Start: 2024-05-15 21:13:00 GMT Package: ugene Version: 50.0+dfsg-1 Installed-Size: 84817 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgl1, libglu1-mesa | libglu1, libqt5core5t64 (>= 5.15.1), libqt5gui5t64 (>= 5.14.1) | libqt5gui5-gles (>= 5.14.1), libqt5network5t64 (>= 5.15.1), libqt5printsupport5t64 (>= 5.0.2), libqt5script5 (>= 5.6.0~beta), libqt5scripttools5 (>= 5.6.0~beta), libqt5svg5 (>= 5.6.0~beta), libqt5test5t64 (>= 5.6.0~beta), libqt5widgets5t64 (>= 5.15.1), libqt5xml5t64 (>= 5.1.0), libsqlite3-0 (>= 3.7.11), libstdc++6 (>= 13.1), libx11-6, libxtst6, zlib1g (>= 1:1.2.3.3), ugene-data Recommends: bedtools, bowtie, bowtie2, bwa, clark, clustalo, clustalw, cutadapt, default-jre-headless, fastqc, hisat2, hmmer, hmmer2, kalign, kraken, macs, mafft, metaphlan2, mrbayes, muscle, ncbi-blast+, phyml, primer3, r-base, samtools, spades, t-coffee, trimmomatic, vcftools, wevote Suggests: cufflinks Description: integrated bioinformatics toolkit Homepage: https://ugene.unipro.ru Description-md5: 9a10717d68a69dfaff1354fa2282b503 Section: science Priority: optional Filename: pool/main/u/ugene/ugene_50.0+dfsg-1_amd64.deb Size: 22366376 MD5sum: 148c9ba3260ad5300f33cdf6edf1cba2 SHA256: 09cc17e086525ade137dbaf19c773f87e40686d10e3c4f3162a32af73cfb36f9 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt ugene=50.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt ugene=50.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-29-amd64 #1 SMP Debian 5.10.216-1 (2024-05-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpi9tror4s 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpi9tror4s 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/proc'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/proc'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/pts'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/pts'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/ptmx'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/ptmx'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpi9tror4s/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', 'update'] 0m4.3s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [168 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9159 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6130 kB] Fetched 15.5 MB in 3s (6086 kB/s) Reading package lists... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', 'update'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', '-yf', 'dist-upgrade'] 0m7.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash libc-bin libc6 libgpg-error0 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4952 kB of archives. After this operation, 304 kB disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.21-2+b1 [1493 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.38-10 [2768 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.38-10 [611 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.49-2 [79.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4952 kB in 0s (41.6 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 ... 5201 files and directories currently installed.) Preparing to unpack .../bash_5.2.21-2+b1_amd64.deb ... Unpacking bash (5.2.21-2+b1) over (5.2.21-2) ... Setting up bash (5.2.21-2+b1) ... 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 ... 5202 files and directories currently installed.) Preparing to unpack .../libc6_2.38-10_amd64.deb ... Unpacking libc6:amd64 (2.38-10) over (2.38-7) ... Setting up libc6:amd64 (2.38-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5202 files and directories currently installed.) Preparing to unpack .../libc-bin_2.38-10_amd64.deb ... Unpacking libc-bin (2.38-10) over (2.38-7) ... Setting up libc-bin (2.38-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5202 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.49-2_amd64.deb ... Unpacking libgpg-error0:amd64 (1.49-2) over (1.47-3+b1) ... Setting up libgpg-error0:amd64 (1.49-2) ... Processing triggers for debianutils (5.17) ... Processing triggers for libc-bin (2.38-10) ... 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', '-yf', 'dist-upgrade'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s DUMP: 15f90ed4eeaa5ddb2b78ad1efeef0695 - 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s INFO: Running scripts post_setup 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_dummy_users'] 0m8.7s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_dummy_users'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_forbid_home'] 0m8.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_forbid_home'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_minimize'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_minimize'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_zz_backports'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_setup_zz_backports'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', 'clean'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', 'clean'] 0m8.8s DEBUG: Recording chroot state 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.3s DUMP: install ok installed apt apt 2.9.2 install ok installed base-files base-files 13.2 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2+b1 install ok installed bsdutils bsdutils 1:2.40-8 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.1~rc2-1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.2 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libblkid1:amd64 libblkid1 2.40-8 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.38-10 install ok installed libc6:amd64 libc6 2.38-10 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1~rc2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1~rc2-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2+b1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.49-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-8 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-5 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-8 install ok installed libss2:amd64 libss2 1.47.1~rc2-1 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240414-1 install ok installed libudev1:amd64 libudev1 255.5-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-8 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.1~rc2-1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-8 install ok installed ncurses-base ncurses-base 6.4+20240414-1 install ok installed ncurses-bin ncurses-bin 6.4+20240414-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-4 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.09-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-8 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'dpkg-divert', '--list'] 0m9.3s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'dpkg-divert', '--list'] 0m9.3s INFO: Running scripts is_testable 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/is_testable_uninstallable'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/is_testable_uninstallable'] 0m9.3s INFO: apt-cache does not know about any of the requested packages 0m9.3s INFO: Running scripts pre_test 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_test_exceptions'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_test_exceptions'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_test_root_password'] 0m9.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_test_root_password'] 0m9.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 0m9.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 0m10.1s DEBUG: No broken symlinks as far as we can find. 0m10.1s INFO: Running scripts pre_install 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_database-server'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_database-server'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_exceptions'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_exceptions'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_extras'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_extras'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 0m10.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 0m10.8s DEBUG: No broken symlinks as far as we can find. 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-cache', 'policy'] 0m11.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-cache', 'policy'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-cache', 'policy', 'ugene'] 0m11.9s DUMP: ugene: Installed: (none) Candidate: 50.0+dfsg-1 Version table: 50.0+dfsg-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-cache', 'policy', 'ugene'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', '-y', 'install', 'ugene=50.0+dfsg-1'] 43m29.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser adwaita-icon-theme alsa-topology-conf alsa-ucm-conf amap-align at-spi2-common at-spi2-core bamtools bcftools bedtools binutils binutils-common binutils-x86-64-linux-gnu biosquid blends-common blt bowtie bowtie2 build-essential bwa bzip2 bzip2-doc ca-certificates ca-certificates-java clustalo clustalw cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cutadapt dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless dialign-tx dialign-tx-data dirmngr dmsetup dpkg-dev exonerate fakeroot fastqc file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lato fonts-lyx fonts-urw-base35 fsa g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gawk gcc gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13 gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme hisat2 hmmer hmmer2 ibverbs-providers icu-devtools isympy-common isympy3 java-common javascript-common jellyfish1 kalign kraken krb5-locales libaec0 libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libamd-comgr2 libamdhip64-5 libapache-pom-java libapparmor1 libargs4j-java libargtable2-0 libasan8 libasound2-data libasound2t64 libassuan0 libatk-bridge2.0-0t64 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.2 libbinutils libblas-dev libblas3 libblosc1 libbrotli1 libbsd0 libbz2-dev libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbor0.10 libcc1-0 libclang-common-17-dev libclang-cpp17t64 libclang-rt-17-dev libclass-inspector-perl libclc-17 libclc-17-dev libclone-perl libcloudproviders0 libcolord2 libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libconvert-binhex-perl libcrypt-dev libcryptsetup12 libctf-nobfd0 libctf0 libcups2t64 libcurl3t64-gnutls libcurl4t64 libdata-dump-perl libdatrie1 libdbus-1-3 libdconf1 libdeflate-dev libdeflate0 libdevmapper1.02.1 libdivsufsort3 libdouble-conversion3 libdpkg-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1t64 libencode-locale-perl libepoxy0 libevdev2 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfakeroot libfcgi-bin libfcgi-perl libfcgi0t64 libfdisk1 libfido2-1 libfile-basedir-perl libfile-desktopentry-perl libfile-fcntllock-perl libfile-listing-perl libfile-mimeinfo-perl libfindbin-libs-perl libfont-afm-perl libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgbm1 libgcc-13-dev libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-bin libgdk-pixbuf2.0-common libgfortran-13-dev libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libgles2 libglib2.0-0t64 libglib2.0-data libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-bin libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhmsbeagle1v5 libhsa-runtime64-1 libhsakmt1 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhtsjdk-java libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwasan0 libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu-dev libicu72 libimagequant0 libinput-bin libinput10 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libisl23 libitm1 libjansson4 libjbig0 libjbzip2-java libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libjs-jquery-ui libjson-c5 libjsoncpp25 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 libksba8 liblapack-dev liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 libldap-common liblerc4 libllvm17t64 libllvmspirvlib17 liblmdb0 liblocale-gettext-perl liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzf1 liblzma-dev liblzo2-2 libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmd4c0 libmime-tools-perl libmjson-java libmpc3 libmpfr6 libmtdev1t64 libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses-dev libncurses6 libncursesw6 libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnlopt0 libnpth0t64 libnspr4 libnss-systemd libnss3 libnuma1 libopengl0 libopenjp2-7 libopenmpi3t64 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpcsclite1 libperl5.38t64 libpixman-1-0 libpkgconf3 libpmix2t64 libpng-dev libpng-tools libpng16-16t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5gui5t64 libqt5network5t64 libqt5printsupport5t64 libqt5qml5 libqt5qmlmodels5 libqt5quick5 libqt5script5 libqt5scripttools5 libqt5svg5 libqt5test5t64 libqt5waylandclient5 libqt5waylandcompositor5 libqt5widgets5t64 libqt5xml5t64 libquadmath0 libraqm0 librdmacm1t64 libreadline-dev libreadline8t64 librhino-java librsvg2-2 librsvg2-common librtmp1 libruby libruby3.1t64 libsasl2-2 libsasl2-modules libsasl2-modules-db libsensors-config libsensors5 libsframe1 libsharpyuv0 libsigsegv2 libsis-base-java libsis-base-jni libsis-jhdf5-java libsis-jhdf5-jni libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsoap-lite-perl libsqlite3-0 libsquid1t64 libssh2-1t64 libssw0 libstdc++-13-dev libsystemd-shared libsz2 libtask-weaken-perl libtcl8.6 libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff6 libtimedate-perl libtirpc-common libtirpc-dev libtirpc3t64 libtk8.6 libtry-tiny-perl libtsan2 libubsan1 libucx0 liburi-perl libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-protocol-perl libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 libxkbcommon0 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml-twig-perl libxml-xpathengine-perl libxml2 libxmlrpc-lite-perl libxmu6 libxmuu1 libxnvctrl0 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libyaml-0-2 libz3-4 linux-libc-dev luit lynx lynx-common macs mafft mailcap make manpages manpages-dev med-config media-types menu mesa-opencl-icd mesa-vulkan-drivers metaphlan metaphlan2-data mrbayes mummer muscle mustang ncbi-blast+ ncbi-data ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl patch perl perl-modules-5.38 perl-openssl-defaults phyml pigz pinentry-curses pkgconf pkgconf-bin poa prank primer3 probcons procps proda psmisc publicsuffix python-babel-localedata python-biopython-doc python-matplotlib-data python-odf-doc python-odf-tools python-tables-data python3 python3-appdirs python3-argcomplete python3-argh python3-attr python3-babel python3-biom-format python3-biopython python3-bottleneck python3-brotli python3-bs4 python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-contourpy python3-cssselect python3-cutadapt python3-cycler python3-cykhash python3-dateutil python3-decorator python3-defusedxml python3-dendropy python3-dnaio python3-et-xmlfile python3-fonttools python3-freetype python3-fs python3-gffutils python3-h5py python3-h5py-serial python3-hisat2 python3-hmmlearn python3-html5lib python3-idna python3-importlib-metadata python3-iniconfig python3-jinja2 python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-msgpack python3-numexpr python3-numpy python3-odf python3-olefile python3-openpyxl python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-psutil python3-pybedtools python3-pyfaidx python3-pygments python3-pyparsing python3-pysam python3-pytest python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-simplejson python3-six python3-sklearn python3-sklearn-lib python3-soupsieve python3-sympy python3-tables python3-tables-lib python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-webencodings python3-xopen python3-yaml python3-zipp python3.11 python3.11-minimal qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended rake readline-common rpcsvc-proto ruby ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools sensible-utils sgml-base shared-mime-info spades systemd systemd-dev systemd-sysv systemd-timesyncd t-coffee tabix tk8.6-blt2.5 tm-align trimmomatic ucf ugene-data unicode-data unzip vcftools w3c-sgml-lib x11-common x11-utils x11-xserver-utils xauth xdg-user-dirs xdg-utils xfonts-encodings xfonts-utils xkb-data xml-core xz-utils zip zlib1g-dev zutty Suggested packages: cron quota texlive-latex-recommended binutils-doc gprofng-gui blends-doc blt-demo bowtie-examples bowtie2-examples clustalx seaview cpp-doc gcc-13-locales cpp-13-doc pinentry-gnome3 tor debian-keyring wise fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib g++-13-multilib gcc-13-doc gawk-doc gcc-multilib autoconf automake libtool flex bison gdb gcc-doc gcc-13-multilib gdb-x86-64-linux-gnu gfortran-multilib gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev parcimonie xloadimage scdaemon hmmer-doc hmmer2-doc apache2 | lighttpd | httpd alsa-utils libasound2-plugins libdigest-hmac-perl libgssapi-perl liblapack-doc libc-devtools glibc-doc colord libasm-java libxz-java libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common git bzr gdbm-l10n low-memory-monitor gpm krb5-doc krb5-user gvfs picard-tools libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs liblcms2-utils libcrypt-ssleay-perl liblzma-doc ncurses-doc libngs-java-doc pciutils pcscd qgnomeplatform-qt5 qt5-image-formats-plugins qt5-qmltooling-plugins readline-doc rhino librsvg2-bin libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql lm-sensors libapache2-mod-perl2 libmime-lite-perl libnet-jabber-perl libstdc++-13-doc tcl8.6 tk8.6 libsub-name-perl libbusiness-isbn-perl libregexp-ipv6-perl libwacom-bin libauthen-ntlm-perl libxml-sax-expatxs-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools make-doc man-browser menu-l10n gksu | kde-cli-tools | ktsuss mrbayes-doc mustang-testdata libnss-mdns fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic keychain libpam-ssh monkeysphere ssh-askpass ed diffutils-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl debhelper pinentry-doc blast2 ncbi-epcr probcons-extra python3-doc python3-venv python-attr-doc python-biom-format-doc dialign dssp emboss fasttree muscle3 phylip python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml python-bottleneck-doc python-charset-normalizer-doc python-cycler-doc python-h5py-doc python3-genshi python-jinja2-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 python3-dev python-openpyxl-doc python-pandas-doc python3-statsmodels python-pil-doc python3-setuptools python-pybedtools-doc python-pygments-doc ttf-bitstream-vera python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python3-dap python-sklearn-doc texlive-fonts-extra python-sympy-doc python3-netcdf4 python-tables-doc vitables tix python3-tk-dbg python3.11-venv python3.11-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib texlive-base texlive-latex-base texlive-plain-generic texlive-fonts-recommended texinfo ri ruby-dev bundler cwltool sgml-base-doc systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved libbpf1 libip4tc2 libpwquality1 libqrencode4 libtss2-esys-3.0.2-0 libtss2-mu-4.0.1-0 libtss2-rc0 libtss2-tcti-device0 polkitd boxshade t-coffee-examples pymol rasmol cufflinks mesa-utils nickle cairo-5c xorg-docs-core Recommended packages: blast2 python3-numba clark wevote The following NEW packages will be installed: adduser adwaita-icon-theme alsa-topology-conf alsa-ucm-conf amap-align at-spi2-common at-spi2-core bamtools bcftools bedtools binutils binutils-common binutils-x86-64-linux-gnu biosquid blends-common blt bowtie bowtie2 build-essential bwa bzip2 bzip2-doc ca-certificates ca-certificates-java clustalo clustalw cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cutadapt dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless dialign-tx dialign-tx-data dirmngr dmsetup dpkg-dev exonerate fakeroot fastqc file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lato fonts-lyx fonts-urw-base35 fsa g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gawk gcc gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13 gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme hisat2 hmmer hmmer2 ibverbs-providers icu-devtools isympy-common isympy3 java-common javascript-common jellyfish1 kalign kraken krb5-locales libaec0 libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libamd-comgr2 libamdhip64-5 libapache-pom-java libapparmor1 libargs4j-java libargtable2-0 libasan8 libasound2-data libasound2t64 libassuan0 libatk-bridge2.0-0t64 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.2 libbinutils libblas-dev libblas3 libblosc1 libbrotli1 libbsd0 libbz2-dev libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbor0.10 libcc1-0 libclang-common-17-dev libclang-cpp17t64 libclang-rt-17-dev libclass-inspector-perl libclc-17 libclc-17-dev libclone-perl libcloudproviders0 libcolord2 libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libconvert-binhex-perl libcrypt-dev libcryptsetup12 libctf-nobfd0 libctf0 libcups2t64 libcurl3t64-gnutls libcurl4t64 libdata-dump-perl libdatrie1 libdbus-1-3 libdconf1 libdeflate-dev libdeflate0 libdevmapper1.02.1 libdivsufsort3 libdouble-conversion3 libdpkg-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1t64 libencode-locale-perl libepoxy0 libevdev2 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfakeroot libfcgi-bin libfcgi-perl libfcgi0t64 libfdisk1 libfido2-1 libfile-basedir-perl libfile-desktopentry-perl libfile-fcntllock-perl libfile-listing-perl libfile-mimeinfo-perl libfindbin-libs-perl libfont-afm-perl libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgbm1 libgcc-13-dev libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-bin libgdk-pixbuf2.0-common libgfortran-13-dev libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libgles2 libglib2.0-0t64 libglib2.0-data libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-bin libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhmsbeagle1v5 libhsa-runtime64-1 libhsakmt1 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhtsjdk-java libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwasan0 libhwloc-plugins libhwloc15 libibverbs1 libice6 libicu-dev libicu72 libimagequant0 libinput-bin libinput10 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libisl23 libitm1 libjansson4 libjbig0 libjbzip2-java libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libjs-jquery-ui libjson-c5 libjsoncpp25 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 libksba8 liblapack-dev liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 libldap-common liblerc4 libllvm17t64 libllvmspirvlib17 liblmdb0 liblocale-gettext-perl liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzf1 liblzma-dev liblzo2-2 libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmd4c0 libmime-tools-perl libmjson-java libmpc3 libmpfr6 libmtdev1t64 libmunge2 libncbi-ngs3 libncbi-vdb3 libncurses-dev libncurses6 libncursesw6 libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnlopt0 libnpth0t64 libnspr4 libnss-systemd libnss3 libnuma1 libopengl0 libopenjp2-7 libopenmpi3t64 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpcsclite1 libperl5.38t64 libpixman-1-0 libpkgconf3 libpmix2t64 libpng-dev libpng-tools libpng16-16t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5gui5t64 libqt5network5t64 libqt5printsupport5t64 libqt5qml5 libqt5qmlmodels5 libqt5quick5 libqt5script5 libqt5scripttools5 libqt5svg5 libqt5test5t64 libqt5waylandclient5 libqt5waylandcompositor5 libqt5widgets5t64 libqt5xml5t64 libquadmath0 libraqm0 librdmacm1t64 libreadline-dev libreadline8t64 librhino-java librsvg2-2 librsvg2-common librtmp1 libruby libruby3.1t64 libsasl2-2 libsasl2-modules libsasl2-modules-db libsensors-config libsensors5 libsframe1 libsharpyuv0 libsigsegv2 libsis-base-java libsis-base-jni libsis-jhdf5-java libsis-jhdf5-jni libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsoap-lite-perl libsqlite3-0 libsquid1t64 libssh2-1t64 libssw0 libstdc++-13-dev libsystemd-shared libsz2 libtask-weaken-perl libtcl8.6 libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff6 libtimedate-perl libtirpc-common libtirpc-dev libtirpc3t64 libtk8.6 libtry-tiny-perl libtsan2 libubsan1 libucx0 liburi-perl libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-protocol-perl libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 libxkbcommon0 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml-twig-perl libxml-xpathengine-perl libxml2 libxmlrpc-lite-perl libxmu6 libxmuu1 libxnvctrl0 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libyaml-0-2 libz3-4 linux-libc-dev luit lynx lynx-common macs mafft mailcap make manpages manpages-dev med-config media-types menu mesa-opencl-icd mesa-vulkan-drivers metaphlan metaphlan2-data mrbayes mummer muscle mustang ncbi-blast+ ncbi-data ncbi-vdb-data netbase ocl-icd-libopencl1 openjdk-17-jre openjdk-17-jre-headless openmpi-bin openmpi-common openssh-client openssl patch perl perl-modules-5.38 perl-openssl-defaults phyml pigz pinentry-curses pkgconf pkgconf-bin poa prank primer3 probcons procps proda psmisc publicsuffix python-babel-localedata python-biopython-doc python-matplotlib-data python-odf-doc python-odf-tools python-tables-data python3 python3-appdirs python3-argcomplete python3-argh python3-attr python3-babel python3-biom-format python3-biopython python3-bottleneck python3-brotli python3-bs4 python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-contourpy python3-cssselect python3-cutadapt python3-cycler python3-cykhash python3-dateutil python3-decorator python3-defusedxml python3-dendropy python3-dnaio python3-et-xmlfile python3-fonttools python3-freetype python3-fs python3-gffutils python3-h5py python3-h5py-serial python3-hisat2 python3-hmmlearn python3-html5lib python3-idna python3-importlib-metadata python3-iniconfig python3-jinja2 python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-msgpack python3-numexpr python3-numpy python3-odf python3-olefile python3-openpyxl python3-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-psutil python3-pybedtools python3-pyfaidx python3-pygments python3-pyparsing python3-pysam python3-pytest python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-simplejson python3-six python3-sklearn python3-sklearn-lib python3-soupsieve python3-sympy python3-tables python3-tables-lib python3-threadpoolctl python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-webencodings python3-xopen python3-yaml python3-zipp python3.11 python3.11-minimal qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended rake readline-common rpcsvc-proto ruby ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools sensible-utils sgml-base shared-mime-info spades systemd systemd-dev systemd-sysv systemd-timesyncd t-coffee tabix tk8.6-blt2.5 tm-align trimmomatic ucf ugene ugene-data unicode-data unzip vcftools w3c-sgml-lib x11-common x11-utils x11-xserver-utils xauth xdg-user-dirs xdg-utils xfonts-encodings xfonts-utils xkb-data xml-core xz-utils zip zlib1g-dev zutty 0 upgraded, 729 newly installed, 0 to remove and 0 not upgraded. Need to get 893 MB of archives. After this operation, 3609 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.0.13-2 [41.6 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 dmsetup amd64 2:1.02.196-1+b1 [82.6 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libdevmapper1.02.1 amd64 2:1.02.196-1+b1 [134 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libjson-c5 amd64 0.17-1+b1 [44.2 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libcryptsetup12 amd64 2:2.7.2-2 [251 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libfdisk1 amd64 2.40-8 [206 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libkmod2 amd64 31+20240202-2 [59.6 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 255.5-1 [1939 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 systemd-dev all 255.5-1 [60.5 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 systemd amd64 255.5-1 [3534 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 255.5-1 [51.2 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.14.10-4+b1 [106 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.14.10-4 [79.0 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.14.10-4+b1 [185 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.14.10-4 [80.1 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.14.10-4+b1 [98.6 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.38 all 5.38.2-4 [2907 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.23-5.1+b1 [73.0 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.23-5.1+b1 [48.8 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libperl5.38t64 amd64 5.38.2-4 [4281 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.38.2-4 [236 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libsigsegv2 amd64 2.14-1+b1 [34.3 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libdouble-conversion3 amd64 3.3.0-1+b1 [41.0 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libqt5core5t64 amd64 5.15.10+dfsg-7.2+b1 [1835 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libqt5script5 amd64 5.15.10+dfsg-3+b1 [694 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:50 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:54 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.0.6-1+b1 [41.0 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.0.6-1+b1 [36.6 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get:74 http://deb.debian.org/debian trixie/main amd64 libegl-mesa0 amd64 24.0.6-1+b1 [119 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libegl1 amd64 1.7.0-1+b1 [34.3 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get:91 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.0.6-1+b1 [8279 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.0.6-1+b1 [151 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libevdev2 amd64 1.13.1+dfsg-1+b1 [32.6 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libmtdev1t64 amd64 1.1.6-1.2 [22.2 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libgudev-1.0-0 amd64 238-5 [14.4 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libwacom-common all 2.10.0-2 [62.5 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libwacom9 amd64 2.10.0-2 [22.4 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libinput-bin amd64 1.25.0-1+b2 [24.8 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libinput10 amd64 1.25.0-1+b2 [128 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libmd4c0 amd64 0.4.8-1+b1 [45.1 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libqt5dbus5t64 amd64 5.15.10+dfsg-7.2+b1 [213 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:113 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libqt5network5t64 amd64 5.15.10+dfsg-7.2+b1 [677 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libxcb-icccm4 amd64 0.4.1-1.1+b1 [26.8 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libxcb-image0 amd64 0.4.0-2+b1 [22.2 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libxcb-shape0 amd64 1.15-1 [106 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libxcb-xinerama0 amd64 1.15-1 [105 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libxcb-xinput0 amd64 1.15-1 [130 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libxcb-xkb1 amd64 1.15-1 [129 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.41-2 [795 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libxkbcommon-x11-0 amd64 1.6.0-1+b1 [16.2 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libqt5gui5t64 amd64 5.15.10+dfsg-7.2+b1 [3444 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libqt5widgets5t64 amd64 5.15.10+dfsg-7.2+b1 [2385 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libqt5scripttools5 amd64 5.15.10+dfsg-3+b1 [212 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 pigz amd64 2.8-1 [62.7 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.4+20240414-1 [135 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.45.3-1 [896 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:145 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 bzip2 amd64 1.0.8-5.1 [40.3 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 krb5-locales all 1.20.1-6 [63.2 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libnss-systemd amd64 255.5-1 [190 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 255.5-1 [261 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 manpages all 6.05.01-1 [1344 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-1.1 [27.8 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.7p1-4 [965 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 systemd-timesyncd amd64 255.5-1 [74.0 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 xz-utils amd64 5.6.1+really5.4.5-1 [503 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b3 [138 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 alsa-topology-conf all 1.2.5.1-2 [15.2 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 alsa-ucm-conf all 1.2.11-1.1 [66.7 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.52.0-1 [75.9 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.14.10-4+b1 [79.1 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-4+b2 [41.9 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-4+b2 [32.4 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b2 [28.7 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 gsettings-desktop-schemas all 46.0-1 [668 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 at-spi2-core amd64 2.52.0-1 [60.8 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5 [159 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 bamtools amd64 2.5.2+dfsg-5 [206 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 python3-argcomplete all 3.3.0-1 [38.9 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 python3-argh all 0.31.2-1 [26.5 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get:209 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get:212 http://deb.debian.org/debian trixie/main amd64 python3-simplejson amd64 3.19.2-1+b1 [69.4 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:224 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.3-1 [109 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14-20240330-1 [136 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:240 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.0-2 [1149 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.83+dfsg1-2 [1634 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 python3-gffutils all 0.13-1 [1041 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get:248 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get:249 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get:250 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:254 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get:255 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:256 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get:257 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get:258 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:259 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:260 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:261 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.12-7 [3869 kB] Get:262 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:263 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:264 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:265 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get:266 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.1.0-1 [2092 kB] Get:267 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get:268 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b1 [299 kB] Get:269 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:270 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get:271 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get:272 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get:273 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get:274 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get:275 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.20-1 [760 kB] Get:276 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:277 http://deb.debian.org/debian trixie/main amd64 binutils-common amd64 2.42-4 [2539 kB] Get:278 http://deb.debian.org/debian trixie/main amd64 libsframe1 amd64 2.42-4 [76.0 kB] Get:279 http://deb.debian.org/debian trixie/main amd64 libbinutils amd64 2.42-4 [520 kB] Get:280 http://deb.debian.org/debian trixie/main amd64 libctf-nobfd0 amd64 2.42-4 [152 kB] Get:281 http://deb.debian.org/debian trixie/main amd64 libctf0 amd64 2.42-4 [87.0 kB] Get:282 http://deb.debian.org/debian trixie/main amd64 libgprofng0 amd64 2.42-4 [772 kB] Get:283 http://deb.debian.org/debian trixie/main amd64 libjansson4 amd64 2.14-2+b2 [39.9 kB] Get:284 http://deb.debian.org/debian trixie/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4 [2215 kB] Get:285 http://deb.debian.org/debian trixie/main amd64 binutils amd64 2.42-4 [80.9 kB] Get:286 http://deb.debian.org/debian trixie/main amd64 libsquid1t64 amd64 1.9g+cvs20050121-15.1 [76.1 kB] Get:287 http://deb.debian.org/debian trixie/main amd64 biosquid amd64 1.9g+cvs20050121-15.1 [79.1 kB] Get:288 http://deb.debian.org/debian trixie/main amd64 menu amd64 2.1.50 [346 kB] Get:289 http://deb.debian.org/debian trixie/main amd64 blends-common all 0.7.6 [14.9 kB] Get:290 http://deb.debian.org/debian trixie/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get:291 http://deb.debian.org/debian trixie/main amd64 bowtie2 amd64 2.5.3-1 [1438 kB] Get:292 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.38-10 [49.5 kB] Get:293 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.7.12-1 [2281 kB] Get:294 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:295 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:296 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.38-10 [1914 kB] Get:297 http://deb.debian.org/debian trixie/main amd64 gcc-13-base amd64 13.2.0-24 [45.3 kB] Get:298 http://deb.debian.org/debian trixie/main amd64 libisl23 amd64 0.26-3+b2 [652 kB] Get:299 http://deb.debian.org/debian trixie/main amd64 libmpc3 amd64 1.3.1-1+b2 [52.1 kB] Get:300 http://deb.debian.org/debian trixie/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-24 [10.3 MB] Get:301 http://deb.debian.org/debian trixie/main amd64 cpp-13 amd64 13.2.0-24 [1276 B] Get:302 http://deb.debian.org/debian trixie/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7 [4724 B] Get:303 http://deb.debian.org/debian trixie/main amd64 cpp amd64 4:13.2.0-7 [1564 B] Get:304 http://deb.debian.org/debian trixie/main amd64 libcc1-0 amd64 14-20240330-1 [42.1 kB] Get:305 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14-20240330-1 [25.8 kB] Get:306 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14-20240330-1 [9216 B] Get:307 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14-20240330-1 [2724 kB] Get:308 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14-20240330-1 [1201 kB] Get:309 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14-20240330-1 [2454 kB] Get:310 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14-20240330-1 [1071 kB] Get:311 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14-20240330-1 [1485 kB] Get:312 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14-20240330-1 [147 kB] Get:313 http://deb.debian.org/debian trixie/main amd64 libgcc-13-dev amd64 13.2.0-24 [2542 kB] Get:314 http://deb.debian.org/debian trixie/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-24 [19.8 MB] Get:315 http://deb.debian.org/debian trixie/main amd64 gcc-13 amd64 13.2.0-24 [486 kB] Get:316 http://deb.debian.org/debian trixie/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7 [1440 B] Get:317 http://deb.debian.org/debian trixie/main amd64 gcc amd64 4:13.2.0-7 [5152 B] Get:318 http://deb.debian.org/debian trixie/main amd64 libstdc++-13-dev amd64 13.2.0-24 [2264 kB] Get:319 http://deb.debian.org/debian trixie/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-24 [11.3 MB] Get:320 http://deb.debian.org/debian trixie/main amd64 g++-13 amd64 13.2.0-24 [15.2 kB] Get:321 http://deb.debian.org/debian trixie/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7 [1200 B] Get:322 http://deb.debian.org/debian trixie/main amd64 g++ amd64 4:13.2.0-7 [1348 B] Get:323 http://deb.debian.org/debian trixie/main amd64 make amd64 4.3-4.1 [396 kB] Get:324 http://deb.debian.org/debian trixie/main amd64 libdpkg-perl all 1.22.6 [631 kB] Get:325 http://deb.debian.org/debian trixie/main amd64 patch amd64 2.7.6-7 [128 kB] Get:326 http://deb.debian.org/debian trixie/main amd64 dpkg-dev all 1.22.6 [1317 kB] Get:327 http://deb.debian.org/debian trixie/main amd64 build-essential amd64 12.10 [4516 B] Get:328 http://deb.debian.org/debian trixie/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get:329 http://deb.debian.org/debian trixie/main amd64 bzip2-doc all 1.0.8-5.1 [505 kB] Get:330 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:331 http://deb.debian.org/debian trixie/main amd64 libargtable2-0 amd64 13-2 [17.6 kB] Get:332 http://deb.debian.org/debian trixie/main amd64 clustalo amd64 1.2.4-8 [267 kB] Get:333 http://deb.debian.org/debian trixie/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get:334 http://deb.debian.org/debian trixie/main amd64 python3-xopen all 1.7.0-2 [16.9 kB] Get:335 http://deb.debian.org/debian trixie/main amd64 python3-dnaio amd64 1.2.0-2 [113 kB] Get:336 http://deb.debian.org/debian trixie/main amd64 python3-cutadapt amd64 4.7-2 [262 kB] Get:337 http://deb.debian.org/debian trixie/main amd64 cutadapt all 4.7-2 [25.1 kB] Get:338 http://deb.debian.org/debian trixie/main amd64 java-common all 0.75 [6640 B] Get:339 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:340 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get:341 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get:342 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get:343 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get:344 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get:345 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.52.0-1 [67.0 kB] Get:346 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.0-3+b1 [129 kB] Get:347 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1 [28.9 kB] Get:348 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b1 [139 kB] Get:349 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get:350 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get:351 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get:352 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get:353 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-1+b2 [191 kB] Get:354 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:355 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:356 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:357 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get:358 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get:359 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get:360 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.22.0-2.1+b1 [11.3 kB] Get:361 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.22.0-2.1+b1 [5640 B] Get:362 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get:363 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB] Get:364 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get:365 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get:366 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get:367 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.41-4 [4635 kB] Get:368 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.41-4 [2727 kB] Get:369 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get:370 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB] Get:371 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get:372 http://deb.debian.org/debian trixie/main amd64 dialign-tx-data all 1.0.2-15 [862 kB] Get:373 http://deb.debian.org/debian trixie/main amd64 dialign-tx amd64 1.0.2-15 [87.6 kB] Get:374 http://deb.debian.org/debian trixie/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get:375 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.40-3 [565 kB] Get:376 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get:377 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get:378 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.40-3 [793 kB] Get:379 http://deb.debian.org/debian trixie/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB] Get:380 http://deb.debian.org/debian trixie/main amd64 libfakeroot amd64 1.33-1 [28.7 kB] Get:381 http://deb.debian.org/debian trixie/main amd64 fakeroot amd64 1.33-1 [74.0 kB] Get:382 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get:383 http://deb.debian.org/debian trixie/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get:384 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B] Get:385 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:386 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get:387 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:388 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:389 http://deb.debian.org/debian trixie/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:390 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:391 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:392 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:393 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:394 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get:395 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-7 [155 kB] Get:396 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.3+dfsg-7 [23.6 kB] Get:397 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.3+dfsg-7 [110 kB] Get:398 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get:399 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.0-2 [29.0 kB] Get:400 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get:401 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get:402 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.0+dfsg-1 [1833 kB] Get:403 http://deb.debian.org/debian trixie/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:404 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get:405 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.16.1-1 [480 kB] Get:406 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get:407 http://deb.debian.org/debian trixie/main amd64 libsis-base-jni amd64 18.09~pre1+git20180928.45fbd31+dfsg-3 [12.5 kB] Get:408 http://deb.debian.org/debian trixie/main amd64 libsis-base-java all 18.09~pre1+git20180928.45fbd31+dfsg-3 [97.8 kB] Get:409 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get:410 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get:411 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get:412 http://deb.debian.org/debian trixie/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get:413 http://deb.debian.org/debian trixie/main amd64 libsis-jhdf5-jni amd64 19.04.1+dfsg-4+b1 [97.0 kB] Get:414 http://deb.debian.org/debian trixie/main amd64 libsis-jhdf5-java all 19.04.1+dfsg-4 [1491 kB] Get:415 http://deb.debian.org/debian trixie/main amd64 fastqc all 0.12.1+dfsg-3 [399 kB] Get:416 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-extra all 2.37-8 [1792 kB] Get:417 http://deb.debian.org/debian trixie/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:418 http://deb.debian.org/debian trixie/main amd64 fsa amd64 1.15.9+dfsg-6 [700 kB] Get:419 http://deb.debian.org/debian trixie/main amd64 libgfortran-13-dev amd64 13.2.0-24 [847 kB] Get:420 http://deb.debian.org/debian trixie/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-24 [10.7 MB] Get:421 http://deb.debian.org/debian trixie/main amd64 gfortran-13 amd64 13.2.0-24 [12.2 kB] Get:422 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7 [1280 B] Get:423 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:13.2.0-7 [1440 B] Get:424 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.40-3 [1094 kB] Get:425 http://deb.debian.org/debian trixie/main amd64 gnupg-utils amd64 2.2.40-3 [928 kB] Get:426 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.40-3 [950 kB] Get:427 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get:428 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.40-3 [695 kB] Get:429 http://deb.debian.org/debian trixie/main amd64 gpg-wks-client amd64 2.2.40-3 [541 kB] Get:430 http://deb.debian.org/debian trixie/main amd64 gpg-wks-server amd64 2.2.40-3 [532 kB] Get:431 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.40-3 [671 kB] Get:432 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.40-3 [847 kB] Get:433 http://deb.debian.org/debian trixie/main amd64 hisat2 amd64 2.2.1-4+b3 [3700 kB] Get:434 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get:435 http://deb.debian.org/debian trixie/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:436 http://deb.debian.org/debian trixie/main amd64 hmmer2 amd64 2.3.2+dfsg-12 [314 kB] Get:437 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get:438 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get:439 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get:440 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get:441 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get:442 http://deb.debian.org/debian trixie/main amd64 isympy-common all 1.12-7 [234 kB] Get:443 http://deb.debian.org/debian trixie/main amd64 isympy3 all 1.12-7 [6164 B] Get:444 http://deb.debian.org/debian trixie/main amd64 javascript-common all 11+nmu1 [6260 B] Get:445 http://deb.debian.org/debian trixie/main amd64 jellyfish1 amd64 1.1.11-9 [132 kB] Get:446 http://deb.debian.org/debian trixie/main amd64 kalign amd64 1:3.4.0-1 [138 kB] Get:447 http://deb.debian.org/debian trixie/main amd64 kraken amd64 1.1.1-4 [752 kB] Get:448 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:449 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-xs-perl amd64 0.04-8+b3 [11.5 kB] Get:450 http://deb.debian.org/debian trixie/main amd64 libalgorithm-merge-perl all 0.08-5 [11.8 kB] Get:451 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get:452 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:453 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get:454 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get:455 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get:456 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:457 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get:458 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get:459 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get:460 http://deb.debian.org/debian trixie/main amd64 libxkbfile1 amd64 1:1.1.0-1+b1 [76.6 kB] Get:461 http://deb.debian.org/debian trixie/main amd64 libxmuu1 amd64 2:1.1.3-3+b2 [21.9 kB] Get:462 http://deb.debian.org/debian trixie/main amd64 libxv1 amd64 2:1.0.11-1.1+b1 [23.4 kB] Get:463 http://deb.debian.org/debian trixie/main amd64 libxxf86dga1 amd64 2:1.1.5-1+b1 [20.7 kB] Get:464 http://deb.debian.org/debian trixie/main amd64 x11-utils amd64 7.7+6+b1 [181 kB] Get:465 http://deb.debian.org/debian trixie/main amd64 libatk-wrapper-java all 0.40.0-3 [63.4 kB] Get:466 http://deb.debian.org/debian trixie/main amd64 libatk-wrapper-java-jni amd64 0.40.0-3+b2 [53.2 kB] Get:467 http://deb.debian.org/debian trixie/main amd64 libauthen-sasl-perl all 2.1700-1 [44.8 kB] Get:468 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get:469 http://deb.debian.org/debian trixie/main amd64 libblosc1 amd64 1.21.5+ds-1+b1 [49.6 kB] Get:470 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get:471 http://deb.debian.org/debian trixie/main amd64 libclang-common-17-dev amd64 1:17.0.6-12 [682 kB] Get:472 http://deb.debian.org/debian trixie/main amd64 libclang-cpp17t64 amd64 1:17.0.6-12 [11.8 MB] Get:473 http://deb.debian.org/debian trixie/main amd64 libclang-rt-17-dev amd64 1:17.0.6-12 [2315 kB] Get:474 http://deb.debian.org/debian trixie/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:475 http://deb.debian.org/debian trixie/main amd64 libclc-17-dev all 1:17.0.6-12 [61.3 kB] Get:476 http://deb.debian.org/debian trixie/main amd64 libclc-17 all 1:17.0.6-12 [9858 kB] Get:477 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get:478 http://deb.debian.org/debian trixie/main amd64 libconvert-binhex-perl all 1.125-3 [27.4 kB] Get:479 http://deb.debian.org/debian trixie/main amd64 libdata-dump-perl all 1.25-1 [28.4 kB] Get:480 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get:481 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:482 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get:483 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get:484 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:485 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:486 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get:487 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get:488 http://deb.debian.org/debian trixie/main amd64 libfcgi0t64 amd64 2.4.2-2.1 [24.6 kB] Get:489 http://deb.debian.org/debian trixie/main amd64 libfcgi-bin amd64 2.4.2-2.1 [11.6 kB] Get:490 http://deb.debian.org/debian trixie/main amd64 libfcgi-perl amd64 0.82+ds-3+b1 [25.4 kB] Get:491 http://deb.debian.org/debian trixie/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:492 http://deb.debian.org/debian trixie/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:493 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get:494 http://deb.debian.org/debian trixie/main amd64 libfile-desktopentry-perl all 0.22-3 [17.6 kB] Get:495 http://deb.debian.org/debian trixie/main amd64 libfile-fcntllock-perl amd64 0.22-4+b3 [30.3 kB] Get:496 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:497 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:498 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:499 http://deb.debian.org/debian trixie/main amd64 libfile-mimeinfo-perl all 0.35-1 [44.4 kB] Get:500 http://deb.debian.org/debian trixie/main amd64 libfont-afm-perl all 1.20-4 [13.1 kB] Get:501 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-bin amd64 2.42.10+dfsg-3+b3 [18.4 kB] Get:502 http://deb.debian.org/debian trixie/main amd64 libgles2 amd64 1.7.0-1+b1 [17.3 kB] Get:503 http://deb.debian.org/debian trixie/main amd64 libglib2.0-data all 2.80.2-1 [1265 kB] Get:504 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b1 [31.1 kB] Get:505 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b1 [180 kB] Get:506 http://deb.debian.org/debian trixie/main amd64 libgpm2 amd64 1.20.7-11 [14.0 kB] Get:507 http://deb.debian.org/debian trixie/main amd64 libgtk-3-bin amd64 3.24.41-4 [84.8 kB] Get:508 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get:509 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get:510 http://deb.debian.org/debian trixie/main amd64 libllvmspirvlib17 amd64 17.0.0-5 [815 kB] Get:511 http://deb.debian.org/debian trixie/main amd64 mesa-opencl-icd amd64 24.0.6-1+b1 [19.8 MB] Get:512 http://deb.debian.org/debian trixie/main amd64 libhmsbeagle1v5 amd64 3.1.2+dfsg-13+b1 [139 kB] Get:513 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:514 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get:515 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:516 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:517 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:518 http://deb.debian.org/debian trixie/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:519 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:520 http://deb.debian.org/debian trixie/main amd64 libhtml-format-perl all 2.16-2 [38.8 kB] Get:521 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:522 http://deb.debian.org/debian trixie/main amd64 libhttp-daemon-perl all 6.16-1 [23.5 kB] Get:523 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:524 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get:525 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get:526 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get:527 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get:528 http://deb.debian.org/debian trixie/main amd64 libio-compress-brotli-perl amd64 0.004001-2+b2 [16.9 kB] Get:529 http://deb.debian.org/debian trixie/main amd64 libio-sessiondata-perl all 1.03-3 [6316 B] Get:530 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:531 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get:532 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get:533 http://deb.debian.org/debian trixie/main amd64 libio-stringy-perl all 2.111-3 [56.5 kB] Get:534 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get:535 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get:536 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get:537 http://deb.debian.org/debian trixie/main amd64 libldap-common all 2.5.17+dfsg-1 [31.5 kB] Get:538 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:539 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:540 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:541 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:542 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get:543 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:544 http://deb.debian.org/debian trixie/main amd64 liblzf1 amd64 3.6-4+b1 [10.4 kB] Get:545 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get:546 http://deb.debian.org/debian trixie/main amd64 liblzo2-2 amd64 2.10-2+b1 [54.8 kB] Get:547 http://deb.debian.org/debian trixie/main amd64 libnet-smtp-ssl-perl all 1.04-2 [6548 B] Get:548 http://deb.debian.org/debian trixie/main amd64 libmailtools-perl all 2.21-3 [88.6 kB] Get:549 http://deb.debian.org/debian trixie/main amd64 libmime-tools-perl all 5.515-1 [203 kB] Get:550 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get:551 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get:552 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.4+20240414-1 [349 kB] Get:553 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b2 [199 kB] Get:554 http://deb.debian.org/debian trixie/main amd64 libxml-twig-perl all 1:3.52-3 [177 kB] Get:555 http://deb.debian.org/debian trixie/main amd64 libnet-dbus-perl amd64 1.2.0-2+b2 [168 kB] Get:556 http://deb.debian.org/debian trixie/main amd64 libnlopt0 amd64 2.7.1-5+b2 [174 kB] Get:557 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get:558 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get:559 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get:560 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:561 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:562 http://deb.debian.org/debian trixie/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get:563 http://deb.debian.org/debian trixie/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get:564 http://deb.debian.org/debian trixie/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get:565 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get:566 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get:567 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.43-5 [360 kB] Get:568 http://deb.debian.org/debian trixie/main amd64 libpng-tools amd64 1.6.43-5 [128 kB] Get:569 http://deb.debian.org/debian trixie/main amd64 libqt5printsupport5t64 amd64 5.15.10+dfsg-7.2+b1 [204 kB] Get:570 http://deb.debian.org/debian trixie/main amd64 libqt5qml5 amd64 5.15.10+dfsg-2+b2 [1361 kB] Get:571 http://deb.debian.org/debian trixie/main amd64 libqt5qmlmodels5 amd64 5.15.10+dfsg-2+b2 [191 kB] Get:572 http://deb.debian.org/debian trixie/main amd64 libqt5quick5 amd64 5.15.10+dfsg-2+b2 [1598 kB] Get:573 http://deb.debian.org/debian trixie/main amd64 libqt5svg5 amd64 5.15.10-2+b2 [134 kB] Get:574 http://deb.debian.org/debian trixie/main amd64 libqt5test5t64 amd64 5.15.10+dfsg-7.2+b1 [148 kB] Get:575 http://deb.debian.org/debian trixie/main amd64 libqt5waylandclient5 amd64 5.15.10-2+b2 [371 kB] Get:576 http://deb.debian.org/debian trixie/main amd64 libqt5waylandcompositor5 amd64 5.15.10-2+b2 [355 kB] Get:577 http://deb.debian.org/debian trixie/main amd64 libqt5xml5t64 amd64 5.15.10+dfsg-7.2+b1 [123 kB] Get:578 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-4 [152 kB] Get:579 http://deb.debian.org/debian trixie/main amd64 librsvg2-2 amd64 2.58.0+dfsg-1 [1937 kB] Get:580 http://deb.debian.org/debian trixie/main amd64 librsvg2-common amd64 2.58.0+dfsg-1 [16.9 kB] Get:581 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.18 [6704 B] Get:582 http://deb.debian.org/debian trixie/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get:583 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get:584 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get:585 http://deb.debian.org/debian trixie/main amd64 rake all 13.0.6-3 [83.9 kB] Get:586 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:587 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get:588 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get:589 http://deb.debian.org/debian trixie/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get:590 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:591 http://deb.debian.org/debian trixie/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get:592 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get:593 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules amd64 2.1.28+dfsg1-6 [66.0 kB] Get:594 http://deb.debian.org/debian trixie/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get:595 http://deb.debian.org/debian trixie/main amd64 libsoap-lite-perl all 1.27-3 [239 kB] Get:596 http://deb.debian.org/debian trixie/main amd64 libssw0 amd64 1.1-14+b1 [21.2 kB] Get:597 http://deb.debian.org/debian trixie/main amd64 libtext-iconv-perl amd64 1.7-8+b3 [14.4 kB] Get:598 http://deb.debian.org/debian trixie/main amd64 libtie-ixhash-perl all 1.23-4 [11.7 kB] Get:599 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:600 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:601 http://deb.debian.org/debian trixie/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [189 kB] Get:602 http://deb.debian.org/debian trixie/main amd64 libx11-protocol-perl all 0.56-9 [120 kB] Get:603 http://deb.debian.org/debian trixie/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:604 http://deb.debian.org/debian trixie/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:605 http://deb.debian.org/debian trixie/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:606 http://deb.debian.org/debian trixie/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b3 [313 kB] Get:607 http://deb.debian.org/debian trixie/main amd64 libxml-sax-expat-perl all 0.51-2 [11.1 kB] Get:608 http://deb.debian.org/debian trixie/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:609 http://deb.debian.org/debian trixie/main amd64 libxml-xpathengine-perl all 0.14-2 [33.5 kB] Get:610 http://deb.debian.org/debian trixie/main amd64 libxmlrpc-lite-perl all 0.717-5 [22.4 kB] Get:611 http://deb.debian.org/debian trixie/main amd64 luit amd64 2.0.20221028-1 [53.8 kB] Get:612 http://deb.debian.org/debian trixie/main amd64 lynx-common all 2.9.1-1 [1193 kB] Get:613 http://deb.debian.org/debian trixie/main amd64 lynx amd64 2.9.1-1 [638 kB] Get:614 http://deb.debian.org/debian trixie/main amd64 python3-cykhash amd64 2.0.0-3 [587 kB] Get:615 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get:616 http://deb.debian.org/debian trixie/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:617 http://deb.debian.org/debian trixie/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-1 [6606 kB] Get:618 http://deb.debian.org/debian trixie/main amd64 python3-sklearn all 1.4.2+dfsg-1 [2247 kB] Get:619 http://deb.debian.org/debian trixie/main amd64 python3-hmmlearn amd64 0.3.0-5 [139 kB] Get:620 http://deb.debian.org/debian trixie/main amd64 macs amd64 3.0.1-2 [4531 kB] Get:621 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] Get:622 http://deb.debian.org/debian trixie/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:623 http://deb.debian.org/debian trixie/main amd64 manpages-dev all 6.05.01-1 [2025 kB] Get:624 http://deb.debian.org/debian trixie/main amd64 med-config all 3.8.1 [11.1 kB] Get:625 http://deb.debian.org/debian trixie/main amd64 mesa-vulkan-drivers amd64 24.0.6-1+b1 [10.2 MB] Get:626 http://deb.debian.org/debian trixie/main amd64 python3-h5py-serial amd64 3.10.0-1+b3 [1400 kB] Get:627 http://deb.debian.org/debian trixie/main amd64 python3-h5py all 3.10.0-1 [14.4 kB] Get:628 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get:629 http://deb.debian.org/debian trixie/main amd64 python3-click all 8.1.7-1 [94.0 kB] Get:630 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [7882 kB] Get:631 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.1.4+dfsg-8 [3015 kB] Get:632 http://deb.debian.org/debian trixie/main amd64 python3-biom-format amd64 2.1.15.2-3 [182 kB] Get:633 http://deb.debian.org/debian trixie/main amd64 python3-dendropy all 4.6.1-1 [277 kB] Get:634 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.0+ds-1+b2 [4646 kB] Get:635 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get:636 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get:637 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.6-2 [37.0 kB] Get:638 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 1.26.18-2 [116 kB] Get:639 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get:640 http://deb.debian.org/debian trixie/main amd64 metaphlan2-data all 2.6.0+ds-4 [204 MB] Get:641 http://deb.debian.org/debian trixie/main amd64 python3-msgpack amd64 1.0.3-3+b1 [96.5 kB] Get:642 http://deb.debian.org/debian trixie/main amd64 metaphlan all 4.0.4-1 [2011 kB] Get:643 http://deb.debian.org/debian trixie/main amd64 mrbayes amd64 3.2.7a-7+b1 [661 kB] Get:644 http://deb.debian.org/debian trixie/main amd64 muscle amd64 1:5.1.0-1 [297 kB] Get:645 http://deb.debian.org/debian trixie/main amd64 mustang amd64 3.2.4-1 [105 kB] Get:646 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get:647 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get:648 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get:649 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get:650 http://deb.debian.org/debian trixie/main amd64 phyml amd64 3:3.3.20220408-3+b1 [1105 kB] Get:651 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get:652 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get:653 http://deb.debian.org/debian trixie/main amd64 poa amd64 2.0+20060928-9 [53.3 kB] Get:654 http://deb.debian.org/debian trixie/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get:655 http://deb.debian.org/debian trixie/main amd64 primer3 amd64 2.6.1-4 [202 kB] Get:656 http://deb.debian.org/debian trixie/main amd64 probcons amd64 1.12-14 [119 kB] Get:657 http://deb.debian.org/debian trixie/main amd64 proda amd64 1.0-14 [65.4 kB] Get:658 http://deb.debian.org/debian trixie/main amd64 psmisc amd64 23.7-1 [266 kB] Get:659 http://deb.debian.org/debian trixie/main amd64 publicsuffix all 20231001.0357-0.1 [125 kB] Get:660 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get:661 http://deb.debian.org/debian trixie/main amd64 python-biopython-doc all 1.83+dfsg1-2 [17.4 MB] Get:662 http://deb.debian.org/debian trixie/main amd64 python-odf-doc all 1.4.2-2 [213 kB] Get:663 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get:664 http://deb.debian.org/debian trixie/main amd64 python3-odf all 1.4.2-2 [78.0 kB] Get:665 http://deb.debian.org/debian trixie/main amd64 python-odf-tools all 1.4.2-2 [28.1 kB] Get:666 http://deb.debian.org/debian trixie/main amd64 python-tables-data all 3.7.0-10 [47.6 kB] Get:667 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.14.0-1 [111 kB] Get:668 http://deb.debian.org/debian trixie/main amd64 python3-bottleneck amd64 1.3.5+ds1-3+b1 [101 kB] Get:669 http://deb.debian.org/debian trixie/main amd64 python3-soupsieve all 2.5-1 [38.1 kB] Get:670 http://deb.debian.org/debian trixie/main amd64 python3-bs4 all 4.12.3-1 [133 kB] Get:671 http://deb.debian.org/debian trixie/main amd64 python3-cssselect all 1.2.0-4 [21.7 kB] Get:672 http://deb.debian.org/debian trixie/main amd64 python3-et-xmlfile all 1.0.1-2.1 [9180 B] Get:673 http://deb.debian.org/debian trixie/main amd64 python3-hisat2 all 2.2.1-4 [13.9 kB] Get:674 http://deb.debian.org/debian trixie/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Get:675 http://deb.debian.org/debian trixie/main amd64 python3-html5lib all 1.1-6 [90.5 kB] Get:676 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get:677 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1 [14.5 kB] Get:678 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get:679 http://deb.debian.org/debian trixie/main amd64 python3-numexpr amd64 2.10.0-2 [101 kB] Get:680 http://deb.debian.org/debian trixie/main amd64 python3-olefile all 0.46-3 [36.1 kB] Get:681 http://deb.debian.org/debian trixie/main amd64 python3-openpyxl all 3.1.2+dfsg-6 [165 kB] Get:682 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get:683 http://deb.debian.org/debian trixie/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get:684 http://deb.debian.org/debian trixie/main amd64 python3-pybedtools amd64 0.10.0-1 [12.3 MB] Get:685 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get:686 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 7.4.4-3 [239 kB] Get:687 http://deb.debian.org/debian trixie/main amd64 python3-tables-lib amd64 3.7.0-10+b1 [674 kB] Get:688 http://deb.debian.org/debian trixie/main amd64 python3-tables all 3.7.0-10 [338 kB] Get:689 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get:690 http://deb.debian.org/debian trixie/main amd64 qt5-gtk-platformtheme amd64 5.15.10+dfsg-7.2+b1 [126 kB] Get:691 http://deb.debian.org/debian trixie/main amd64 qttranslations5-l10n all 5.15.10-2 [1834 kB] Get:692 http://deb.debian.org/debian trixie/main amd64 qtwayland5 amd64 5.15.10-2+b2 [203 kB] Get:693 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-13 [230 kB] Get:694 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:695 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:696 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.0-2 [28.2 MB] Get:697 http://deb.debian.org/debian trixie/main amd64 r-cran-boot all 1.3-30-1 [622 kB] Get:698 http://deb.debian.org/debian trixie/main amd64 r-cran-cluster amd64 2.1.6-1 [568 kB] Get:699 http://deb.debian.org/debian trixie/main amd64 r-cran-foreign amd64 0.8.86-1 [250 kB] Get:700 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-60.0.1-1 [1118 kB] Get:701 http://deb.debian.org/debian trixie/main amd64 r-cran-kernsmooth amd64 2.23-22-1 [90.9 kB] Get:702 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-5-1 [1394 kB] Get:703 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get:704 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:705 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:706 http://deb.debian.org/debian trixie/main amd64 r-cran-survival amd64 3.5-8-1 [6149 kB] Get:707 http://deb.debian.org/debian trixie/main amd64 r-cran-rpart amd64 4.1.23-1 [685 kB] Get:708 http://deb.debian.org/debian trixie/main amd64 r-cran-class amd64 7.3-22-2 [87.3 kB] Get:709 http://deb.debian.org/debian trixie/main amd64 r-cran-nnet amd64 7.3-19-2 [111 kB] Get:710 http://deb.debian.org/debian trixie/main amd64 r-cran-spatial amd64 7.3-17-1 [128 kB] Get:711 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:712 http://deb.debian.org/debian trixie/main amd64 r-recommended all 4.4.0-2 [2572 B] Get:713 http://deb.debian.org/debian trixie/main amd64 r-base all 4.4.0-2 [14.3 kB] Get:714 http://deb.debian.org/debian trixie/main amd64 xauth amd64 1:1.1.2-1 [36.0 kB] Get:715 http://deb.debian.org/debian trixie/main amd64 r-base-dev all 4.4.0-2 [4512 B] Get:716 http://deb.debian.org/debian trixie/main amd64 r-base-html all 4.4.0-2 [62.6 kB] Get:717 http://deb.debian.org/debian trixie/main amd64 r-doc-html all 4.4.0-2 [580 kB] Get:718 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get:719 http://deb.debian.org/debian trixie/main amd64 spades amd64 3.15.5+dfsg-7 [9020 kB] Get:720 http://deb.debian.org/debian trixie/main amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1032 kB] Get:721 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.19+ds-1.1+b1 [476 kB] Get:722 http://deb.debian.org/debian trixie/main amd64 tm-align amd64 20190822+dfsg-2 [865 kB] Get:723 http://deb.debian.org/debian trixie/main amd64 trimmomatic all 0.39+dfsg-2 [758 kB] Get:724 http://deb.debian.org/debian trixie/main amd64 ugene-data all 50.0+dfsg-1 [7638 kB] Get:725 http://deb.debian.org/debian trixie/main amd64 ugene amd64 50.0+dfsg-1 [22.4 MB] Get:726 http://deb.debian.org/debian trixie/main amd64 vcftools amd64 0.1.16-3+b1 [431 kB] Get:727 http://deb.debian.org/debian trixie/main amd64 x11-xserver-utils amd64 7.7+10+b1 [163 kB] Get:728 http://deb.debian.org/debian trixie/main amd64 xdg-user-dirs amd64 0.18-1 [54.4 kB] Get:729 http://deb.debian.org/debian trixie/main amd64 zutty amd64 0.15.2.20240411+dfsg1-1 [180 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 893 MB in 23s (38.5 MB/s) Selecting previously unselected package libapparmor1: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 ... 5205 files and directories currently installed.) Preparing to unpack .../0-libapparmor1_3.0.13-2_amd64.deb ... Unpacking libapparmor1:amd64 (3.0.13-2) ... Selecting previously unselected package dmsetup. Preparing to unpack .../1-dmsetup_2%3a1.02.196-1+b1_amd64.deb ... Unpacking dmsetup (2:1.02.196-1+b1) ... Selecting previously unselected package libdevmapper1.02.1:amd64. Preparing to unpack .../2-libdevmapper1.02.1_2%3a1.02.196-1+b1_amd64.deb ... Unpacking libdevmapper1.02.1:amd64 (2:1.02.196-1+b1) ... Selecting previously unselected package libjson-c5:amd64. Preparing to unpack .../3-libjson-c5_0.17-1+b1_amd64.deb ... Unpacking libjson-c5:amd64 (0.17-1+b1) ... Selecting previously unselected package libcryptsetup12:amd64. Preparing to unpack .../4-libcryptsetup12_2%3a2.7.2-2_amd64.deb ... Unpacking libcryptsetup12:amd64 (2:2.7.2-2) ... Selecting previously unselected package libfdisk1:amd64. Preparing to unpack .../5-libfdisk1_2.40-8_amd64.deb ... Unpacking libfdisk1:amd64 (2.40-8) ... Selecting previously unselected package libkmod2:amd64. Preparing to unpack .../6-libkmod2_31+20240202-2_amd64.deb ... Unpacking libkmod2:amd64 (31+20240202-2) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../7-libsystemd-shared_255.5-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (255.5-1) ... Selecting previously unselected package systemd-dev. Preparing to unpack .../8-systemd-dev_255.5-1_all.deb ... Unpacking systemd-dev (255.5-1) ... Selecting previously unselected package systemd. Preparing to unpack .../9-systemd_255.5-1_amd64.deb ... Unpacking systemd (255.5-1) ... Setting up libapparmor1:amd64 (3.0.13-2) ... Setting up libjson-c5:amd64 (0.17-1+b1) ... Setting up libfdisk1:amd64 (2.40-8) ... Setting up libkmod2:amd64 (31+20240202-2) ... Setting up libsystemd-shared:amd64 (255.5-1) ... Setting up systemd-dev (255.5-1) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.196-1+b1) ... Setting up libcryptsetup12:amd64 (2:2.7.2-2) ... Setting up systemd (255.5-1) ... Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service → /usr/lib/systemd/system/getty@.service. Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target → /usr/lib/systemd/system/remote-fs.target. Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service → /usr/lib/systemd/system/systemd-pstore.service. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. [ESC][0;1;31m"/home" already exists and is not a directory.[ESC][0m Setting up dmsetup (2:1.02.196-1+b1) ... Selecting previously unselected package systemd-sysv. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc-dev:amd64. Preparing to unpack .../456-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libx11-protocol-perl. Preparing to unpack .../457-libx11-protocol-perl_0.56-9_all.deb ... Unpacking libx11-protocol-perl (0.56-9) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../458-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../459-libxml-sax-base-perl_1.09-3_all.deb ... 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Selecting previously unselected package libxmlrpc-lite-perl. Preparing to unpack .../465-libxmlrpc-lite-perl_0.717-5_all.deb ... Unpacking libxmlrpc-lite-perl (0.717-5) ... Selecting previously unselected package luit. Preparing to unpack .../466-luit_2.0.20221028-1_amd64.deb ... Adding 'diversion of /usr/bin/luit to /usr/bin/luit.x11-utils by luit' Adding 'diversion of /usr/share/man/man1/luit.1.gz to /usr/share/man/man1/luit.x11-utils.1.gz by luit' Unpacking luit (2.0.20221028-1) ... Selecting previously unselected package lynx-common. Preparing to unpack .../467-lynx-common_2.9.1-1_all.deb ... Unpacking lynx-common (2.9.1-1) ... Selecting previously unselected package lynx. Preparing to unpack .../468-lynx_2.9.1-1_amd64.deb ... Unpacking lynx (2.9.1-1) ... Selecting previously unselected package python3-cykhash. Preparing to unpack .../469-python3-cykhash_2.0.0-3_amd64.deb ... Unpacking python3-cykhash (2.0.0-3) ... Selecting previously unselected package python3-joblib. 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Setting up xz-utils (5.6.1+really5.4.5-1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up perl-modules-5.38 (5.38.2-4) ... Setting up libquadmath0:amd64 (14-20240330-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libhwloc15:amd64 (2.10.0-1+b1) ... Setting up libmpc3:amd64 (1.3.1-1+b2) ... Setting up systemd-timesyncd (255.5-1) ... Creating group 'systemd-timesync' with GID 997. Creating user 'systemd-timesync' (systemd Time Synchronization) with UID 997 and GID 997. Created symlink /etc/systemd/system/dbus-org.freedesktop.timesync1.service → /usr/lib/systemd/system/systemd-timesyncd.service. Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service → /usr/lib/systemd/system/systemd-timesyncd.service. Setting up libatomic1:amd64 (14-20240330-1) ... Setting up patch (2.7.6-7) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up icu-devtools (72.1-4+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libncursesw6:amd64 (6.4+20240414-1) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up lynx-common (2.9.1-1) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-5) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libglapi-mesa:amd64 (24.0.6-1+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up libvulkan1:amd64 (1.3.280.0-1) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up libubsan1:amd64 (14-20240330-1) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up fonts-dejavu-extra (2.37-8) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up libpcre2-posix3:amd64 (10.42-4+b1) ... Setting up alsa-topology-conf (1.2.5.1-2) ... Setting up libmtdev1t64:amd64 (1.1.6-1.2) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Setting up libclang-common-17-dev:amd64 (1:17.0.6-12) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up libhwasan0:amd64 (14-20240330-1) ... Setting up pigz (2.8-1) ... Setting up libclc-17 (1:17.0.6-12) ... Setting up at-spi2-common (2.52.0-1) ... Setting up python-biopython-doc (1.83+dfsg1-2) ... Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up bamtools (2.5.2+dfsg-5) ... Setting up dialign-tx (1.0.2-15) ... Setting up dbus-session-bus-common (1.14.10-4) ... Setting up libasan8:amd64 (14-20240330-1) ... Setting up libclang-rt-17-dev:amd64 (1:17.0.6-12) ... Setting up procps (2:4.0.4-4) ... Setting up libblosc1:amd64 (1.21.5+ds-1+b1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up gpgconf (2.2.40-3) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmd4c0:amd64 (0.4.8-1+b1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1+b1) ... Setting up libwayland-egl1:amd64 (1.22.0-2.1+b1) ... Setting up libperl5.38t64:amd64 (5.38.2-4) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libtsan2:amd64 (14-20240330-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.42-4) ... Setting up dbus-system-bus-common (1.14.10-4) ... Setting up menu (2.1.50) ... Setting up libfido2-1:amd64 (1.14.0-1+b2) ... Setting up libisl23:amd64 (0.26-3+b2) ... Setting up libc-dev-bin (2.38-10) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up tabix (1.19+ds-1.1+b1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up libssw0:amd64 (1.1-14+b1) ... Setting up libevdev2:amd64 (1.13.1+dfsg-1+b1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up publicsuffix (20231001.0357-0.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up python-tables-data (3.7.0-10) ... Setting up exonerate (2.4.0-5+b1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsquid1t64:amd64 (1.9g+cvs20050121-15.1) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libcc1-0:amd64 (14-20240330-1) ... Setting up dbus-bin (1.14.10-4+b1) ... Setting up libargs4j-java (2.33-2) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up gpg (2.2.40-3) ... Setting up libgudev-1.0-0:amd64 (238-5) ... Setting up liblsan0:amd64 (14-20240330-1) ... Setting up libblas-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.1.3-1) ... Setting up libitm1:amd64 (14-20240330-1) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libargtable2-0 (13-2) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libwacom-common (2.10.0-2) ... Setting up libxkbcommon0:amd64 (1.6.0-1+b1) ... Setting up libwayland-client0:amd64 (1.22.0-2.1+b1) ... Setting up libctf0:amd64 (2.42-4) ... Setting up pinentry-curses (1.2.1-3+b2) ... Setting up manpages-dev (6.05.01-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up gpg-agent (2.2.40-3) ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket → /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket → /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket → /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket → /usr/lib/systemd/user/gpg-agent.socket. Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up kraken (1.1.1-4) ... Setting up libxcb-xinput0:amd64 (1.15-1) ... Setting up libpng-tools (1.6.43-5) ... Setting up alsa-ucm-conf (1.2.11-1.1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libwacom9:amd64 (2.10.0-2) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-24) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up gpgsm (2.2.40-3) ... Setting up libcommons-parent-java (56-1) ... Setting up libxcb-keysyms1:amd64 (0.4.0-1+b2) ... Setting up libxcb-shape0:amd64 (1.15-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libcloudproviders0:amd64 (0.3.6-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxcb-render-util0:amd64 (0.3.9-1+b1) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libxcb-icccm4:amd64 (0.4.1-1.1+b1) ... Setting up dbus-daemon (1.14.10-4+b1) ... Setting up clustalo (1.2.4-8) ... Setting up tm-align (20190822+dfsg-2) ... Setting up biosquid (1.9g+cvs20050121-15.1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up libcolord2:amd64 (1.4.7-1+b1) ... Setting up libxcb-util1:amd64 (0.4.0-1+b1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up libinput-bin (1.25.0-1+b2) ... Setting up libxcb-xkb1:amd64 (1.15-1) ... Setting up libxcb-image0:amd64 (0.4.0-2+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libdconf1:amd64 (0.40.0-4+b2) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up dirmngr (2.2.40-3) ... Created symlink /etc/systemd/user/sockets.target.wants/dirmngr.socket → /usr/lib/systemd/user/dirmngr.socket. Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.38.2-4) ... Setting up libgprofng0:amd64 (2.42-4) ... Setting up libxcb-xinerama0:amd64 (1.15-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-12) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libdata-dump-perl (1.25-1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libxml-xpathengine-perl (0.14-2) ... Setting up dbus (1.14.10-4+b1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libio-compress-brotli-perl (0.004001-2+b2) ... Setting up shared-mime-info (2.4-4) ... Setting up python-odf-doc (1.4.2-2) ... Setting up libxkbcommon-x11-0:amd64 (1.6.0-1+b1) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libdpkg-perl (1.22.6) ... Setting up libtimedate-perl (2.3300-2) ... Setting up gpg-wks-server (2.2.40-3) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libgcc-13-dev:amd64 (13.2.0-24) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up libwayland-cursor0:amd64 (1.22.0-2.1+b1) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up mummer (3.23+dfsg-8) ... Setting up hmmer2 (2.3.2+dfsg-12) ... Setting up libpam-systemd:amd64 (255.5-1) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libfcgi-perl (0.82+ds-3+b1) ... Setting up libc6-dev:amd64 (2.38-10) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libxkbfile1:amd64 (1:1.1.0-1+b1) ... Setting up lynx (2.9.1-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libgfortran-13-dev:amd64 (13.2.0-24) ... Setting up mailcap (3.70+nmu1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up liburi-perl (5.28-1) ... Setting up libxmuu1:amd64 (2:1.1.3-3+b2) ... Setting up libx11-protocol-perl (0.56-9) ... Setting up libstdc++-13-dev:amd64 (13.2.0-24) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libllvmspirvlib17:amd64 (17.0.0-5) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up binutils-x86-64-linux-gnu (2.42-4) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7) ... Setting up libio-sessiondata-perl (1.03-3) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libinput10:amd64 (1.25.0-1+b2) ... Setting up vcftools (0.1.16-3+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libibverbs1:amd64 (50.0-2+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libncurses-dev:amd64 (6.4+20240414-1) ... Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libtie-ixhash-perl (1.23-4) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libpcre2-dev:amd64 (10.42-4+b1) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up cpp-13 (13.2.0-24) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libfont-afm-perl (1.20-4) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libgbm1:amd64 (24.0.6-1+b1) ... Setting up ibverbs-providers:amd64 (50.0-2+b1) ... Setting up libfile-fcntllock-perl (0.22-4+b3) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up openssh-client (1:9.7p1-4) ... Setting up libio-stringy-perl (2.111-3) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-24) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libauthen-sasl-perl (2.1700-1) ... Setting up libconvert-binhex-perl (1.125-3) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.6-1+b1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up python3 (3.11.8-1) ... Setting up rubygems-integration (1.18) ... Setting up fsa (1.15.9+dfsg-6) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up binutils (2.42-4) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up libreadline-dev:amd64 (8.2-4) ... Setting up python3-freetype (2.4.0-1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up gfortran-13-x86-64-linux-gnu (13.2.0-24) ... Setting up python3-webencodings (0.5.1-5) ... Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-tz (2024.1-2) ... Setting up dpkg-dev (1.22.6) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up bowtie2 (2.5.3-1) ... Setting up python3-cykhash (2.0.0-3) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up ncbi-blast+ (2.12.0+ds-4+b1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-simplejson (3.19.2-1+b1) ... Setting up libclang-cpp17t64 (1:17.0.6-12) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up dbus-user-session (1.14.10-4+b1) ... Setting up libqt5core5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up libegl-mesa0:amd64 (24.0.6-1+b1) ... Setting up python3-packaging (24.0-1) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up python3-certifi (2023.11.17-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up python3-cycler (0.12.1-1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libxv1:amd64 (2:1.0.11-1.1+b1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up gcc-13 (13.2.0-24) ... Setting up python3-idna (3.6-2) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up python3-html5lib (1.1-6) ... Setting up libfile-desktopentry-perl (0.22-3) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-3) ... Setting up hisat2 (2.2.1-4+b3) ... Setting up xauth (1:1.1.2-1) ... Setting up libgdk-pixbuf2.0-bin (2.42.10+dfsg-3+b3) ... Setting up python3-lxml:amd64 (5.1.0-1) ... Setting up cpp (4:13.2.0-7) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up libegl1:amd64 (1.7.0-1+b1) ... Setting up python3-et-xmlfile (1.0.1-2.1) ... Setting up gnupg (2.2.40-3) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up librdmacm1t64:amd64 (50.0-2+b1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-msgpack (1.0.3-3+b1) ... Setting up libcairo-gobject2:amd64 (1.18.0-3+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-argcomplete (3.3.0-1) ... Setting up python3-cssselect (1.2.0-4) ... Setting up python3-appdirs (1.4.4-4) ... Setting up libalgorithm-diff-xs-perl:amd64 (0.04-8+b3) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up python3-soupsieve (2.5-1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libalgorithm-merge-perl (0.08-5) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-7) ... Setting up python3-more-itertools (10.2.0-1) ... Setting up mesa-opencl-icd:amd64 (24.0.6-1+b1) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.12-7) ... Setting up mesa-vulkan-drivers:amd64 (24.0.6-1+b1) ... Setting up libfile-mimeinfo-perl (0.35-1) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-argh (0.31.2-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up metaphlan2-data (2.6.0+ds-4) ... Settings: Output files: "/usr/share/metaphlan2/db_v20/mpa_v20_m200.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: /var/lib/metaphlan2-data/markers.fasta Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:06 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 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: 00:00:34 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: 00:00:18 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 Split 1, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.01651e+08 (target: 133417046) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (133417047) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 73481450 for bucket 1 (Using difference cover) Sorting block time: 00:01:09 Returning block of 73481451 for bucket 1 Getting block 2 of 7 Reserving size (133417047) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 112624089 for bucket 2 (Using difference cover) Sorting block time: 00:01:48 Returning block of 112624090 for bucket 2 Getting block 3 of 7 Reserving size (133417047) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 114872559 for bucket 3 (Using difference cover) Sorting block time: 00:01:45 Returning block of 114872560 for bucket 3 Getting block 4 of 7 Reserving size (133417047) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 96915131 for bucket 4 (Using difference cover) Sorting block time: 00:01:22 Returning block of 96915132 for bucket 4 Getting block 5 of 7 Reserving size (133417047) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 110535719 for bucket 5 (Using difference cover) Sorting block time: 00:01:31 Returning block of 110535720 for bucket 5 Getting block 6 of 7 Reserving size (133417047) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 79173124 for bucket 6 (Using difference cover) Sorting block time: 00:01:06 Returning block of 79173125 for bucket 6 Getting block 7 of 7 Reserving size (133417047) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 123955509 for bucket 7 (Using difference cover) Sorting block time: 00:01:53 Returning block of 123955510 for bucket 7 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.tmp Wrote 177889404 bytes to secondary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.2.bt2.tmp 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: 00:18:14 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 177889396 Using parameters --bmax 133417047 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 133417047 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:35 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: 00:00:18 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 Split 1, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.01651e+08 (target: 133417046) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (133417047) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 91718666 for bucket 1 (Using difference cover) Sorting block time: 00:01:24 Returning block of 91718667 for bucket 1 Getting block 2 of 7 Reserving size (133417047) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 107401525 for bucket 2 (Using difference cover) Sorting block time: 00:01:46 Returning block of 107401526 for bucket 2 Getting block 3 of 7 Reserving size (133417047) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 113723363 for bucket 3 (Using difference cover) Sorting block time: 00:01:50 Returning block of 113723364 for bucket 3 Getting block 4 of 7 Reserving size (133417047) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 95758918 for bucket 4 (Using difference cover) Sorting block time: 00:01:31 Returning block of 95758919 for bucket 4 Getting block 5 of 7 Reserving size (133417047) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 104659734 for bucket 5 (Using difference cover) Sorting block time: 00:01:39 Returning block of 104659735 for bucket 5 Getting block 6 of 7 Reserving size (133417047) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 116767199 for bucket 6 (Using difference cover) Sorting block time: 00:01:31 Returning block of 116767200 for bucket 6 Getting block 7 of 7 Reserving size (133417047) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 81528176 for bucket 7 (Using difference cover) Sorting block time: 00:00:58 Returning block of 81528177 for bucket 7 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.tmp Wrote 177889404 bytes to secondary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.2.bt2.tmp 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: 00:17:40 Renaming /usr/share/metaphlan2/db_v20/mpa_v20_m200.3.bt2.tmp to /usr/share/metaphlan2/db_v20/mpa_v20_m200.3.bt2 Renaming /usr/share/metaphlan2/db_v20/mpa_v20_m200.4.bt2.tmp to /usr/share/metaphlan2/db_v20/mpa_v20_m200.4.bt2 Renaming /usr/share/metaphlan2/db_v20/mpa_v20_m200.1.bt2.tmp to /usr/share/metaphlan2/db_v20/mpa_v20_m200.1.bt2 Renaming /usr/share/metaphlan2/db_v20/mpa_v20_m200.2.bt2.tmp to /usr/share/metaphlan2/db_v20/mpa_v20_m200.2.bt2 Renaming /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.1.bt2.tmp to /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.1.bt2 Renaming /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.2.bt2.tmp to /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.2.bt2 Metaphlan2 data are properly created. Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-7) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libqt5dbus5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libglx-mesa0:amd64 (24.0.6-1+b1) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-hisat2 (2.2.1-4) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-24) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up bowtie (1.3.1-3) ... Setting up python3-joblib (1.3.2-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.4.6-4) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up python3-olefile (0.46-3) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ... Setting up libpng-dev:amd64 (1.6.43-5) ... Setting up libqt5network5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libhmsbeagle1v5:amd64 (3.1.2+dfsg-13+b1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up libqt5script5:amd64 (5.15.10+dfsg-3+b1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3) ... Setting up isympy-common (1.12-7) ... Setting up libxxf86dga1:amd64 (2:1.1.5-1+b1) ... Setting up mrbayes (3.2.7a-7+b1) ... Setting up libqt5xml5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up python3-yaml (6.0.1-2) ... Setting up dconf-service (0.40.0-4+b2) ... Setting up libhtml-format-perl (2.16-2) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libqt5test5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-click (8.1.7-1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up x11-xserver-utils (7.7+10+b1) ... Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up python3-bs4 (4.12.3-1) ... Setting up gcc (4:13.2.0-7) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-fs (2.4.16-4) ... Setting up librsvg2-2:amd64 (2.58.0+dfsg-1) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-xopen (1.7.0-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up libnet-smtp-ssl-perl (1.04-2) ... Setting up libmailtools-perl (2.21-3) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libqt5qml5:amd64 (5.15.10+dfsg-2+b2) ... Setting up gfortran-13 (13.2.0-24) ... Setting up python3-openpyxl (3.1.2+dfsg-6) ... Setting up isympy3 (1.12-7) ... Setting up libatspi2.0-0t64:amd64 (2.52.0-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up r-base-core (4.4.0-2) ... Creating config file /etc/R/Renviron with new version Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up librsvg2-common:amd64 (2.58.0+dfsg-1) ... Setting up r-cran-lattice (0.22-5-1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up python3-reportlab (4.2.0-2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up zutty (0.15.2.20240411+dfsg1-1) ... update-alternatives: using /usr/bin/zutty to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode Setting up libhttp-daemon-perl (6.16-1) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up r-cran-cluster (2.1.6-1) ... Setting up x11-utils (7.7+6+b1) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up spades (3.15.5+dfsg-7) ... Setting up python3-contourpy (1.0.7-3) ... Setting up libsis-jhdf5-jni (19.04.1+dfsg-4+b1) ... Setting up libatk-wrapper-java (0.40.0-3) ... Setting up libngs-java:amd64 (3.0.3+dfsg-7) ... Setting up python3-dendropy (4.6.1-1) ... Setting up libhtsjdk-java (4.1.0+dfsg-1) ... Setting up python3-dnaio (1.2.0-2) ... Setting up python3-odf (1.4.2-2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.52.0-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up g++-13 (13.2.0-24) ... Setting up r-cran-boot (1.3-30-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-pybedtools (0.10.0-1) ... Setting up libqt5qmlmodels5:amd64 (5.15.10+dfsg-2+b2) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b2) ... Setting up libsis-jhdf5-java (19.04.1+dfsg-4) ... Setting up python3-tables-lib (3.7.0-10+b1) ... Setting up r-cran-spatial (7.3-17-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-8) ... Setting up python-odf-tools (1.4.2-2) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-1) ... Setting up python3-h5py-serial (3.10.0-1+b3) ... Setting up python3-tk:amd64 (3.12.3-1) ... Setting up r-cran-foreign (0.8.86-1) ... Setting up libmime-tools-perl (5.515-1) ... Setting up gfortran (4:13.2.0-7) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libatk-wrapper-java-jni:amd64 (0.40.0-3+b2) ... Setting up libqt5gui5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up r-base-html (4.4.0-2) ... Setting up python3-pandas (2.1.4+dfsg-8) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-cutadapt (4.7-2) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-h5py (3.10.0-1) ... Setting up python3-bottleneck (1.3.5+ds1-3+b1) ... Setting up python3-sklearn (1.4.2+dfsg-1) ... Setting up python3-numexpr (2.10.0-2) ... Setting up libxml-simple-perl (2.25-2) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up r-cran-kernsmooth (2.23-22-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up g++ (4:13.2.0-7) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up build-essential (12.10) ... Setting up libqt5quick5:amd64 (5.15.10+dfsg-2+b2) ... Setting up libgtk-3-common (3.24.41-4) ... Setting up gsettings-desktop-schemas (46.0-1) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up libucx0:amd64 (1.16.0+ds-5) ... Setting up r-base-dev (4.4.0-2) ... Setting up r-cran-class (7.3-22-2) ... Setting up libqt5widgets5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up cutadapt (4.7-2) ... Setting up python3-hmmlearn (0.3.0-5) ... Setting up libqt5svg5:amd64 (5.15.10-2+b2) ... Setting up r-cran-survival (3.5-8-1) ... Setting up python3-tables (3.7.0-10) ... Setting up libqt5waylandclient5:amd64 (5.15.10-2+b2) ... Setting up libqt5waylandcompositor5:amd64 (5.15.10-2+b2) ... Setting up python3-biom-format (2.1.15.2-3) ... Setting up libgtk-3-0t64:amd64 (3.24.41-4) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up at-spi2-core (2.52.0-1) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up phyml (3:3.3.20220408-3+b1) ... Setting up macs (3.0.1-2) ... Setting up libqt5printsupport5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libqt5scripttools5:amd64 (5.15.10+dfsg-3+b1) ... Setting up qtwayland5:amd64 (5.15.10-2+b2) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up libgtk-3-bin (3.24.41-4) ... Setting up qt5-gtk-platformtheme:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up ugene (50.0+dfsg-1) ... Setting up r-recommended (4.4.0-2) ... Setting up r-base (4.4.0-2) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up python3-fonttools (4.46.0-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up libxml-parser-perl (2.47-1+b2) ... Setting up python3-matplotlib (3.6.3-2) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up libxml-twig-perl (1:3.52-3) ... Setting up libnet-dbus-perl (1.2.0-2+b2) ... Setting up ruby (1:3.1+nmu1) ... Setting up rake (13.0.6-3) ... Setting up libxml-sax-expat-perl (0.51-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libsoap-lite-perl (1.27-3) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libxmlrpc-lite-perl (0.717-5) ... Processing triggers for libc-bin (2.38-10) ... Processing triggers for systemd (255.5-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up trimmomatic (0.39+dfsg-2) ... Setting up fastqc (0.12.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Setting up metaphlan (4.0.4-1) ... Setting up python3-gffutils (0.13-1) ... Setting up bcftools (1.20-1) ... Processing triggers for menu (2.1.50) ... Setting up blends-common (0.7.6) ... Setting up med-config (3.8.1) ... info: Selecting GID from range 100 to 999 ... info: Adding group `med' (GID 153) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Processing triggers for ca-certificates-java (20240118) ... done. 43m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'apt-get', '-y', 'install', 'ugene=50.0+dfsg-1'] 43m30.9s INFO: Running scripts post_install 43m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_install_exceptions'] 43m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', 'tmp/scripts/post_install_exceptions'] 43m51.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 43m53.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 43m58.6s ERROR: WARN: Broken symlinks: /etc/vconsole.conf -> default/keyboard /etc/default/locale -> ../locale.conf /usr/lib/x86_64-linux-gnu/qt-default/qtchooser/default.conf -> ../../../../share/qtchooser/qt5-x86_64-linux-gnu.conf (libqt5core5t64:amd64) 43m59.2s INFO: /bin converted to /usr/bin by /usr merge 43m59.2s INFO: /lib converted to /usr/lib by /usr merge 43m59.2s INFO: /lib/firmware converted to /usr/lib/firmware by /usr merge 43m59.2s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 43m59.2s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 43m59.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 43m59.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 44m2.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', '-ac', '--ignore-obsolete'] 52m57.8s DUMP: debsums: missing file /srv/piuparts.debian.org/tmp/tmpi9tror4s/var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 52m57.8s DEBUG: Command failed (status=2), but ignoring error: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi9tror4s', '-ac', '--ignore-obsolete'] 52m57.8s ERROR: FAIL: debsums reports modifications inside the chroot: debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 53m0.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/shm'] 53m0.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/shm'] 53m0.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/console'] 53m0.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/console'] 53m0.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/ptmx'] 53m0.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/ptmx'] 53m0.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/pts'] 53m0.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/dev/pts'] 53m0.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/proc'] 53m0.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9tror4s/proc'] 53m0.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 53m1.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi9tror4s'] 53m1.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpi9tror4s 53m1.5s ERROR: piuparts run ends. ret=1 End: 2024-05-15 22:06:14 GMT