Start: 2018-12-11 20:30:19 UTC [stable] 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 [sid] 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 --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stable -d sid -B 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 0.95~201811291053~0.94-24-g107b4297 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stable -d sid -B reference-chroot-metadata.dat --apt metaphlan2-data=2.6.0+ds-4 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-8-amd64 #1 SMP Debian 4.9.130-2 (2018-10-27) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpr9wKm2 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpr9wKm2 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/proc'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/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/tmpr9wKm2/dev/pts'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/pts'] 0m2.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/ptmx'] 0m2.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/ptmx'] 0m2.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/console'] 0m2.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/console'] 0m2.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/shm'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/shm'] 0m2.5s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ stretch main 0m2.5s DEBUG: Created policy-rc.d and chmodded it. 0m2.6s DEBUG: Created resolv.conf. 0m2.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpr9wKm2/tmp/scripts/ 0m2.6s INFO: Running scripts post_chroot_unpack 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', 'update'] 0m4.4s DUMP: Ign:1 http://mirror.bm.debian.org/debian stretch InRelease Hit:2 http://mirror.bm.debian.org/debian stretch Release Reading package lists... 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', 'update'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', '-yf', 'dist-upgrade'] 0m5.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', '-yf', 'dist-upgrade'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.5s DUMP: 41b22e4ba8141cb867e2975265289448 - 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.5s INFO: Running scripts post_setup 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_experimental'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_experimental'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_forbid_home'] 0m8.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_forbid_home'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_minimize'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_minimize'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_zz_backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_setup_zz_backports'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.1s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.8 install ok installed base-files base-files 9.9+deb9u6 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~deb9u3 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 1.4.8 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+deb9u3 install ok installed libc6:amd64 libc6 2.24-11+deb9u3 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+deb9u6 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u6 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+deb9u3 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+deb9u4 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 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.1s DEBUG: Loading chroot meta data from reference-chroot-metadata.dat 0m8.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpr9wKm2'] 0m9.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpr9wKm2'] 0m9.8s INFO: Running scripts is_testable 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/is_testable_uninstallable'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/is_testable_uninstallable'] 0m9.8s INFO: Running scripts pre_test 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_test_exceptions'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_test_exceptions'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_test_root_password'] 0m9.9s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_test_root_password'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m10.3s 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 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data'] 0m10.3s INFO: apt-cache knows about the following packages: metaphlan2-data 0m10.3s INFO: Running scripts pre_install 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_database-server'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_database-server'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_exceptions'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_exceptions'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_extras'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_extras'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-cache', 'policy'] 0m10.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian stretch/main amd64 Packages release v=9.6,o=Debian,a=stable,n=stretch,l=Debian,c=main,b=amd64 origin mirror.bm.debian.org Pinned packages: 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-cache', 'policy'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-cache', 'policy', 'metaphlan2-data'] 0m10.6s DUMP: metaphlan2-data: Installed: (none) Candidate: 2.6.0+ds-2 Version table: 2.6.0+ds-2 500 500 http://mirror.bm.debian.org/debian stretch/main amd64 Packages 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-cache', 'policy', 'metaphlan2-data'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', '-y', 'install', 'metaphlan2-data'] 47m27.8s DUMP: Reading package lists... Building dependency tree... 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.bm.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:2 http://mirror.bm.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:3 http://mirror.bm.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:4 http://mirror.bm.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:5 http://mirror.bm.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u1 [83.4 kB] Get:6 http://mirror.bm.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://mirror.bm.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:8 http://mirror.bm.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:9 http://mirror.bm.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:10 http://mirror.bm.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0f-3+deb9u2 [1344 kB] Get:11 http://mirror.bm.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://mirror.bm.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://mirror.bm.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://mirror.bm.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://mirror.bm.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:16 http://mirror.bm.debian.org/debian stretch/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:17 http://mirror.bm.debian.org/debian stretch/main amd64 bowtie2 amd64 2.3.0-2 [1166 kB] Get:18 http://mirror.bm.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 (55.1 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. Preparing to unpack .../02-python-minimal_2.7.13-2_amd64.deb ... Unpacking python-minimal (2.7.13-2) ... Selecting previously unselected package mime-support. Preparing to unpack .../03-mime-support_3.60_all.deb ... Unpacking mime-support (3.60) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../04-libexpat1_2.2.0-2+deb9u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.0-2+deb9u1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../05-libffi6_3.2.1-6_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-6) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-3_all.deb ... Unpacking readline-common (7.0-3) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../07-libreadline7_7.0-3_amd64.deb ... Unpacking libreadline7:amd64 (7.0-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../08-libsqlite3-0_3.16.2-5+deb9u1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../09-libssl1.1_1.1.0f-3+deb9u2_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0f-3+deb9u2) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../10-libpython2.7-stdlib_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7. Preparing to unpack .../11-python2.7_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7 (2.7.13-2+deb9u3) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../12-libpython-stdlib_2.7.13-2_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.13-2) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Setting up python2.7-minimal (2.7.13-2+deb9u3) ... Setting up python-minimal (2.7.13-2) ... Selecting previously unselected package python. (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 ... 5236 files and directories currently installed.) Preparing to unpack .../python_2.7.13-2_amd64.deb ... Unpacking python (2.7.13-2) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../libatomic1_6.3.0-18+deb9u1_amd64.deb ... Unpacking libatomic1:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../libtbb2_4.3~20150611-2_amd64.deb ... Unpacking libtbb2:amd64 (4.3~20150611-2) ... Selecting previously unselected package bowtie2. Preparing to unpack .../bowtie2_2.3.0-2_amd64.deb ... Unpacking bowtie2 (2.3.0-2) ... Selecting previously unselected package metaphlan2-data. Preparing to unpack .../metaphlan2-data_2.6.0+ds-2_all.deb ... Unpacking metaphlan2-data (2.6.0+ds-2) ... Setting up libatomic1:amd64 (6.3.0-18+deb9u1) ... Setting up readline-common (7.0-3) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u1) ... Setting up mime-support (3.60) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libtbb2:amd64 (4.3~20150611-2) ... Processing triggers for libc-bin (2.24-11+deb9u3) ... Setting up libssl1.1:amd64 (1.1.0f-3+deb9u2) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up bowtie2 (2.3.0-2) ... Setting up metaphlan2-data (2.6.0+ds-2) ... Settings: Output files: "/usr/share/metaphlan2/db_v20/mpa_v20_m200.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: /var/lib/metaphlan2-data/markers.fasta Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:11 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:13 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: 00:01:18 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:13 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:40 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: 00:17:03 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_m200.1.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: 00:23:18 Reading reference sizes Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:12 Time to reverse reference sequence: 00:00:02 bmax according to bmaxDivN setting: 177889396 Using parameters --bmax 133417047 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 133417047 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:01:19 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:14 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:38 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: 00:17:16 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: 00:23:16 Metaphlan2 data are properly created. Processing triggers for libc-bin (2.24-11+deb9u3) ... 47m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', '-y', 'install', 'metaphlan2-data'] 47m27.8s INFO: Running scripts post_install 47m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_install_exceptions'] 47m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/post_install_exceptions'] 47m27.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpr9wKm2'] 47m29.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpr9wKm2'] 47m29.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpr9wKm2 to sid 47m29.0s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ sid main 47m29.0s INFO: Running scripts pre_distupgrade 47m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 47m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 47m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_exceptions'] 47m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_exceptions'] 47m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 47m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 47m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_zz_database-server'] 47m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_zz_database-server'] 47m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 47m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 47m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', 'update'] 47m35.4s DUMP: Get:1 http://mirror.bm.debian.org/debian sid InRelease [237 kB] Get:2 http://mirror.bm.debian.org/debian sid/main amd64 Packages [8310 kB] Get:3 http://mirror.bm.debian.org/debian sid/main Translation-en [6243 kB] Fetched 14.8 MB in 4s (3151 kB/s) Reading package lists... 47m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', 'update'] 47m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpr9wKm2', 'apt-get', '-yf', 'dist-upgrade'] Piuparts interrupted by the user, exiting... 80m0.9s DEBUG: kill -15 30227 80m1.2s DEBUG: kill -15 4484 80m1.4s DEBUG: kill -15 4473 80m1.7s DEBUG: kill -15 4469 80m1.9s DEBUG: kill -15 4468 80m2.2s DEBUG: kill -15 4447 80m8.6s DEBUG: kill -15 25673 80m8.8s DEBUG: kill -15 25672 80m15.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/shm'] 80m15.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/shm'] 80m15.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/console'] 80m15.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/console'] 80m15.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/ptmx'] 80m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/ptmx'] 80m15.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/pts'] 80m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/dev/pts'] 80m15.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/proc'] 80m15.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpr9wKm2/proc'] 80m15.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpr9wKm2'] 80m15.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpr9wKm2'] 80m15.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpr9wKm2 80m15.9s ERROR: piuparts run ends. *** Process KILLED - exceed maximum run time *** ret=-124 End: 2018-12-11 21:50:36 UTC