dfsg-3+deb10u7 install ok installed libldap-common libldap-common 2.4.47+dfsg-3+deb10u7 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncurses5:amd64 libncurses5 6.1+20181013-2+deb10u2 install ok installed libncurses6:amd64 libncurses6 6.1+20181013-2+deb10u2 install ok installed libncursesw5:amd64 libncursesw5 6.1+20181013-2+deb10u2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.36.0-2+deb10u1 install ok installed libnlopt0:amd64 libnlopt0 2.4.2+dfsg-8+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libprocps7:amd64 libprocps7 2:3.3.15-2 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2+deb10u1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u1 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1+deb10u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1+deb10u2 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u3 install ok installed libssw0:amd64 libssw0 1.1-2 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo5:amd64 libtinfo5 6.1+20181013-2+deb10u2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.1-1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed lsb-base lsb-base 10.2019051400 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed multiarch-support multiarch-support 2.28-10+deb10u1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed procps procps 2:3.3.15-2 install ok installed python python 2.7.16-1 install ok installed python-joblib python-joblib 0.13.0-2 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python-yaml python-yaml 3.13-2 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u1 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u1 install ok installed readline-common readline-common 7.0-5 install ok installed samtools samtools 1.9-4 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed spades spades 3.13.0+dfsg2-2 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'remove', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'procps', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'spades'] 0m32.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bamtools bwa libbamtools2.4.0 libbamtools2.5.1 libcurl3-gnutls libdeflate0 libexpat1 libgomp1 libgssapi-krb5-2 libhat-trie0 libhts1 libhts2 libidn11 libjemalloc1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libncurses5 libncurses6 libnghttp2-14 libnlopt0 libprocps7 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libssw0 libunistring0 libyaml-0-2 lsb-base mime-support procps python python-joblib python-minimal python-yaml python2 python2-minimal python2.7 python2.7-minimal readline-common samtools spades 0 upgraded, 0 newly installed, 55 to remove and 0 not upgraded. After this operation, 62.1 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 ... 6182 files and directories currently installed.) Removing spades (3.13.0+dfsg2-2) ... Removing bamtools (2.5.1+dfsg-3) ... Removing bwa (0.7.17-3) ... Removing libbamtools2.4.0 (2.4.1+dfsg-1) ... Removing libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Removing libhts1:amd64 (1.3.2-2) ... Removing samtools (1.9-4) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python-yaml (3.13-2) ... Removing python-joblib (0.13.0-2) ... Removing python (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Removing libhat-trie0:amd64 (0.1.2-2) ... Removing libidn11:amd64 (1.33-2.2) ... Removing libjemalloc1 (3.6.0-9.1) ... Removing libjsoncpp1:amd64 (1.7.4-3) ... Removing libkrb5-3:amd64 (1.17-3+deb10u4) ... Removing libk5crypto3:amd64 (1.17-3+deb10u4) ... Removing libkrb5support0:amd64 (1.17-3+deb10u4) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Removing libldap-common (2.4.47+dfsg-3+deb10u7) ... Removing libncurses5:amd64 (6.1+20181013-2+deb10u2) ... Removing procps (2:3.3.15-2) ... Removing libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libnlopt0:amd64 (2.4.2+dfsg-8+b1) ... Removing libprocps7:amd64 (2:3.3.15-2) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... Removing python2-minimal (2.7.16-1) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing libssw0:amd64 (1.1-2) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libyaml-0-2:amd64 (0.2.1-1) ... Removing lsb-base (10.2019051400) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... find: '/usr/lib/python2.7': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Removing libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Removing mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'remove', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'procps', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools', 'spades'] 0m32.8s INFO: Running scripts post_remove 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_remove_exceptions'] 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_remove_exceptions'] 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--purge', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'procps', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools'] 0m32.9s DUMP: dpkg: warning: ignoring request to remove bamtools which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed dpkg: warning: ignoring request to remove libbamtools2.4.0 which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.1 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 4638 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... dpkg: warning: ignoring request to remove libhat-trie0 which isn't installed dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libjemalloc1 which isn't installed dpkg: warning: ignoring request to remove libjsoncpp1 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.47+dfsg-3+deb10u7) ... dpkg: warning: ignoring request to remove libncurses5 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnlopt0 which isn't installed dpkg: warning: ignoring request to remove libprocps7 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1n-0+deb10u3) ... dpkg: warning: ignoring request to remove libssw0 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove lsb-base which isn't installed Purging configuration files for mime-support (3.62) ... Purging configuration files for procps (2:3.3.15-2) ... Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-joblib which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-yaml which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.16-2+deb10u1) ... Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--purge', 'bamtools', 'bwa', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhat-trie0:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libjemalloc1', 'libjsoncpp1:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libncurses5:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnlopt0:amd64', 'libprocps7:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libssw0:amd64', 'libunistring0:amd64', 'libyaml-0-2:amd64', 'lsb-base', 'mime-support', 'procps', 'python', 'python-joblib', 'python-minimal', 'python-yaml', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'samtools'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--purge', 'spades'] 0m32.9s DUMP: dpkg: warning: ignoring request to remove spades which isn't installed 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--purge', 'spades'] 0m32.9s INFO: Running scripts post_purge 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_purge_exceptions'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_purge_exceptions'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--purge', '--pending'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--purge', '--pending'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--remove', '--pending'] 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg', '--remove', '--pending'] 0m33.0s INFO: Running scripts post_test 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_test_exceptions'] 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'tmp/scripts/post_test_exceptions'] 0m33.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m33.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg-divert', '--list'] 0m33.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'dpkg-divert', '--list'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'clean'] 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnccxs99d', 'apt-get', 'clean'] 0m33.2s DEBUG: Recording chroot state 0m34.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/shm'] 0m34.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/shm'] 0m34.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/console'] 0m34.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/console'] 0m34.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/ptmx'] 0m34.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/ptmx'] 0m34.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/pts'] 0m34.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/dev/pts'] 0m34.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/proc'] 0m34.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnccxs99d/proc'] 0m34.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m34.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnccxs99d'] 0m34.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpnccxs99d 0m34.4s INFO: PASS: Upgrading between Debian distributions. 0m34.4s INFO: PASS: All tests. 0m34.4s INFO: piuparts run ends. ret=0 End: 2022-12-31 10:16:31 GMT