Start: 2025-10-10 04:59:13 GMT [stable] Package: racon Version: 1.5.0-3 Installed-Size: 3167 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libedlib1 (>= 1.2.7-3~), libgcc-s1 (>= 3.0), libspoa7.0.0 (>= 4.0.5), libstdc++6 (>= 12), zlib1g (>= 1:1.1.4) Recommends: python3, rampler Description: consensus module for raw de novo DNA assembly of long uncorrected reads Homepage: https://github.com/lbcb-sci/racon Description-md5: 0245f53dd68b53cce76f4a5dd8d8a554 Section: science Priority: optional Filename: pool/main/r/racon/racon_1.5.0-3_amd64.deb Size: 3115248 MD5sum: 602de8da7f51b1ac954f76963f5399a6 SHA256: eba84b0023a9c8748a5fae490d259993f306b0d2e1b9c2efb89535d5458a9241 [testing] [sid] Package: racon Version: 1.5.0-4 Installed-Size: 3171 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libedlib1 (>= 1.2.3), libgcc-s1 (>= 3.0), libspoa7.0.0 (>= 4.0.5), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4) Recommends: python3, rampler Description: consensus module for raw de novo DNA assembly of long uncorrected reads Homepage: https://github.com/lbcb-sci/racon Description-md5: 0245f53dd68b53cce76f4a5dd8d8a554 Section: science Priority: optional Filename: pool/main/r/racon/racon_1.5.0-4_amd64.deb Size: 3116828 MD5sum: febeb177f8a7c5364aa24a04719e5515 SHA256: c3a0ced64d68cc1338862839137e43168043ebd2a0e1b983adb5c357f34e9c03 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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/trixie-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt racon=1.5.0-4 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 1.6.1~202508211944~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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/trixie-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt racon=1.5.0-4 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-40-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.153-1 (2025-09-20) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpm5vrprjp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpm5vrprjp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/proc'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/proc'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/pts'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/pts'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/ptmx'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/ptmx'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpm5vrprjp/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: cc6be03135582e5dd4c9ee869186ad39 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_dummy_users'] 0m3.2s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_dummy_users'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_forbid_home'] 0m3.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_forbid_home'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.2s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_minimize'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_minimize'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8+deb13u1 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69~deb13u1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1~deb13u1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.8-1~deb13u1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.8-1~deb13u1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4+deb13u1 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m3.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'show', '--no-all-versions', 'racon'] 0m3.8s DUMP: Package: racon Version: 1.5.0-3 Installed-Size: 3167 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libedlib1 (>= 1.2.7-3~), libgcc-s1 (>= 3.0), libspoa7.0.0 (>= 4.0.5), libstdc++6 (>= 12), zlib1g (>= 1:1.1.4) Recommends: python3, rampler Description-en: consensus module for raw de novo DNA assembly of long uncorrected reads Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. . Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected. . Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip. . Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads including dual overlaps. . A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be subsampled to decrease the total execution time (accuracy might be lower) while target sequences can be split into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well. Description-md5: 0245f53dd68b53cce76f4a5dd8d8a554 Homepage: https://github.com/lbcb-sci/racon Section: science Priority: optional Filename: pool/main/r/racon/racon_1.5.0-3_amd64.deb Size: 3115248 MD5sum: 602de8da7f51b1ac954f76963f5399a6 SHA256: eba84b0023a9c8748a5fae490d259993f306b0d2e1b9c2efb89535d5458a9241 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'show', '--no-all-versions', 'racon'] 0m3.8s INFO: apt-cache knows about the following packages: racon 0m3.8s INFO: Running scripts pre_install 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy'] 0m3.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.1,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy', 'racon'] 0m3.9s DUMP: racon: Installed: (none) Candidate: 1.5.0-3 Version table: 1.5.0-3 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy', 'racon'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-y', 'install', 'racon'] 0m5.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libedlib1 libspoa7.0.0 Recommended packages: python3 rampler The following NEW packages will be installed: libedlib1 libspoa7.0.0 racon 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 3208 kB of archives. After this operation, 3614 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libedlib1 amd64 1.2.7-6+b3 [18.1 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libspoa7.0.0 amd64 4.1.4-2+b1 [74.1 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 racon amd64 1.5.0-3 [3115 kB] Fetched 3208 kB in 0s (48.3 MB/s) Selecting previously unselected package libedlib1: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 ... 4939 files and directories currently installed.) Preparing to unpack .../libedlib1_1.2.7-6+b3_amd64.deb ... Unpacking libedlib1:amd64 (1.2.7-6+b3) ... Selecting previously unselected package libspoa7.0.0:amd64. Preparing to unpack .../libspoa7.0.0_4.1.4-2+b1_amd64.deb ... Unpacking libspoa7.0.0:amd64 (4.1.4-2+b1) ... Selecting previously unselected package racon. Preparing to unpack .../racon_1.5.0-3_amd64.deb ... Unpacking racon (1.5.0-3) ... Setting up libspoa7.0.0:amd64 (4.1.4-2+b1) ... Setting up libedlib1:amd64 (1.2.7-6+b3) ... Setting up racon (1.5.0-3) ... Processing triggers for libc-bin (2.41-12) ... 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-y', 'install', 'racon'] 0m5.0s INFO: Running scripts post_install 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_install_exceptions'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_install_exceptions'] 0m5.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m5.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m5.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpm5vrprjp to testing 0m5.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m5.3s INFO: Running scripts pre_distupgrade 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'update'] 0m7.1s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [147 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9706 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6461 kB] Fetched 16.3 MB in 1s (16.0 MB/s) Reading package lists... 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'update'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-yf', 'dist-upgrade'] 0m12.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-15-base The following packages will be upgraded: apt base-files bash bsdutils gcc-14-base grep init-system-helpers libapt-pkg7.0 libaudit-common libaudit1 libblkid1 libedlib1 libgcc-s1 libgmp10 libhogweed6t64 liblastlog2-2 liblzma5 libmount1 libnettle8t64 libpcre2-8-0 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libsystemd0 libudev1 libuuid1 libzstd1 login login.defs mount openssl-provider-legacy passwd tzdata util-linux 35 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 16.3 MB of archives. After this operation, 746 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 base-files amd64 14 [72.9 kB] Get:2 http://deb.debian.org/debian forky/main amd64 bash amd64 5.3-1 [1556 kB] Get:3 http://deb.debian.org/debian forky/main amd64 grep amd64 3.12-1 [443 kB] Get:4 http://deb.debian.org/debian forky/main amd64 liblastlog2-2 amd64 2.41.2-1 [28.9 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libuuid1 amd64 2.41.2-1 [38.1 kB] Get:6 http://deb.debian.org/debian forky/main amd64 bsdutils amd64 1:2.41.2-1 [93.4 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libblkid1 amd64 2.41.2-1 [173 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libmount1 amd64 2.41.2-1 [211 kB] Get:9 http://deb.debian.org/debian forky/main amd64 libsmartcols1 amd64 2.41.2-1 [144 kB] Get:10 http://deb.debian.org/debian forky/main amd64 util-linux amd64 2.41.2-1 [1257 kB] Get:11 http://deb.debian.org/debian forky/main amd64 mount amd64 2.41.2-1 [162 kB] Get:12 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Get:13 http://deb.debian.org/debian forky/main amd64 libsystemd0 amd64 258-1 [466 kB] Get:14 http://deb.debian.org/debian forky/main amd64 gcc-15-base amd64 15.2.0-4 [52.8 kB] Get:15 http://deb.debian.org/debian forky/main amd64 libgcc-s1 amd64 15.2.0-4 [71.7 kB] Get:16 http://deb.debian.org/debian forky/main amd64 liblzma5 amd64 5.8.1-2 [310 kB] Get:17 http://deb.debian.org/debian forky/main amd64 openssl-provider-legacy amd64 3.5.4-1 [308 kB] Get:18 http://deb.debian.org/debian forky/main amd64 libzstd1 amd64 1.5.7+dfsg-2 [308 kB] Get:19 http://deb.debian.org/debian forky/main amd64 libssl3t64 amd64 3.5.4-1 [2446 kB] Get:20 http://deb.debian.org/debian forky/main amd64 libstdc++6 amd64 15.2.0-4 [738 kB] Get:21 http://deb.debian.org/debian forky/main amd64 libudev1 amd64 258-1 [156 kB] Get:22 http://deb.debian.org/debian forky/main amd64 libapt-pkg7.0 amd64 3.1.8 [1206 kB] Get:23 http://deb.debian.org/debian forky/main amd64 apt amd64 3.1.8 [1483 kB] Get:24 http://deb.debian.org/debian forky/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Get:26 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.1.2-1 [60.4 kB] Get:27 http://deb.debian.org/debian forky/main amd64 login amd64 1:4.16.0-2+really2.41.2-1 [105 kB] Get:28 http://deb.debian.org/debian forky/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Get:29 http://deb.debian.org/debian forky/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Get:30 http://deb.debian.org/debian forky/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Get:31 http://deb.debian.org/debian forky/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Get:32 http://deb.debian.org/debian forky/main amd64 login.defs all 1:4.18.0-1 [211 kB] Get:33 http://deb.debian.org/debian forky/main amd64 passwd amd64 1:4.18.0-1 [1284 kB] Get:34 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get:35 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get:36 http://deb.debian.org/debian forky/main amd64 libedlib1 amd64 1.2.7-7 [18.5 kB] Preconfiguring packages ... Fetched 16.3 MB in 0s (134 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4969 files and directories currently installed.) Preparing to unpack .../base-files_14_amd64.deb ... Unpacking base-files (14) over (13.8+deb13u1) ... Setting up base-files (14) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (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 ... 4977 files and directories currently installed.) Preparing to unpack .../archives/apt_3.1.8_amd64.deb ... Unpacking apt (3.1.8) over (3.0.3) ... Setting up apt (3.1.8) ... (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 ... 4975 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.69_all.deb ... Unpacking init-system-helpers (1.69) over (1.69~deb13u1) ... Setting up init-system-helpers (1.69) ... (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 ... 4975 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.1.2-1_all.deb ... Unpacking libaudit-common (1:4.1.2-1) over (1:4.0.2-2) ... Setting up libaudit-common (1:4.1.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4975 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.1.2-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.1.2-1) over (1:4.0.2-2+b2) ... Setting up libaudit1:amd64 (1:4.1.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4974 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.41.2-1_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41.2-1) over (1:4.16.0-2+really2.41-5) ... Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-5) over (2:6.3.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-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 ... 4966 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.10.2-1_amd64.deb ... Unpacking libnettle8t64:amd64 (3.10.2-1) over (3.10.1-1) ... Setting up libnettle8t64:amd64 (3.10.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4966 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.10.2-1_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.10.2-1) over (3.10.1-1) ... Setting up libhogweed6t64:amd64 (3.10.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4966 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.46-1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.46-1) over (10.46-1~deb13u1) ... Setting up libpcre2-8-0:amd64 (10.46-1) ... (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 ... 4966 files and directories currently installed.) Preparing to unpack .../login.defs_1%3a4.18.0-1_all.deb ... Unpacking login.defs (1:4.18.0-1) over (1:4.17.4-2) ... Preparing to unpack .../passwd_1%3a4.18.0-1_amd64.deb ... Unpacking passwd (1:4.18.0-1) over (1:4.17.4-2) ... Preparing to unpack .../tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) over (2025b-4+deb13u1) ... Preparing to unpack .../gcc-14-base_14.3.0-8_amd64.deb ... Unpacking gcc-14-base:amd64 (14.3.0-8) over (14.2.0-19) ... Preparing to unpack .../libedlib1_1.2.7-7_amd64.deb ... Unpacking libedlib1:amd64 (1.2.7-7) over (1.2.7-6+b3) ... Setting up gcc-14-base:amd64 (14.3.0-8) ... Setting up login.defs (1:4.18.0-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Oct 10 04:59:25 UTC 2025. Universal Time is now: Fri Oct 10 04:59:25 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libedlib1:amd64 (1.2.7-7) ... Setting up passwd (1:4.18.0-1) ... Setting up mount (2.41.2-1) ... Setting up login (1:4.16.0-2+really2.41.2-1) ... Processing triggers for debianutils (5.23.2) ... Processing triggers for libc-bin (2.41-12) ... 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-yf', 'dist-upgrade'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.8s DUMP: c9e676531033ea4b441efee9d26bbc8a - 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'show', '--no-all-versions', 'racon'] 0m14.1s DUMP: Package: racon Status: install ok installed Priority: optional Section: science Installed-Size: 3167 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 1.5.0-3 Depends: libc6 (>= 2.34), libedlib1 (>= 1.2.7-3~), libgcc-s1 (>= 3.0), libspoa7.0.0 (>= 4.0.5), libstdc++6 (>= 12), zlib1g (>= 1:1.1.4) Recommends: python3, rampler Description: consensus module for raw de novo DNA assembly of long uncorrected reads Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. . Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected. . Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip. . Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads including dual overlaps. . A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be subsampled to decrease the total execution time (accuracy might be lower) while target sequences can be split into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well. Description-md5: Homepage: https://github.com/lbcb-sci/racon 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'show', '--no-all-versions', 'racon'] 0m14.1s INFO: apt-cache does not know about any of the requested packages 0m14.1s INFO: Running scripts post_distupgrade 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m14.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m14.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpm5vrprjp to sid 0m14.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m14.5s INFO: Running scripts pre_distupgrade 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'update'] 0m18.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [207 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7446 kB] Fetched 17.9 MB in 3s (6602 kB/s) Reading package lists... 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'update'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-yf', 'dist-upgrade'] 0m23.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libdb5.3t64 liblastlog2-2 libmount1 libsmartcols1 libspoa7.0.0 libuuid1 login mount racon util-linux 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6024 kB of archives. After this operation, 667 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41.2-3 [38.4 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41.2-3 [174 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41.2-3 [211 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41.2-3 [145 kB] Get:5 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41.2-3 [1164 kB] Get:6 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41.2-3 [163 kB] Get:7 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41.2-3 [105 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-10 [709 kB] Get:9 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41.2-3 [29.3 kB] Get:10 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41.2-3 [93.5 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libspoa7.0.0 amd64 4.1.5-1 [75.6 kB] Get:12 http://deb.debian.org/debian sid/main amd64 racon amd64 1.5.0-4 [3117 kB] Fetched 6024 kB in 3s (1870 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4965 files and directories currently installed.) Preparing to unpack .../libuuid1_2.41.2-3_amd64.deb ... Unpacking libuuid1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libuuid1:amd64 (2.41.2-3) ... (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 ... 4965 files and directories currently installed.) Preparing to unpack .../libblkid1_2.41.2-3_amd64.deb ... Unpacking libblkid1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libblkid1:amd64 (2.41.2-3) ... (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 ... 4965 files and directories currently installed.) Preparing to unpack .../libmount1_2.41.2-3_amd64.deb ... Unpacking libmount1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libmount1:amd64 (2.41.2-3) ... (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 ... 4965 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.41.2-3_amd64.deb ... Unpacking libsmartcols1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libsmartcols1:amd64 (2.41.2-3) ... (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 ... 4965 files and directories currently installed.) Preparing to unpack .../util-linux_2.41.2-3_amd64.deb ... Unpacking util-linux (2.41.2-3) over (2.41.2-1) ... Setting up util-linux (2.41.2-3) ... (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 ... 4930 files and directories currently installed.) Preparing to unpack .../mount_2.41.2-3_amd64.deb ... Unpacking mount (2.41.2-3) over (2.41.2-1) ... Preparing to unpack .../login_1%3a4.16.0-2+really2.41.2-3_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41.2-3) over (1:4.16.0-2+really2.41.2-1) ... Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-10_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-10) over (5.3.28+dfsg2-9) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4930 files and directories currently installed.) Preparing to unpack .../liblastlog2-2_2.41.2-3_amd64.deb ... Unpacking liblastlog2-2:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up liblastlog2-2:amd64 (2.41.2-3) ... (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 ... 4930 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.41.2-3_amd64.deb ... Unpacking bsdutils (1:2.41.2-3) over (1:2.41.2-1) ... Preparing to unpack .../libspoa7.0.0_4.1.5-1_amd64.deb ... Unpacking libspoa7.0.0:amd64 (4.1.5-1) over (4.1.4-2+b1) ... Preparing to unpack .../racon_1.5.0-4_amd64.deb ... Unpacking racon (1.5.0-4) over (1.5.0-3) ... Setting up bsdutils (1:2.41.2-3) ... Setting up libspoa7.0.0:amd64 (4.1.5-1) ... Setting up mount (2.41.2-3) ... Setting up login (1:4.16.0-2+really2.41.2-3) ... Setting up racon (1.5.0-4) ... Processing triggers for libc-bin (2.41-12) ... 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-yf', 'dist-upgrade'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.5s DUMP: 380e29d71b2fa71794a874e8aace2664 - 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'show', '--no-all-versions', 'racon'] 0m24.8s DUMP: Package: racon Version: 1.5.0-4 Installed-Size: 3171 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libedlib1 (>= 1.2.3), libgcc-s1 (>= 3.0), libspoa7.0.0 (>= 4.0.5), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4) Recommends: python3, rampler Description-en: consensus module for raw de novo DNA assembly of long uncorrected reads Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. . Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected. . Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip. . Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads including dual overlaps. . A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be subsampled to decrease the total execution time (accuracy might be lower) while target sequences can be split into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well. Description-md5: 0245f53dd68b53cce76f4a5dd8d8a554 Homepage: https://github.com/lbcb-sci/racon Section: science Priority: optional Filename: pool/main/r/racon/racon_1.5.0-4_amd64.deb Size: 3116828 MD5sum: febeb177f8a7c5364aa24a04719e5515 SHA256: c3a0ced64d68cc1338862839137e43168043ebd2a0e1b983adb5c357f34e9c03 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'show', '--no-all-versions', 'racon'] 0m24.8s INFO: apt-cache knows about the following packages: racon 0m24.8s INFO: Running scripts pre_install 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_database-server'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_database-server'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_exceptions'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_extras'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_extras'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy'] 0m24.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy', 'racon'] 0m24.9s DUMP: racon: Installed: 1.5.0-4 Candidate: 1.5.0-4 Version table: *** 1.5.0-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy', 'racon'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-y', 'install', 'racon'] 0m25.4s DUMP: Reading package lists... Building dependency tree... Reading state information... racon is already the newest version (1.5.0-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-y', 'install', 'racon'] 0m25.4s INFO: Running scripts post_install 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_install_exceptions'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_install_exceptions'] 0m25.4s INFO: Running scripts post_distupgrade 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_exceptions'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_exceptions'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m25.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m25.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m25.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m26.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m26.2s INFO: Running scripts pre_install 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_database-server'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_database-server'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_exceptions'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_exceptions'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_extras'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_extras'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy'] 0m26.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy', 'racon'] 0m26.3s DUMP: racon: Installed: 1.5.0-4 Candidate: 1.5.0-4 Version table: *** 1.5.0-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-cache', 'policy', 'racon'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-y', 'install', 'racon=1.5.0-4'] 0m27.0s DUMP: Reading package lists... Building dependency tree... Reading state information... racon is already the newest version (1.5.0-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', '-y', 'install', 'racon=1.5.0-4'] 0m27.0s INFO: Running scripts post_install 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_install_exceptions'] 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_install_exceptions'] 0m27.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m27.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m27.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', '-ac', '--ignore-obsolete'] 0m28.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', '-ac', '--ignore-obsolete'] 0m28.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m28.2s DUMP: 0.15.9~deb12u1 0m28.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m28.2s INFO: Running adequate version 0.15.9~deb12u1 now. 0m28.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'racon'] 0m28.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'racon'] 0m28.4s INFO: Running scripts pre_remove 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_exceptions'] 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/pre_remove_exceptions'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m29.1s DUMP: install ok installed apt apt 3.1.8 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.3-1 install ok installed bsdutils bsdutils 1:2.41.2-3 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-8 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-4 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.41.2-3 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libedlib1:amd64 libedlib1 1.2.7-7 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-4 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.2-3 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.2-3 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.2-3 install ok installed libspoa7.0.0:amd64 libspoa7.0.0 4.1.5-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssl3t64:amd64 libssl3t64 3.5.4-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-4 install ok installed libsystemd0:amd64 libsystemd0 258-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 258-1 install ok installed libuuid1:amd64 libuuid1 2.41.2-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-2 install ok installed login login 1:4.16.0-2+really2.41.2-3 install ok installed login.defs login.defs 1:4.18.0-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41.2-3 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.4-1 install ok installed passwd passwd 1:4.18.0-1 install ok installed perl-base perl-base 5.40.1-6 install ok installed racon racon 1.5.0-4 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.2-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'remove', '--allow-remove-essential', 'libedlib1:amd64', 'libspoa7.0.0:amd64', 'racon'] 0m30.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libedlib1 libspoa7.0.0 racon 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. After this operation, 3620 kB 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 ... 4929 files and directories currently installed.) Removing racon (1.5.0-4) ... Removing libedlib1:amd64 (1.2.7-7) ... Removing libspoa7.0.0:amd64 (4.1.5-1) ... Processing triggers for libc-bin (2.41-12) ... 0m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'remove', '--allow-remove-essential', 'libedlib1:amd64', 'libspoa7.0.0:amd64', 'racon'] 0m30.3s INFO: Running scripts post_remove 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_remove_exceptions'] 0m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_remove_exceptions'] 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--purge', 'libedlib1:amd64', 'libspoa7.0.0:amd64'] 0m30.4s DUMP: dpkg: warning: ignoring request to remove libedlib1 which isn't installed dpkg: warning: ignoring request to remove libspoa7.0.0 which isn't installed 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--purge', 'libedlib1:amd64', 'libspoa7.0.0:amd64'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--purge', 'racon'] 0m30.4s DUMP: dpkg: warning: ignoring request to remove racon which isn't installed 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--purge', 'racon'] 0m30.4s INFO: Running scripts post_purge 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_purge_exceptions'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_purge_exceptions'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--purge', '--pending'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--purge', '--pending'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--remove', '--pending'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg', '--remove', '--pending'] 0m30.4s INFO: Running scripts post_test 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_test_exceptions'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'tmp/scripts/post_test_exceptions'] 0m30.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m30.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg-divert', '--list'] 0m30.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m30.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'dpkg-divert', '--list'] 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'clean'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp', 'apt-get', 'clean'] 0m30.8s DEBUG: Recording chroot state 0m32.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/shm'] 0m32.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/shm'] 0m32.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/console'] 0m32.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/console'] 0m32.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/ptmx'] 0m32.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/ptmx'] 0m32.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/pts'] 0m32.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/dev/pts'] 0m32.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/proc'] 0m32.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp/proc'] 0m32.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m32.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpm5vrprjp'] 0m32.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpm5vrprjp 0m32.5s INFO: PASS: Upgrading between Debian distributions. 0m32.5s INFO: PASS: All tests. 0m32.5s INFO: piuparts run ends. ret=0 End: 2025-10-10 04:59:46 GMT