Start: 2019-05-02 20:01:19 UTC [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/python2.7/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://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2buster/reference-chroot-metadata.dat --apt 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 0.99~201905021005~0.98-61-g1dc90988 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://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2buster/reference-chroot-metadata.dat --apt metaphlan2-data=2.6.0+ds-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.9.0-9-amd64 #1 SMP Debian 4.9.168-1 (2019-04-12) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp2I9kMq 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp2I9kMq 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/proc'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/proc'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/pts'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/pts'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/ptmx'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/ptmx'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/console'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/console'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/shm'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/shm'] 0m2.4s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ stretch main 0m2.5s DEBUG: Created policy-rc.d and chmodded it. 0m2.5s DEBUG: Created resolv.conf. 0m2.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp2I9kMq/tmp/scripts/ 0m2.5s INFO: Running scripts post_chroot_unpack 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', 'update'] 0m7.0s DUMP: Ign:1 http://mirror-ubc.debian.org/debian stretch InRelease Get:2 http://mirror-ubc.debian.org/debian stretch Release [118 kB] Get:3 http://mirror-ubc.debian.org/debian stretch Release.gpg [2434 B] Get:4 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages [7082 kB] Get:5 http://mirror-ubc.debian.org/debian stretch/main Translation-en [5384 kB] Fetched 12.6 MB in 3s (3567 kB/s) Reading package lists... 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', 'update'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-yf', 'dist-upgrade'] 0m7.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libsystemd0 libudev1 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 475 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian stretch/main amd64 base-files amd64 9.9+deb9u9 [67.4 kB] Get:2 http://mirror-ubc.debian.org/debian stretch/main amd64 libsystemd0 amd64 232-25+deb9u11 [281 kB] Get:3 http://mirror-ubc.debian.org/debian stretch/main amd64 libudev1 amd64 232-25+deb9u11 [126 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 475 kB in 0s (27.1 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4408 files and directories currently installed.) Preparing to unpack .../base-files_9.9+deb9u9_amd64.deb ... Unpacking base-files (9.9+deb9u9) over (9.9+deb9u8) ... Setting up base-files (9.9+deb9u9) ... Installing new version of config file /etc/debian_version ... (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 ... 4408 files and directories currently installed.) Preparing to unpack .../libsystemd0_232-25+deb9u11_amd64.deb ... Unpacking libsystemd0:amd64 (232-25+deb9u11) over (232-25+deb9u8) ... Setting up libsystemd0:amd64 (232-25+deb9u11) ... (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 ... 4408 files and directories currently installed.) Preparing to unpack .../libudev1_232-25+deb9u11_amd64.deb ... Unpacking libudev1:amd64 (232-25+deb9u11) over (232-25+deb9u8) ... Setting up libudev1:amd64 (232-25+deb9u11) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-yf', 'dist-upgrade'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.2s DUMP: 9469031779ec19dbf5f373c37a12ce7f - 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.2s INFO: Running scripts post_setup 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_dummy_users'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_dummy_users'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_forbid_home'] 0m9.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_forbid_home'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.2s DUMP: dpkg: error: error writing to '': Broken pipe Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_minimize'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_minimize'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_zz_backports'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_setup_zz_backports'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.3s 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+deb9u9 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 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 install ok installed e2fsprogs e2fsprogs 1.43.4-2 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 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 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u11 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u11 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+deb9u5 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 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2buster/reference-chroot-metadata.dat 0m9.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 0m10.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 0m10.0s INFO: Running scripts is_testable 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/is_testable_uninstallable'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/is_testable_uninstallable'] 0m10.0s INFO: Running scripts pre_test 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_test_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_test_exceptions'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_test_root_password'] 0m10.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_test_root_password'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m10.2s 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 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m10.2s INFO: apt-cache knows about the following packages: metaphlan2-data 0m10.2s INFO: Running scripts pre_install 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_database-server'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_database-server'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_exceptions'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_exceptions'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_extras'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_extras'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy'] 0m10.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages release v=9.9,o=Debian,a=stable,n=stretch,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy', 'metaphlan2-data'] 0m10.4s DUMP: metaphlan2-data: Installed: (none) Candidate: 2.6.0+ds-2 Version table: 2.6.0+ds-2 500 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy', 'metaphlan2-data'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-y', 'install', 'metaphlan2-data'] 32m11.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bowtie2 libatomic1 libexpat1 libffi6 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 Suggested packages: bowtie2-examples python-doc python-tk python2.7-doc binutils binfmt-support readline-doc Recommended packages: bzip2 file xz-utils The following NEW packages will be installed: bowtie2 libatomic1 libexpat1 libffi6 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 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. Need to get 212 MB of archives. After this operation, 799 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:2 http://mirror-ubc.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:3 http://mirror-ubc.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:4 http://mirror-ubc.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:5 http://mirror-ubc.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u1 [83.4 kB] Get:6 http://mirror-ubc.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://mirror-ubc.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:8 http://mirror-ubc.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:9 http://mirror-ubc.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:10 http://mirror-ubc.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0j-1~deb9u1 [1354 kB] Get:11 http://mirror-ubc.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://mirror-ubc.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://mirror-ubc.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://mirror-ubc.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://mirror-ubc.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:16 http://mirror-ubc.debian.org/debian stretch/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:17 http://mirror-ubc.debian.org/debian stretch/main amd64 bowtie2 amd64 2.3.0-2 [1166 kB] Get:18 http://mirror-ubc.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 (66.0 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4410 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2+deb9u3) ... Selecting previously unselected package python-minimal. 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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: 00:00:08 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: 00:00:26 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:08 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:17 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: 00:11:20 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: 00:15:43 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: 00:00:06 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: 00:00:25 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:08 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:14 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: 00:11:35 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: 00:15:47 Metaphlan2 data are properly created. Processing triggers for libc-bin (2.24-11+deb9u4) ... 32m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-y', 'install', 'metaphlan2-data'] 32m11.1s INFO: Running scripts post_install 32m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_install_exceptions'] 32m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_install_exceptions'] 32m11.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 32m11.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 32m11.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp2I9kMq to buster 32m11.4s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ buster main 32m11.4s INFO: Running scripts pre_distupgrade 32m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 32m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 32m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_exceptions'] 32m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_exceptions'] 32m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 32m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 32m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 32m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 32m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 32m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 32m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', 'update'] 32m15.9s DUMP: Get:1 http://mirror-ubc.debian.org/debian buster InRelease [163 kB] Get:2 http://mirror-ubc.debian.org/debian buster/main amd64 Packages [7908 kB] Get:3 http://mirror-ubc.debian.org/debian buster/main Translation-en [5978 kB] Fetched 14.0 MB in 3s (4108 kB/s) Reading package lists... 32m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', 'update'] 32m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-yf', 'dist-upgrade'] 65m3.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: fdisk gcc-8-base libcom-err2 libext2fs2 libgmp10 libgnutls30 libhogweed4 libidn2-0 libncursesw6 libnettle6 libp11-kit0 libpython2-stdlib libseccomp2 libtasn1-6 libtinfo6 libunistring2 libzstd1 python2 python2-minimal The following packages will be upgraded: adduser apt base-files base-passwd bash bowtie2 bsdutils coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fslibs e2fsprogs findutils gpgv grep gzip hostname init-system-helpers libacl1 libapt-pkg5.0 libatomic1 libattr1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcomerr2 libdb5.3 libdebconfclient0 libexpat1 libfdisk1 libffi6 libgcc1 libgcrypt20 libgpg-error0 liblz4-1 liblzma5 libmount1 libncursesw5 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++6 libsystemd0 libtbb2 libtinfo5 libudev1 libuuid1 login metaphlan2-data mime-support mount multiarch-support ncurses-base ncurses-bin passwd perl-base python python-minimal python2.7 python2.7-minimal readline-common sed sensible-utils sysvinit-utils tar util-linux zlib1g 89 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 245 MB of archives. After this operation, 16.9 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian buster/main amd64 base-files amd64 10.1 [69.4 kB] Get:2 http://mirror-ubc.debian.org/debian buster/main amd64 libc6 amd64 2.28-8 [2867 kB] Get:3 http://mirror-ubc.debian.org/debian buster/main amd64 libc-bin amd64 2.28-8 [791 kB] Get:4 http://mirror-ubc.debian.org/debian buster/main amd64 gcc-8-base amd64 8.3.0-6 [191 kB] Get:5 http://mirror-ubc.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:6 http://mirror-ubc.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2 [325 kB] Get:7 http://mirror-ubc.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:8 http://mirror-ubc.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:9 http://mirror-ubc.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:10 http://mirror-ubc.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:11 http://mirror-ubc.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3 [236 kB] Get:12 http://mirror-ubc.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4 [250 kB] Get:13 http://mirror-ubc.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1 [214 kB] Get:14 http://mirror-ubc.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1 [141 kB] Get:15 http://mirror-ubc.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:16 http://mirror-ubc.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1 [76.4 kB] Get:17 http://mirror-ubc.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:18 http://mirror-ubc.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2 [318 kB] Get:19 http://mirror-ubc.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:20 http://mirror-ubc.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.6-2 [1112 kB] Get:21 http://mirror-ubc.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:22 http://mirror-ubc.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1 [75.1 kB] Get:23 http://mirror-ubc.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:24 http://mirror-ubc.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:25 http://mirror-ubc.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:26 http://mirror-ubc.debian.org/debian buster/main amd64 debconf all 1.5.71 [145 kB] Get:27 http://mirror-ubc.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:28 http://mirror-ubc.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:29 http://mirror-ubc.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:30 http://mirror-ubc.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:31 http://mirror-ubc.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:32 http://mirror-ubc.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:33 http://mirror-ubc.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9 [45.2 kB] Get:34 http://mirror-ubc.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:35 http://mirror-ubc.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:36 http://mirror-ubc.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:37 http://mirror-ubc.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:38 http://mirror-ubc.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:39 http://mirror-ubc.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5 [556 kB] Get:40 http://mirror-ubc.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1 [94.1 kB] Get:41 http://mirror-ubc.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1 [583 kB] Get:42 http://mirror-ubc.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:43 http://mirror-ubc.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.0 [966 kB] Get:44 http://mirror-ubc.debian.org/debian buster/main amd64 apt amd64 1.8.0 [1354 kB] Get:45 http://mirror-ubc.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1 [52.9 kB] Get:46 http://mirror-ubc.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1 [153 kB] Get:47 http://mirror-ubc.debian.org/debian buster/main amd64 libudev1 amd64 241-3 [148 kB] Get:48 http://mirror-ubc.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:49 http://mirror-ubc.debian.org/debian buster/main amd64 dpkg amd64 1.19.6 [2206 kB] Get:50 http://mirror-ubc.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:51 http://mirror-ubc.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:52 http://mirror-ubc.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1 [68.3 kB] Get:53 http://mirror-ubc.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1 [64.1 kB] Get:54 http://mirror-ubc.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1 [220 kB] Get:55 http://mirror-ubc.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1 [64.1 kB] Get:56 http://mirror-ubc.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1 [574 kB] Get:57 http://mirror-ubc.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:58 http://mirror-ubc.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:59 http://mirror-ubc.debian.org/debian buster/main amd64 gzip amd64 1.9-3 [128 kB] Get:60 http://mirror-ubc.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:61 http://mirror-ubc.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:62 http://mirror-ubc.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:63 http://mirror-ubc.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:64 http://mirror-ubc.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:65 http://mirror-ubc.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2 [132 kB] Get:66 http://mirror-ubc.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:67 http://mirror-ubc.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:68 http://mirror-ubc.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:69 http://mirror-ubc.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:70 http://mirror-ubc.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:71 http://mirror-ubc.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2 [406 kB] Get:72 http://mirror-ubc.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6 [1511 kB] Get:73 http://mirror-ubc.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:74 http://mirror-ubc.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:75 http://mirror-ubc.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:76 http://mirror-ubc.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:77 http://mirror-ubc.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2 [320 kB] Get:78 http://mirror-ubc.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2 [118 kB] Get:79 http://mirror-ubc.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2 [258 kB] Get:80 http://mirror-ubc.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:81 http://mirror-ubc.debian.org/debian buster/main amd64 libsystemd0 amd64 241-3 [329 kB] Get:82 http://mirror-ubc.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1b-2 [1530 kB] Get:83 http://mirror-ubc.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:84 http://mirror-ubc.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2 [305 kB] Get:85 http://mirror-ubc.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:86 http://mirror-ubc.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:87 http://mirror-ubc.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:88 http://mirror-ubc.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:89 http://mirror-ubc.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-2 [640 kB] Get:90 http://mirror-ubc.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2 [1910 kB] Get:91 http://mirror-ubc.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2 [1367 kB] Get:92 http://mirror-ubc.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2 [395 kB] Get:93 http://mirror-ubc.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:94 http://mirror-ubc.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:95 http://mirror-ubc.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:96 http://mirror-ubc.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:97 http://mirror-ubc.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:98 http://mirror-ubc.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:99 http://mirror-ubc.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:100 http://mirror-ubc.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:101 http://mirror-ubc.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:102 http://mirror-ubc.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:103 http://mirror-ubc.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1 [72.7 kB] Get:104 http://mirror-ubc.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B] Get:105 http://mirror-ubc.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get:106 http://mirror-ubc.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get:107 http://mirror-ubc.debian.org/debian buster/main amd64 metaphlan2-data all 2.6.0+ds-4 [204 MB] Get:108 http://mirror-ubc.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-8 [215 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 245 MB in 3s (69.6 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 ... 5344 files and directories currently installed.) Preparing to unpack .../base-files_10.1_amd64.deb ... Unpacking base-files (10.1) over (9.9+deb9u9) ... Setting up base-files (10.1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... (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 ... 5345 files and directories currently installed.) Preparing to unpack .../libc6_2.28-8_amd64.deb ... Unpacking libc6:amd64 (2.28-8) over (2.24-11+deb9u4) ... Setting up libc6:amd64 (2.28-8) ... Installing new version of config file /etc/ld.so.conf.d/x86_64-linux-gnu.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 ... 5343 files and directories currently installed.) Preparing to unpack .../libc-bin_2.28-8_amd64.deb ... Unpacking libc-bin (2.28-8) over (2.24-11+deb9u4) ... Setting up libc-bin (2.28-8) ... Updating /etc/nsswitch.conf to current default. Selecting previously unselected package gcc-8-base:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5343 files and directories currently installed.) Preparing to unpack .../gcc-8-base_8.3.0-6_amd64.deb ... Unpacking gcc-8-base:amd64 (8.3.0-6) ... Setting up gcc-8-base:amd64 (8.3.0-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5349 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a8.3.0-6_amd64.deb ... Unpacking libgcc1:amd64 (1:8.3.0-6) over (1:6.3.0-18+deb9u1) ... Setting up libgcc1:amd64 (1:8.3.0-6) ... Selecting previously unselected package libtinfo6:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5349 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20181013-2_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2) ... Setting up libtinfo6:amd64 (6.1+20181013-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5359 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6.1_amd64.deb ... Unpacking debianutils (4.8.6.1) over (4.8.1.1) ... Setting up debianutils (4.8.6.1) ... (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 ... 5359 files and directories currently installed.) Preparing to unpack .../archives/bash_5.0-4_amd64.deb ... Unpacking bash (5.0-4) over (4.4-5) ... Setting up bash (5.0-4) ... Installing new version of config file /etc/bash.bashrc ... Installing new version of config file /etc/skel/.profile ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 5360 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.33.1-0.1_amd64.deb ... Unpacking bsdutils (1:2.33.1-0.1) over (1:2.29.2-1+deb9u1) ... Setting up bsdutils (1:2.33.1-0.1) ... (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 ... 5360 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3_amd64.deb ... Unpacking coreutils (8.30-3) over (8.26-3) ... Setting up coreutils (8.30-3) ... Selecting previously unselected package libzstd1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5360 files and directories currently installed.) Preparing to unpack .../libzstd1_1.3.8+dfsg-3_amd64.deb ... Unpacking libzstd1:amd64 (1.3.8+dfsg-3) ... Setting up libzstd1:amd64 (1.3.8+dfsg-3) ... Selecting previously unselected package libgmp10:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5366 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.1.2+dfsg-4_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-4) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-4) ... Selecting previously unselected package libnettle6:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5372 files and directories currently installed.) Preparing to unpack .../libnettle6_3.4.1-1_amd64.deb ... Unpacking libnettle6:amd64 (3.4.1-1) ... Setting up libnettle6:amd64 (3.4.1-1) ... Selecting previously unselected package libhogweed4:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5380 files and directories currently installed.) Preparing to unpack .../libhogweed4_3.4.1-1_amd64.deb ... Unpacking libhogweed4:amd64 (3.4.1-1) ... Setting up libhogweed4:amd64 (3.4.1-1) ... Selecting previously unselected package libunistring2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5383 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-1_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-1) ... Setting up libunistring2:amd64 (0.9.10-1) ... Selecting previously unselected package libidn2-0:amd64. (Reading database ... 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Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-jessie-stable.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-wheezy-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-wheezy-stable.gpg ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5483 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.8.4-3_amd64.deb ... Unpacking libaudit1:amd64 (1:2.8.4-3) over (1:2.6.7-2) ... Setting up libaudit1:amd64 (1:2.8.4-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5483 files and directories currently installed.) Preparing to unpack .../debconf_1.5.71_all.deb ... Unpacking debconf (1.5.71) over (1.5.61) ... Setting up debconf (1.5.71) ... (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 ... 5466 files and directories currently installed.) Preparing to unpack .../libselinux1_2.8-1+b1_amd64.deb ... Unpacking libselinux1:amd64 (2.8-1+b1) over (2.6-3+b3) ... Setting up libselinux1:amd64 (2.8-1+b1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5463 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.5-1.1_amd64.deb ... Unpacking passwd (1:4.5-1.1) over (1:4.4-4.1) ... Setting up passwd (1:4.5-1.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5444 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.8.4-5_amd64.deb ... Unpacking libgcrypt20:amd64 (1.8.4-5) over (1.7.6-2+deb9u3) ... Setting up libgcrypt20:amd64 (1.8.4-5) ... (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 ... 5444 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-1) over (1:1.2.8.dfsg-5) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-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 ... 5444 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.12-1_amd64.deb ... Unpacking gpgv (2.2.12-1) over (2.1.18-8~deb9u4) ... Setting up gpgv (2.2.12-1) ... (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 ... 5444 files and directories currently installed.) Preparing to unpack .../libstdc++6_8.3.0-6_amd64.deb ... Unpacking libstdc++6:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Setting up libstdc++6:amd64 (8.3.0-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5444 files and directories currently installed.) Preparing to unpack .../archives/apt_1.8.0_amd64.deb ... Unpacking apt (1.8.0) over (1.4.9) ... Preparing to unpack .../libapt-pkg5.0_1.8.0_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.8.0) over (1.4.9) ... Setting up libapt-pkg5.0:amd64 (1.8.0) ... (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 ... 5461 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.8.3-1_amd64.deb ... Unpacking liblz4-1:amd64 (1.8.3-1) over (0.0~r131-2+b1) ... Setting up liblz4-1:amd64 (1.8.3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5460 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1_amd64.deb ... Unpacking liblzma5:amd64 (5.2.4-1) over (5.2.2-1.2+b1) ... Setting up liblzma5:amd64 (5.2.4-1) ... (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 ... 5459 files and directories currently installed.) Preparing to unpack .../libudev1_241-3_amd64.deb ... Unpacking libudev1:amd64 (241-3) over (232-25+deb9u11) ... Setting up libudev1:amd64 (241-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5459 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-6_amd64.deb ... Unpacking tar (1.30+dfsg-6) over (1.29b-1.1) ... Setting up tar (1.30+dfsg-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5457 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.19.6_amd64.deb ... Unpacking dpkg (1.19.6) over (1.18.25) ... Setting up dpkg (1.19.6) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (Reading database ... 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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 ... 5473 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 ... 5489 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2_all.deb ... Unpacking ncurses-base (6.1+20181013-2) over (6.0+20161126-1+deb9u2) ... Setting up ncurses-base (6.1+20181013-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5491 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_2.93-8_amd64.deb ... Unpacking sysvinit-utils (2.93-8) over (2.88dsf-59.9) ... 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 sysvinit-utils (2.93-8) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5491 files and directories currently installed.) Preparing to unpack .../libsystemd0_241-3_amd64.deb ... Unpacking libsystemd0:amd64 (241-3) over (232-25+deb9u11) ... Setting up libsystemd0:amd64 (241-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5491 files and directories currently installed.) Preparing to unpack .../libssl1.1_1.1.1b-2_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1b-2) over (1.1.0j-1~deb9u1) ... Preparing to unpack .../mime-support_3.62_all.deb ... Unpacking mime-support (3.62) over (3.60) ... Preparing to unpack .../python2.7_2.7.16-2_amd64.deb ... Unpacking python2.7 (2.7.16-2) over (2.7.13-2+deb9u3) ... Preparing to unpack .../libdb5.3_5.3.28+dfsg1-0.5_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg1-0.5) over (5.3.28-12+deb9u1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg1-0.5) ... (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 ... 5493 files and directories currently installed.) Preparing to unpack .../0-libexpat1_2.2.6-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-1) over (2.2.0-2+deb9u1) ... Preparing to unpack .../1-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) over (7.0-3) ... 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Setting up python2.7-minimal (2.7.16-2) ... 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 ... 5501 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 ... Unpacking libpython-stdlib:amd64 (2.7.16-1) over (2.7.13-2) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package python2. Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Preparing to unpack .../libpam-runtime_1.3.1-5_all.deb ... Unpacking libpam-runtime (1.3.1-5) over (1.1.8-3.6) ... Setting up libpam-runtime (1.3.1-5) ... (Reading database ... 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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) ... Setting up bowtie2 (2.3.4.3-1) ... 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: 00:00:07 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: 00:00:27 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:09 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:14 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: 00:11:07 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: 00:15:26 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: 00:00:27 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:11 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:17 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: 00:12:03 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: 00:16:35 Metaphlan2 data are properly created. Processing triggers for libc-bin (2.28-8) ... 65m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-yf', 'dist-upgrade'] 65m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 65m4.9s DUMP: 1f5f6190360ca25127ecb0a5bef1b37d - 65m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 65m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 65m5.2s 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 65m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 65m5.2s INFO: apt-cache knows about the following packages: metaphlan2-data 65m5.2s INFO: Running scripts pre_install 65m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_database-server'] 65m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_database-server'] 65m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_exceptions'] 65m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_exceptions'] 65m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_extras'] 65m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_extras'] 65m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture'] 65m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture'] 65m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 65m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 65m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy'] 65m5.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian buster/main amd64 Packages release o=Debian,a=testing,n=buster,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 65m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy'] 65m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy', 'metaphlan2-data'] 65m5.5s 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://mirror-ubc.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 65m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy', 'metaphlan2-data'] 65m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-y', 'install', 'metaphlan2-data'] 65m6.1s 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. 65m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-y', 'install', 'metaphlan2-data'] 65m6.1s INFO: Running scripts post_install 65m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_install_exceptions'] 65m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_install_exceptions'] 65m6.1s INFO: Running scripts post_distupgrade 65m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_base_cleanup'] 65m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_base_cleanup'] 65m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_exceptions'] 65m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_exceptions'] 65m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 65m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 65m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 65m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 65m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_zz_backports'] 65m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_distupgrade_zz_backports'] 65m6.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m6.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m6.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m7.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m7.3s INFO: Running scripts pre_install 65m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_database-server'] 65m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_database-server'] 65m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_exceptions'] 65m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_exceptions'] 65m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_extras'] 65m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_extras'] 65m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture'] 65m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture'] 65m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 65m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 65m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy'] 65m7.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian buster/main amd64 Packages release o=Debian,a=testing,n=buster,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 65m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy'] 65m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy', 'metaphlan2-data'] 65m7.5s 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://mirror-ubc.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 65m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-cache', 'policy', 'metaphlan2-data'] 65m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 65m8.1s 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. 65m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 65m8.1s INFO: Running scripts post_install 65m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_install_exceptions'] 65m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'tmp/scripts/post_install_exceptions'] 65m8.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m8.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 65m8.6s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.0 install ok installed base-files base-files 10.1 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bowtie2 bowtie2 2.3.4.3-1 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.6 install ok installed e2fslibs:amd64 e2fslibs 1.44.5-1 install ok installed e2fsprogs e2fsprogs 1.44.5-1 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.0 install ok installed libatomic1:amd64 libatomic1 8.3.0-6 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9 install ok installed libc-bin libc-bin 2.28-8 install ok installed libc6:amd64 libc6 2.28-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1 install ok installed libcomerr2:amd64 libcomerr2 1.44.5-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libexpat1:amd64 libexpat1 2.2.6-1 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw5:amd64 libncursesw5 6.1+20181013-2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-2 install ok installed libss2:amd64 libss2 1.44.5-1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1b-2 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtbb2:amd64 libtbb2 2018~U6-4 install ok installed libtinfo5:amd64 libtinfo5 6.1+20181013-2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2 install ok installed libudev1:amd64 libudev1 241-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed metaphlan2-data metaphlan2-data 2.6.0+ds-4 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed multiarch-support multiarch-support 2.28-8 install ok installed ncurses-base ncurses-base 6.1+20181013-2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6 install ok installed python python 2.7.16-1 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2 install ok installed readline-common readline-common 7.0-5 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1 65m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 65m8.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', '-ac', '--ignore-obsolete'] 65m10.3s DUMP: debsums: missing file /srv/piuparts.debian.org/tmp/tmp2I9kMq/var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 65m10.3s DEBUG: Command failed (status=2), but ignoring error: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp2I9kMq', '-ac', '--ignore-obsolete'] 65m10.3s ERROR: FAIL: debsums reports modifications inside the chroot: debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 65m10.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/shm'] 65m10.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/shm'] 65m10.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/console'] 65m10.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/console'] 65m10.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/ptmx'] 65m10.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/ptmx'] 65m10.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/pts'] 65m10.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/dev/pts'] 65m10.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/proc'] 65m10.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2I9kMq/proc'] 65m10.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m11.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp2I9kMq'] 65m11.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp2I9kMq 65m11.3s ERROR: piuparts run ends. ret=1 End: 2019-05-02 21:06:30 UTC