Start: 2021-08-19 02:55:48 GMT [bullseye] Package: metaphlan2-data Version: 2.6.0+ds-4 Installed-Size: 753107 Maintainer: Debian Med Packaging Team Architecture: all Depends: debconf (>= 0.5) | debconf-2.0, bowtie2 Description: data package for Metagenomic Phylogenetic Analysis Homepage: https://bitbucket.org/biobakery/metaphlan2 Description-md5: f0775409e41de9fba49cda4590c73ce4 Section: science Priority: optional Filename: pool/main/m/metaphlan2-data/metaphlan2-data_2.6.0+ds-4_all.deb Size: 204323768 MD5sum: de685246213a02dcedfee6e464f7ac11 SHA256: f38a6e3f49d7b03ba80d9fdd5647b9f9f2dfb38d43b28618053e8ef2c60db7d7 [bullseye-next] Package: metaphlan2-data Version: 2.6.0+ds-4 Installed-Size: 753107 Maintainer: Debian Med Packaging Team Architecture: all Depends: debconf (>= 0.5) | debconf-2.0, bowtie2 Description: data package for Metagenomic Phylogenetic Analysis Homepage: https://bitbucket.org/biobakery/metaphlan2 Description-md5: f0775409e41de9fba49cda4590c73ce4 Section: science Priority: optional Filename: pool/main/m/metaphlan2-data/metaphlan2-data_2.6.0+ds-4_all.deb Size: 204323768 MD5sum: de685246213a02dcedfee6e464f7ac11 SHA256: f38a6e3f49d7b03ba80d9fdd5647b9f9f2dfb38d43b28618053e8ef2c60db7d7 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/bullseye_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt metaphlan2-data=2.6.0+ds-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 1.1.4 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/bullseye_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt metaphlan2-data=2.6.0+ds-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpv54bw3ot 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpv54bw3ot 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/pts'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/console'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/console'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/shm'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/shm'] 0m1.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpv54bw3ot/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', 'update'] 0m2.4s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [113 kB] Fetched 113 kB in 0s (991 kB/s) Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s DUMP: e5893bf5d89f83f99f0dc7018e11583b - 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s INFO: Running scripts post_setup 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+b3 install ok installed bsdutils bsdutils 1:2.36.1-8 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.9 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2 install ok installed grep grep 3.6-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13 install ok installed libc6:amd64 libc6 2.31-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.36.1-8 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9 install ok installed libpam-runtime libpam-runtime 1.4.0-9 install ok installed libpam0g:amd64 libpam0g 1.4.0-9 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1k-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-6 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2 install ok installed libtirpc-common libtirpc-common 1.3.1-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1 install ok installed libudev1:amd64 libudev1 247.3-6 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8 install ok installed ncurses-base ncurses-base 6.2+20201114-2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1 install ok installed util-linux util-linux 2.36.1-8 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m3.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m4.3s DUMP: Package: metaphlan2-data Version: 2.6.0+ds-4 Installed-Size: 753107 Maintainer: Debian Med Packaging Team Architecture: all Depends: debconf (>= 0.5) | debconf-2.0, bowtie2 Description-en: data package for Metagenomic Phylogenetic Analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species. . MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at src/utils/markers_info.txt.bz2 or here) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing: . * unambiguous taxonomic assignments; * accurate estimation of organismal relative abundance; * species-level resolution for bacteria, archaea, eukaryotes and viruses; * strain identification and tracking * orders of magnitude speedups compared to existing methods. * metagenomic strain-level population genomics . This package contains the data for metaphlan2. Description-md5: f0775409e41de9fba49cda4590c73ce4 Homepage: https://bitbucket.org/biobakery/metaphlan2 Section: science Priority: optional Filename: pool/main/m/metaphlan2-data/metaphlan2-data_2.6.0+ds-4_all.deb Size: 204323768 MD5sum: de685246213a02dcedfee6e464f7ac11 SHA256: f38a6e3f49d7b03ba80d9fdd5647b9f9f2dfb38d43b28618053e8ef2c60db7d7 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m4.3s INFO: apt-cache knows about the following packages: metaphlan2-data 0m4.3s INFO: Running scripts pre_install 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_extras'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy'] 0m4.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.0,o=Debian,a=stable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy', 'metaphlan2-data'] 0m4.4s DUMP: metaphlan2-data: Installed: (none) Candidate: 2.6.0+ds-4 Version table: 2.6.0+ds-4 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy', 'metaphlan2-data'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-y', 'install', 'metaphlan2-data'] 15m56.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bowtie2 libexpat1 libgdbm-compat4 libgdbm6 libmpdec3 libncursesw6 libperl5.32 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libtbb2 media-types perl perl-modules-5.32 python3 python3-minimal python3.9 python3.9-minimal readline-common Suggested packages: bowtie2-examples gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates netbase The following NEW packages will be installed: bowtie2 libexpat1 libgdbm-compat4 libgdbm6 libmpdec3 libncursesw6 libperl5.32 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libtbb2 media-types metaphlan2-data perl perl-modules-5.32 python3 python3-minimal python3.9 python3.9-minimal readline-common 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 220 MB of archives. After this operation, 847 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4 [4117 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2 [132 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 metaphlan2-data all 2.6.0+ds-4 [204 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 220 MB in 7s (30.0 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6655 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.19-2_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.19-2) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../3-libperl5.32_5.32.1-4_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.32.1-4_amd64.deb ... Unpacking perl (5.32.1-4) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8920 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.2+20201114-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.2+20201114-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.34.1-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.34.1-3) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (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 ... 9358 files and directories currently installed.) Preparing to unpack .../python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../libtbb2_2020.3-1_amd64.deb ... Unpacking libtbb2:amd64 (2020.3-1) ... Selecting previously unselected package bowtie2. Preparing to unpack .../bowtie2_2.4.2-2+b3_amd64.deb ... Unpacking bowtie2 (2.4.2-2+b3) ... Selecting previously unselected package metaphlan2-data. Preparing to unpack .../metaphlan2-data_2.6.0+ds-4_all.deb ... Unpacking metaphlan2-data (2.6.0+ds-4) ... Setting up media-types (4.0.0) ... Setting up perl-modules-5.32 (5.32.1-4) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libtbb2:amd64 (2020.3-1) ... Setting up libncursesw6:amd64 (6.2+20201114-2) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up readline-common (8.1-1) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up libperl5.32:amd64 (5.32.1-4) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up perl (5.32.1-4) ... Setting up python3.9 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up metaphlan2-data (2.6.0+ds-4) ... Settings: Output files: "/usr/share/metaphlan2/db_v20/mpa_v20_m200.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: /var/lib/metaphlan2-data/markers.fasta Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:03 bmax according to bmaxDivN setting: 177889396 Using parameters --bmax 133417047 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 133417047 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:19 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:06 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:15 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 7.11558e+08 (target: 133417046) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 711557587 for bucket 1 (Using difference cover) Sorting block time: 00:05:39 Returning block of 711557588 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 193247476 fchr[G]: 355349181 fchr[T]: 534730948 fchr[$]: 711557587 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 304203219 bytes to primary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.1.bt2 Wrote 177889404 bytes to secondary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 711557587 bwtLen: 711557588 sz: 177889397 bwtSz: 177889397 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 44472350 offsSz: 177889400 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3706030 numLines: 3706030 ebwtTotLen: 237185920 ebwtTotSz: 237185920 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:08:28 Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:03 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 177889396 Using parameters --bmax 133417047 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 133417047 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:14 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:05 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:12 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 7.11558e+08 (target: 133417046) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 711557587 for bucket 1 (Using difference cover) Sorting block time: 00:04:42 Returning block of 711557588 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 193247476 fchr[G]: 355349181 fchr[T]: 534730948 fchr[$]: 711557587 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 304203219 bytes to primary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.1.bt2 Wrote 177889404 bytes to secondary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 711557587 bwtLen: 711557588 sz: 177889397 bwtSz: 177889397 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 44472350 offsSz: 177889400 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3706030 numLines: 3706030 ebwtTotLen: 237185920 ebwtTotSz: 237185920 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:06:54 Metaphlan2 data are properly created. Processing triggers for libc-bin (2.31-13) ... 15m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-y', 'install', 'metaphlan2-data'] 15m56.3s INFO: Running scripts post_install 15m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_install_exceptions'] 15m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_install_exceptions'] 15m56.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 15m56.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 15m56.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpv54bw3ot to bullseye-next 15m56.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 15m56.8s INFO: Running scripts pre_distupgrade 15m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 15m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 15m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_exceptions'] 15m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_exceptions'] 15m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 15m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 15m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_zz_database-server'] 15m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_zz_database-server'] 15m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 15m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 15m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', 'update'] 15m58.5s DUMP: Get:1 http://security.debian.org bullseye-security InRelease [44.1 kB] Hit:2 http://deb.debian.org/debian bullseye InRelease Get:3 http://deb.debian.org/debian bullseye-updates InRelease [36.8 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [43.9 kB] Get:5 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [19.2 kB] Get:6 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [10.1 kB] Get:7 http://security.debian.org bullseye-security/main amd64 Packages [25.8 kB] Get:8 http://security.debian.org bullseye-security/main Translation-en [12.8 kB] Fetched 193 kB in 1s (283 kB/s) Reading package lists... 15m58.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', 'update'] 15m58.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-yf', 'dist-upgrade'] 16m0.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libperl5.32 perl perl-base perl-modules-5.32 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 8841 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://security.debian.org bullseye-security/main amd64 libperl5.32 amd64 5.32.1-4+deb11u1 [4098 kB] Get:2 http://security.debian.org bullseye-security/main amd64 perl amd64 5.32.1-4+deb11u1 [293 kB] Get:3 http://security.debian.org bullseye-security/main amd64 perl-base amd64 5.32.1-4+deb11u1 [1627 kB] Get:4 http://security.debian.org bullseye-security/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u1 [2823 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8841 kB in 0s (76.9 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 ... 9422 files and directories currently installed.) Preparing to unpack .../libperl5.32_5.32.1-4+deb11u1_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4+deb11u1) over (5.32.1-4) ... Preparing to unpack .../perl_5.32.1-4+deb11u1_amd64.deb ... Unpacking perl (5.32.1-4+deb11u1) over (5.32.1-4) ... Preparing to unpack .../perl-base_5.32.1-4+deb11u1_amd64.deb ... Unpacking perl-base (5.32.1-4+deb11u1) over (5.32.1-4) ... Setting up perl-base (5.32.1-4+deb11u1) ... (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 ... 9422 files and directories currently installed.) Preparing to unpack .../perl-modules-5.32_5.32.1-4+deb11u1_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u1) over (5.32.1-4) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u1) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u1) ... Setting up perl (5.32.1-4+deb11u1) ... Processing triggers for libc-bin (2.31-13) ... 16m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-yf', 'dist-upgrade'] 16m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 16m1.0s DUMP: 638c1e79cb616c30ea715877aa65987b - 16m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 16m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 16m1.2s DUMP: Package: metaphlan2-data Version: 2.6.0+ds-4 Installed-Size: 753107 Maintainer: Debian Med Packaging Team Architecture: all Depends: debconf (>= 0.5) | debconf-2.0, bowtie2 Description-en: data package for Metagenomic Phylogenetic Analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species. . MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at src/utils/markers_info.txt.bz2 or here) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing: . * unambiguous taxonomic assignments; * accurate estimation of organismal relative abundance; * species-level resolution for bacteria, archaea, eukaryotes and viruses; * strain identification and tracking * orders of magnitude speedups compared to existing methods. * metagenomic strain-level population genomics . This package contains the data for metaphlan2. Description-md5: f0775409e41de9fba49cda4590c73ce4 Homepage: https://bitbucket.org/biobakery/metaphlan2 Section: science Priority: optional Filename: pool/main/m/metaphlan2-data/metaphlan2-data_2.6.0+ds-4_all.deb Size: 204323768 MD5sum: de685246213a02dcedfee6e464f7ac11 SHA256: f38a6e3f49d7b03ba80d9fdd5647b9f9f2dfb38d43b28618053e8ef2c60db7d7 16m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 16m1.2s INFO: apt-cache knows about the following packages: metaphlan2-data 16m1.2s INFO: Running scripts pre_install 16m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_database-server'] 16m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_database-server'] 16m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_exceptions'] 16m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_exceptions'] 16m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_extras'] 16m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_extras'] 16m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture'] 16m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture'] 16m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture_i386'] 16m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture_i386'] 16m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy'] 16m1.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=stable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.0,o=Debian,a=stable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 16m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy'] 16m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy', 'metaphlan2-data'] 16m1.4s DUMP: metaphlan2-data: Installed: 2.6.0+ds-4 Candidate: 2.6.0+ds-4 Version table: *** 2.6.0+ds-4 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 16m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy', 'metaphlan2-data'] 16m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-y', 'install', 'metaphlan2-data'] 16m1.8s DUMP: Reading package lists... Building dependency tree... Reading state information... metaphlan2-data is already the newest version (2.6.0+ds-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 16m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-y', 'install', 'metaphlan2-data'] 16m1.8s INFO: Running scripts post_install 16m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_install_exceptions'] 16m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_install_exceptions'] 16m1.8s INFO: Running scripts post_distupgrade 16m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_base_cleanup'] 16m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_base_cleanup'] 16m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_exceptions'] 16m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_exceptions'] 16m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 16m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 16m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_squeeze-backports'] 16m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_squeeze-backports'] 16m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_zz_backports'] 16m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_distupgrade_zz_backports'] 16m1.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m2.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m2.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m2.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m2.6s INFO: Running scripts pre_install 16m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_database-server'] 16m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_database-server'] 16m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_exceptions'] 16m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_exceptions'] 16m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_extras'] 16m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_extras'] 16m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture'] 16m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture'] 16m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture_i386'] 16m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/pre_install_foreign_architecture_i386'] 16m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy'] 16m2.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=stable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.0,o=Debian,a=stable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 16m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy'] 16m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy', 'metaphlan2-data'] 16m2.7s DUMP: metaphlan2-data: Installed: 2.6.0+ds-4 Candidate: 2.6.0+ds-4 Version table: *** 2.6.0+ds-4 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 16m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-cache', 'policy', 'metaphlan2-data'] 16m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 16m3.1s DUMP: Reading package lists... Building dependency tree... Reading state information... metaphlan2-data is already the newest version (2.6.0+ds-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 16m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 16m3.1s INFO: Running scripts post_install 16m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_install_exceptions'] 16m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', 'tmp/scripts/post_install_exceptions'] 16m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m3.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', '-ac', '--ignore-obsolete'] 16m20.4s DUMP: debsums: missing file /srv/piuparts.debian.org/tmp/tmpv54bw3ot/var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 16m20.4s DEBUG: Command failed (status=2), but ignoring error: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot', '-ac', '--ignore-obsolete'] 16m20.4s ERROR: FAIL: debsums reports modifications inside the chroot: debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 16m20.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/shm'] 16m20.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/shm'] 16m20.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/console'] 16m20.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/console'] 16m20.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/ptmx'] 16m20.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/ptmx'] 16m20.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/pts'] 16m21.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/dev/pts'] 16m21.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/proc'] 16m21.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot/proc'] 16m21.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m21.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv54bw3ot'] 16m21.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpv54bw3ot 16m21.2s ERROR: piuparts run ends. ret=1 End: 2021-08-19 03:12:10 GMT