Start: 2020-06-20 11:40:06 GMT [stretch] Package: metaphlan2-data Version: 2.6.0+ds-2 Installed-Size: 753104 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-2_all.deb Size: 203825192 MD5sum: 5c6e0be2a3698b3fd52c0048fd8626af SHA256: 7539d2ece52874e4664924de76e608894d6a2e188fb0fa76f092bb0bae3720d0 [buster] 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 --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/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 1.1.2~202004292038~1.1.1-19-g418151e2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat --apt metaphlan2-data=2.6.0+ds-4 0m0.0s INFO: Running on: Linux piu-slave-conova-01 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpzkv0rdoc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpzkv0rdoc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/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/tmpzkv0rdoc/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/tmpzkv0rdoc/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/console'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/console'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/shm'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/shm'] 0m1.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.7s DEBUG: Created resolv.conf. 0m1.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpzkv0rdoc/tmp/scripts/ 0m1.7s INFO: Running scripts post_chroot_unpack 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', 'update'] 0m2.4s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s DUMP: 2daaae1f7720409bbe2f25258a2c8995 - 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s INFO: Running scripts post_setup 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.9 install ok installed base-files base-files 9.9+deb9u12 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.9 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u6 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 0m3.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 0m3.8s INFO: Running scripts is_testable 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s INFO: Running scripts pre_test 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_test_root_password'] 0m3.8s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_test_root_password'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m4.0s DUMP: Package: metaphlan2-data Version: 2.6.0+ds-2 Installed-Size: 753104 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-2_all.deb Size: 203825192 MD5sum: 5c6e0be2a3698b3fd52c0048fd8626af SHA256: 7539d2ece52874e4664924de76e608894d6a2e188fb0fa76f092bb0bae3720d0 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m4.0s INFO: apt-cache knows about the following packages: metaphlan2-data 0m4.0s INFO: Running scripts pre_install 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy'] 0m4.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.12,o=Debian,a=oldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy', 'metaphlan2-data'] 0m4.1s DUMP: metaphlan2-data: Installed: (none) Candidate: 2.6.0+ds-2 Version table: 2.6.0+ds-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy', 'metaphlan2-data'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'install', 'metaphlan2-data'] 27m8.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bowtie2 bzip2 file libatomic1 libexpat1 libffi6 libmagic-mgc libmagic1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsqlite3-0 libssl1.1 libtbb2 mime-support python python-minimal python2.7 python2.7-minimal readline-common xz-utils Suggested packages: bowtie2-examples bzip2-doc python-doc python-tk python2.7-doc binutils binfmt-support readline-doc The following NEW packages will be installed: bowtie2 bzip2 file libatomic1 libexpat1 libffi6 libmagic-mgc libmagic1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsqlite3-0 libssl1.1 libtbb2 metaphlan2-data mime-support python python-minimal python2.7 python2.7-minimal readline-common xz-utils 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 212 MB of archives. After this operation, 805 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 bzip2 amd64 1.0.6-8.1 [47.5 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libmagic-mgc amd64 1:5.30-1+deb9u3 [222 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libmagic1 amd64 1:5.30-1+deb9u3 [111 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 file amd64 1:5.30-1+deb9u3 [64.2 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:21 http://deb.debian.org/debian stretch/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 bowtie2 amd64 2.3.0-2 [1166 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 metaphlan2-data all 2.6.0+ds-2 [204 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 212 MB in 3s (63.4 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. 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Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up file (1:5.30-1+deb9u3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up bowtie2 (2.3.0-2) ... Setting up metaphlan2-data (2.6.0+ds-2) ... 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: 00:00:06 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:05 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: 00:00:13 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: 00:00:08 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: 00:10:50 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: 00:14:07 Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:05 Time to reverse reference sequence: 00:00:02 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: 00:00:11 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: 00:00:07 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: 00:09:34 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: 00:12:31 Metaphlan2 data are properly created. Processing triggers for libc-bin (2.24-11+deb9u4) ... 27m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'install', 'metaphlan2-data'] 27m8.6s INFO: Running scripts post_install 27m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_install_exceptions'] 27m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_install_exceptions'] 27m8.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 27m8.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 27m8.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpzkv0rdoc to buster 27m8.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 27m8.9s INFO: Running scripts pre_distupgrade 27m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 27m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 27m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_exceptions'] 27m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_exceptions'] 27m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 27m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 27m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 27m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 27m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 27m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 27m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', 'update'] 27m12.4s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [121 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7905 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5969 kB] Fetched 14.0 MB in 2s (5173 kB/s) Reading package lists... 27m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', 'update'] 27m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'upgrade'] 52m34.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: apt bash coreutils dash dpkg e2fslibs e2fsprogs gpgv libapt-pkg5.0 libatomic1 libblkid1 libc-bin libc6 libcomerr2 libexpat1 libfdisk1 libgcc1 libgpg-error0 libmount1 libncursesw5 libpam-modules libpam-modules-bin libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++6 libsystemd0 libtbb2 libtinfo5 libudev1 libuuid1 login mount ncurses-base ncurses-bin perl-base python python-minimal python2.7 python2.7-minimal util-linux The following packages will be upgraded: adduser base-files base-passwd bowtie2 bsdutils bzip2 debconf debian-archive-keyring debianutils diffutils file findutils grep gzip hostname init-system-helpers libacl1 libattr1 libaudit-common libaudit1 libbz2-1.0 libcap-ng0 libdb5.3 libdebconfclient0 libffi6 libgcrypt20 liblz4-1 liblzma5 libmagic-mgc libmagic1 libpam-runtime libpam0g libpcre3 libselinux1 libsemanage-common libsemanage1 libsepol1 metaphlan2-data mime-support multiarch-support passwd readline-common sed sensible-utils sysvinit-utils tar xz-utils zlib1g 48 upgraded, 0 newly installed, 0 to remove and 46 not upgraded. Need to get 214 MB of archives. After this operation, 1453 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u4 [69.8 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:3 http://deb.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:4 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:5 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:6 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:7 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3 [128 kB] Get:8 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:9 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:10 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:12 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:13 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:14 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:15 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71 [145 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:26 http://deb.debian.org/debian buster/main amd64 bzip2 amd64 1.0.6-9.2~deb10u1 [48.4 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:28 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:29 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:30 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1 [75.1 kB] Get:31 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5 [556 kB] Get:36 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1 [52.9 kB] Get:37 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1 [153 kB] Get:38 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1 [94.1 kB] Get:39 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:40 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u1 [66.4 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u1 [117 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u1 [242 kB] Get:43 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:44 http://deb.debian.org/debian buster/main amd64 xz-utils amd64 5.2.4-1 [183 kB] Get:45 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:47 http://deb.debian.org/debian buster/main amd64 metaphlan2-data all 2.6.0+ds-4 [204 MB] Get:48 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10 [215 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 214 MB in 1s (113 MB/s) (Reading database ... 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Setting up bowtie2 (2.3.4.3-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up bzip2 (1.0.6-9.2~deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up xz-utils (5.2.4-1) ... Setting up libffi6:amd64 (3.2.1-9) ... 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: 00:00:06 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:05 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: 00:00:13 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:04 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:07 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: 00:09:10 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: 00:12:13 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: 00:00:05 Time to reverse reference sequence: 00:00:01 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: 00:00:06 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:06 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: 00:09:33 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: 00:12:37 Metaphlan2 data are properly created. Setting up file (1:5.35-4+deb10u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 52m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'upgrade'] 52m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-yf', 'dist-upgrade'] 52m49.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: ca-certificates e2fsprogs-l10n fdisk gcc-8-base libcom-err2 libext2fs2 libgmp10 libgnutls30 libgpg-error-l10n libgpm2 libhogweed4 libidn2-0 libncursesw6 libnettle6 libp11-kit0 libpython2-stdlib libseccomp2 libtasn1-6 libtinfo6 libunistring2 libzstd1 openssl python2 python2-minimal The following packages will be upgraded: apt bash coreutils dash dpkg e2fslibs e2fsprogs gpgv libapt-pkg5.0 libatomic1 libblkid1 libc-bin libc6 libcomerr2 libexpat1 libfdisk1 libgcc1 libgpg-error0 libmount1 libncursesw5 libpam-modules libpam-modules-bin libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++6 libsystemd0 libtbb2 libtinfo5 libudev1 libuuid1 login mount ncurses-base ncurses-bin perl-base python python-minimal python2.7 python2.7-minimal util-linux 46 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. Need to get 33.0 MB of archives. After this operation, 21.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libc6 amd64 2.28-10 [2867 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libc-bin amd64 2.28-10 [789 kB] Get:3 http://deb.debian.org/debian buster/main amd64 gcc-8-base amd64 8.3.0-6 [191 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u2 [325 kB] Get:6 http://deb.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:7 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:8 http://deb.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3 [236 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4 [250 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1 [214 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1 [141 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1+deb10u1 [76.7 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2 [318 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u3 [1124 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:19 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u1 [584 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2 [966 kB] Get:22 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2 [1418 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u4 [331 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u4 [150 kB] Get:25 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.7 [2208 kB] Get:26 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:30 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:31 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:37 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:38 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:39 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:40 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:41 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:42 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:43 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6 [1511 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:46 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u3 [1538 kB] Get:50 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3 [641 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:55 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:57 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:58 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:59 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:62 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:64 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u3 [844 kB] Get:65 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20190110 [157 kB] Get:66 http://deb.debian.org/debian buster/main amd64 e2fsprogs-l10n all 1.44.5-1+deb10u3 [504 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B] Get:68 http://deb.debian.org/debian buster/main amd64 libgpg-error-l10n all 1.35-1 [97.6 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libgpm2 amd64 1.20.7-5 [35.1 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.0 MB in 0s (34.3 MB/s) (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 ... 5625 files and directories currently installed.) Preparing to unpack .../mount_2.33.1-0.1_amd64.deb ... Unpacking mount (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Preparing to unpack .../util-linux_2.33.1-0.1_amd64.deb ... Unpacking util-linux (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Replacing files in old package login (1:4.4-4.1) ... Selecting previously unselected package fdisk. Preparing to unpack .../fdisk_2.33.1-0.1_amd64.deb ... Unpacking fdisk (2.33.1-0.1) ... Setting up fdisk (2.33.1-0.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5642 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1_amd64.deb ... Unpacking login (1:4.5-1.1) over (1:4.4-4.1) ... Setting up login (1:4.5-1.1) ... Installing new version of config file /etc/securetty ... (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 ... 5632 files and directories currently installed.) Preparing to unpack .../perl-base_5.28.1-6_amd64.deb ... Unpacking perl-base (5.28.1-6) over (5.24.1-3+deb9u6) ... Setting up perl-base (5.28.1-6) ... (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 ... 5658 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw5:amd64 (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up libncursesw5:amd64 (6.1+20181013-2+deb10u2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5658 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2+deb10u2_all.deb ... Unpacking ncurses-base (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up ncurses-base (6.1+20181013-2+deb10u2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5660 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.3.1-5_amd64.deb ... Unpacking libpam-modules-bin (1.3.1-5) over (1.1.8-3.6) ... Setting up libpam-modules-bin (1.3.1-5) ... (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 ... 5660 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.3.1-5_amd64.deb ... Unpacking libpam-modules:amd64 (1.3.1-5) over (1.1.8-3.6) ... Setting up libpam-modules:amd64 (1.3.1-5) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/limits.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5661 files and directories currently installed.) Preparing to unpack .../0-libssl1.1_1.1.1d-0+deb10u3_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u3) over (1.1.0l-1~deb9u1) ... Preparing to unpack .../1-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../2-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) over (2.2.0-2+deb9u3) ... 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Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... (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 ... 5671 files and directories currently installed.) Preparing to unpack .../python_2.7.16-1_amd64.deb ... Unpacking python (2.7.16-1) over (2.7.13-2) ... Preparing to unpack .../libpython-stdlib_2.7.16-1_amd64.deb ... 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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 ... 5661 files and directories currently installed.) Preparing to unpack .../0-openssl_1.1.1d-0+deb10u3_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../1-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package e2fsprogs-l10n. Preparing to unpack .../2-e2fsprogs-l10n_1.44.5-1+deb10u3_all.deb ... Unpacking e2fsprogs-l10n (1.44.5-1+deb10u3) ... Preparing to unpack .../3-libatomic1_8.3.0-6_amd64.deb ... Unpacking libatomic1:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Selecting previously unselected package libgpg-error-l10n. Preparing to unpack .../4-libgpg-error-l10n_1.35-1_all.deb ... Unpacking libgpg-error-l10n (1.35-1) ... Selecting previously unselected package libgpm2:amd64. Preparing to unpack .../5-libgpm2_1.20.7-5_amd64.deb ... Unpacking libgpm2:amd64 (1.20.7-5) ... Preparing to unpack .../6-libtbb2_2018~U6-4_amd64.deb ... Unpacking libtbb2:amd64 (2018~U6-4) over (4.3~20150611-2) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up apt (1.8.2) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Setting up libgpm2:amd64 (1.20.7-5) ... Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up e2fsprogs-l10n (1.44.5-1+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u3) ... Setting up libsqlite3-0:amd64 (3.27.2-3) ... Setting up libatomic1:amd64 (8.3.0-6) ... Setting up util-linux (2.33.1-0.1) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives Setting up mount (2.33.1-0.1) ... Setting up libcomerr2:amd64 (1.44.5-1+deb10u3) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libgpg-error-l10n (1.35-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for mime-support (3.62) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 52m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-yf', 'dist-upgrade'] 52m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 52m50.1s DUMP: 56a5cadd0a92977eff42722d4f028736 - 52m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 52m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 52m50.4s 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 52m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 52m50.4s INFO: apt-cache knows about the following packages: metaphlan2-data 52m50.4s INFO: Running scripts pre_install 52m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_database-server'] 52m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_database-server'] 52m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_exceptions'] 52m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_exceptions'] 52m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_extras'] 52m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_extras'] 52m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture'] 52m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture'] 52m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 52m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 52m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy'] 52m50.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.4,o=Debian,a=stable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 52m50.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy'] 52m50.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy', 'metaphlan2-data'] 52m50.5s 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 buster/main amd64 Packages 100 /var/lib/dpkg/status 52m50.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy', 'metaphlan2-data'] 52m50.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'install', 'metaphlan2-data'] 52m51.0s 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. 52m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'install', 'metaphlan2-data'] 52m51.0s INFO: Running scripts post_install 52m51.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_install_exceptions'] 52m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_install_exceptions'] 52m51.0s INFO: Running scripts post_distupgrade 52m51.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_base_cleanup'] 52m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_base_cleanup'] 52m51.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_exceptions'] 52m51.2s DUMP: Running pam-auth-update... 52m51.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_exceptions'] 52m51.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 52m51.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 52m51.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 52m51.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 52m51.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_zz_backports'] 52m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_distupgrade_zz_backports'] 52m51.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m51.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m51.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m52.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m52.2s INFO: Running scripts pre_install 52m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_database-server'] 52m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_database-server'] 52m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_exceptions'] 52m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_exceptions'] 52m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_extras'] 52m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_extras'] 52m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture'] 52m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture'] 52m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 52m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 52m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy'] 52m52.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.4,o=Debian,a=stable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 52m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy'] 52m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy', 'metaphlan2-data'] 52m52.3s 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 buster/main amd64 Packages 100 /var/lib/dpkg/status 52m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-cache', 'policy', 'metaphlan2-data'] 52m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 52m52.7s 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. 52m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 52m52.7s INFO: Running scripts post_install 52m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_install_exceptions'] 52m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', 'tmp/scripts/post_install_exceptions'] 52m52.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m53.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m53.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', '-ac', '--ignore-obsolete'] 52m55.1s DUMP: debsums: missing file /srv/piuparts.debian.org/tmp/tmpzkv0rdoc/var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 52m55.1s DEBUG: Command failed (status=2), but ignoring error: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc', '-ac', '--ignore-obsolete'] 52m55.1s ERROR: FAIL: debsums reports modifications inside the chroot: debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 52m55.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/shm'] 52m55.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/shm'] 52m55.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/console'] 52m55.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/console'] 52m55.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/ptmx'] 52m55.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/ptmx'] 52m55.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/pts'] 52m55.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/dev/pts'] 52m55.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/proc'] 52m55.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc/proc'] 52m55.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m56.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpzkv0rdoc'] 52m56.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpzkv0rdoc 52m56.1s ERROR: piuparts run ends. ret=1 End: 2020-06-20 12:33:02 GMT