0s autopkgtest [14:03:28]: starting date and time: 2024-07-12 14:03:28+0000 0s autopkgtest [14:03:28]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [14:03:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9h9cjvnb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade sortmerna --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-40.secgroup --name adt-oracular-amd64-sortmerna-20240712-140327-juju-7f2275-prod-proposed-migration-environment-2-9b24dcc4-7a04-46fc-9bfb-12c855dd690e --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 823s autopkgtest [14:17:11]: testbed dpkg architecture: amd64 824s autopkgtest [14:17:12]: testbed apt version: 2.9.6 824s autopkgtest [14:17:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 869s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 869s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 869s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [345 kB] 869s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [45.3 kB] 869s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 869s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [99.7 kB] 869s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [73.0 kB] 869s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B] 869s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 869s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 869s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 869s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [240 kB] 870s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [374 kB] 870s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B] 870s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 870s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B] 870s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 871s Fetched 1378 kB in 0s (4578 kB/s) 871s Reading package lists... 888s Reading package lists... 889s Building dependency tree... 889s Reading state information... 890s Calculating upgrade... 890s The following packages will be upgraded: 890s binutils binutils-common binutils-x86-64-linux-gnu gir1.2-glib-2.0 890s libbinutils libc-bin libc-dev-bin libc-devtools libc6 libc6-dev 890s libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data libgprofng0 890s libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssl 891s 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 891s Need to get 21.2 MB of archives. 891s After this operation, 423 kB of additional disk space will be used. 891s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB] 891s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB] 891s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB] 891s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB] 891s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB] 891s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.2.2-1ubuntu1 [2138 kB] 891s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 gir1.2-glib-2.0 amd64 2.80.4-1ubuntu1 [182 kB] 891s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-0t64 amd64 2.80.4-1ubuntu1 [1545 kB] 891s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB] 891s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB] 891s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.2.2-1ubuntu1 [1122 kB] 891s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.62.1-2 [75.1 kB] 891s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42.50.20240710-1ubuntu1 [860 kB] 891s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42.50.20240710-1ubuntu1 [95.6 kB] 891s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42.50.20240710-1ubuntu1 [97.6 kB] 891s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240710-1ubuntu1 [2477 kB] 891s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42.50.20240710-1ubuntu1 [574 kB] 891s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42.50.20240710-1ubuntu1 [18.1 kB] 891s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42.50.20240710-1ubuntu1 [243 kB] 891s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42.50.20240710-1ubuntu1 [14.4 kB] 891s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libnss3 amd64 2:3.102-1 [1399 kB] 891s Preconfiguring packages ... 891s Fetched 21.2 MB in 0s (85.2 MB/s) 892s (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 ... 74487 files and directories currently installed.) 892s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ... 892s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 892s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ... 892s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 892s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ... 892s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 892s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ... 892s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 892s Setting up libc6:amd64 (2.39-3.1ubuntu3) ... 892s Error: Could not restart systemd, systemd binary not working 893s (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 ... 74487 files and directories currently installed.) 893s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ... 893s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 893s Setting up libc-bin (2.39-3.1ubuntu3) ... 893s (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 ... 74487 files and directories currently installed.) 893s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_amd64.deb ... 893s Unpacking libssl3t64:amd64 (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 893s Setting up libssl3t64:amd64 (3.2.2-1ubuntu1) ... 893s (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 ... 74487 files and directories currently installed.) 893s Preparing to unpack .../00-gir1.2-glib-2.0_2.80.4-1ubuntu1_amd64.deb ... 893s Unpacking gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 893s Preparing to unpack .../01-libglib2.0-0t64_2.80.4-1ubuntu1_amd64.deb ... 893s Unpacking libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 893s Preparing to unpack .../02-libglib2.0-data_2.80.4-1ubuntu1_all.deb ... 893s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 893s Preparing to unpack .../03-locales_2.39-3.1ubuntu3_all.deb ... 893s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 893s Preparing to unpack .../04-openssl_3.2.2-1ubuntu1_amd64.deb ... 893s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 893s Preparing to unpack .../05-libnghttp2-14_1.62.1-2_amd64.deb ... 893s Unpacking libnghttp2-14:amd64 (1.62.1-2) over (1.62.1-1) ... 893s Preparing to unpack .../06-libgprofng0_2.42.50.20240710-1ubuntu1_amd64.deb ... 893s Unpacking libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 893s Preparing to unpack .../07-libctf0_2.42.50.20240710-1ubuntu1_amd64.deb ... 893s Unpacking libctf0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 893s Preparing to unpack .../08-libctf-nobfd0_2.42.50.20240710-1ubuntu1_amd64.deb ... 893s Unpacking libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 894s Preparing to unpack .../09-binutils-x86-64-linux-gnu_2.42.50.20240710-1ubuntu1_amd64.deb ... 894s Unpacking binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 894s Preparing to unpack .../10-libbinutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 894s Unpacking libbinutils:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 894s Preparing to unpack .../11-binutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 894s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 894s Preparing to unpack .../12-binutils-common_2.42.50.20240710-1ubuntu1_amd64.deb ... 894s Unpacking binutils-common:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 894s Preparing to unpack .../13-libsframe1_2.42.50.20240710-1ubuntu1_amd64.deb ... 894s Unpacking libsframe1:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 894s Preparing to unpack .../14-libnss3_2%3a3.102-1_amd64.deb ... 894s Unpacking libnss3:amd64 (2:3.102-1) over (2:3.101-1) ... 894s Setting up binutils-common:amd64 (2.42.50.20240710-1ubuntu1) ... 894s Setting up libnghttp2-14:amd64 (1.62.1-2) ... 894s Setting up libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) ... 894s Setting up libnss3:amd64 (2:3.102-1) ... 894s Setting up locales (2.39-3.1ubuntu3) ... 895s Generating locales (this might take a while)... 896s en_US.UTF-8... done 896s Generation complete. 896s Setting up libsframe1:amd64 (2.42.50.20240710-1ubuntu1) ... 896s Setting up libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) ... 896s No schema files found: doing nothing. 896s Setting up libglib2.0-data (2.80.4-1ubuntu1) ... 896s Setting up gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) ... 896s Setting up libbinutils:amd64 (2.42.50.20240710-1ubuntu1) ... 896s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 896s Setting up openssl (3.2.2-1ubuntu1) ... 896s Installing new version of config file /etc/ssl/openssl.cnf ... 896s Setting up libc-devtools (2.39-3.1ubuntu3) ... 896s Setting up libctf0:amd64 (2.42.50.20240710-1ubuntu1) ... 896s Setting up libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) ... 896s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ... 896s Setting up binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) ... 896s Setting up binutils (2.42.50.20240710-1ubuntu1) ... 896s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 896s Processing triggers for systemd (256-1ubuntu1) ... 897s Processing triggers for man-db (2.12.1-2) ... 899s Reading package lists... 899s Building dependency tree... 899s Reading state information... 899s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 900s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 900s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 900s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 900s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 901s Reading package lists... 901s Reading package lists... 901s Building dependency tree... 901s Reading state information... 902s Calculating upgrade... 902s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 902s Reading package lists... 903s Building dependency tree... 903s Reading state information... 903s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 918s autopkgtest [14:18:46]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 918s autopkgtest [14:18:46]: @@@@@@@@@@@@@@@@@@@@ apt-source sortmerna 920s Get:1 http://ftpmaster.internal/ubuntu oracular/universe sortmerna 4.3.7-1build1 (dsc) [2207 B] 920s Get:2 http://ftpmaster.internal/ubuntu oracular/universe sortmerna 4.3.7-1build1 (tar) [31.4 MB] 920s Get:3 http://ftpmaster.internal/ubuntu oracular/universe sortmerna 4.3.7-1build1 (diff) [10.7 kB] 920s gpgv: Signature made Wed Jun 5 12:53:53 2024 UTC 920s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 920s gpgv: Can't check signature: No public key 920s dpkg-source: warning: cannot verify inline signature for ./sortmerna_4.3.7-1build1.dsc: no acceptable signature found 921s autopkgtest [14:18:49]: testing package sortmerna version 4.3.7-1build1 930s autopkgtest [14:18:58]: build not needed 950s autopkgtest [14:19:18]: test run-unit-test: preparing testbed 959s Reading package lists... 959s Building dependency tree... 959s Reading state information... 959s Starting pkgProblemResolver with broken count: 0 959s Starting 2 pkgProblemResolver with broken count: 0 959s Done 960s The following additional packages will be installed: 960s libgflags2.2 librocksdb9.2 libsnappy1v5 sortmerna 960s The following NEW packages will be installed: 960s autopkgtest-satdep libgflags2.2 librocksdb9.2 libsnappy1v5 sortmerna 960s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 960s Need to get 3882 kB/3883 kB of archives. 960s After this operation, 12.6 MB of additional disk space will be used. 960s Get:1 /tmp/autopkgtest.UyEb2G/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 960s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgflags2.2 amd64 2.2.2-2build1 [74.5 kB] 960s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 960s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 librocksdb9.2 amd64 9.2.1-3 [3273 kB] 960s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 sortmerna amd64 4.3.7-1build1 [504 kB] 961s Fetched 3882 kB in 0s (22.8 MB/s) 961s Selecting previously unselected package libgflags2.2. 961s (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 ... 74486 files and directories currently installed.) 961s Preparing to unpack .../libgflags2.2_2.2.2-2build1_amd64.deb ... 961s Unpacking libgflags2.2 (2.2.2-2build1) ... 961s Selecting previously unselected package libsnappy1v5:amd64. 961s Preparing to unpack .../libsnappy1v5_1.2.1-1_amd64.deb ... 961s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 961s Selecting previously unselected package librocksdb9.2. 961s Preparing to unpack .../librocksdb9.2_9.2.1-3_amd64.deb ... 961s Unpacking librocksdb9.2 (9.2.1-3) ... 961s Selecting previously unselected package sortmerna. 961s Preparing to unpack .../sortmerna_4.3.7-1build1_amd64.deb ... 961s Unpacking sortmerna (4.3.7-1build1) ... 961s Selecting previously unselected package autopkgtest-satdep. 961s Preparing to unpack .../1-autopkgtest-satdep.deb ... 961s Unpacking autopkgtest-satdep (0) ... 961s Setting up libsnappy1v5:amd64 (1.2.1-1) ... 961s Setting up libgflags2.2 (2.2.2-2build1) ... 961s Setting up librocksdb9.2 (9.2.1-3) ... 961s Setting up sortmerna (4.3.7-1build1) ... 961s /usr/share/sortmerna/scripts/run.py:258: SyntaxWarning: invalid escape sequence '\(' 961s logd['results']['num_hits'][1] = int((re.split(' = | \(', line)[1]).strip()) 961s /usr/share/sortmerna/scripts/run.py:260: SyntaxWarning: invalid escape sequence '\(' 961s logd['results']['num_fail'][1] = int((re.split(' = | \(', line)[1]).strip()) 961s Setting up autopkgtest-satdep (0) ... 961s Processing triggers for man-db (2.12.1-2) ... 962s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 975s (Reading database ... 74526 files and directories currently installed.) 975s Removing autopkgtest-satdep (0) ... 988s autopkgtest [14:19:56]: test run-unit-test: [----------------------- 988s === Test 0 (superficial verifications) === 988s [process:1393] === Options processing starts ... === 988s Found value: sortmerna 988s Found flag: --version 988s [process:1483] Processing option: version with value: 988s 988s SortMeRNA version 4.3.7 988s Build Date: Jun 5 2024 988s sortmerna_build_git_sha:@0@ 988s sortmerna_build_git_date:@2024/06/05 12:53:49@ 988s [process:1393] === Options processing starts ... === 988s Found value: sortmerna 988s Found flag: -h 988s [process:1483] Processing option: h with value: 988s 988s Program: SortMeRNA version 4.3.7 988s Copyright: 2016-2020 Clarity Genomics BVBA: 988s Turnhoutseweg 30, 2340 Beerse, Belgium 988s 2014-2016 Knight Lab: 988s Department of Pediatrics, UCSD, La Jolla 988s 2012-2014 Bonsai Bioinformatics Research Group: 988s LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe 988s Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the 988s implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 988s See the GNU Lesser General Public License for more details. 988s Contributors: Jenya Kopylova jenya.kopylov@gmail.com 988s Laurent Noé laurent.noe@lifl.fr 988s Pierre Pericard pierre.pericard@lifl.fr 988s Daniel McDonald wasade@gmail.com 988s Mikaël Salson mikael.salson@lifl.fr 988s Hélène Touzet helene.touzet@lifl.fr 988s Rob Knight robknight@ucsd.edu 988s 988s Usage: sortmerna -ref FILE [-ref FILE] -reads FWD_READS [-reads REV_READS] [OPTIONS]: 988s ------------------------------------------------------------------------------------------------------------- 988s | option type-format description default | 988s ------------------------------------------------------------------------------------------------------------- 988s 988s [REQUIRED] 988s --ref PATH Required Reference file (FASTA) absolute or relative path. 988s 988s Use mutliple times, once per a reference file 988s 988s 988s --reads PATH Required Raw reads file (FASTA/FASTQ/FASTA.GZ/FASTQ.GZ). 988s 988s Use twice for files with paired reads. 988s The file extensions are Not important. The program automatically 988s recognizes the file format as flat/compressed, fasta/fastq 988s 988s 988s 988s [COMMON] 988s --workdir PATH Optional Workspace directory USRDIR/sortmerna/run/ 988s 988s Default structure: WORKDIR/ 988s idx/ (References index) 988s kvdb/ (Key-value storage for alignments) 988s out/ (processing output) 988s readb/ (pre-processed reads/index) 988s 988s 988s --kvdb PATH Optional Directory for Key-value database WORKDIR/kvdb 988s 988s KVDB is used for storing the alignment results. 988s 988s 988s --idx-dir PATH Optional Directory for storing Reference index. WORKDIR/idx 988s 988s 988s --readb PATH Optional Storage for pre-processed reads WORKDIR/readb/ 988s 988s Directory storing the split reads, or the random access index of compressed reads 988s 988s 988s --fastx BOOL Optional Output aligned reads into FASTA/FASTQ file 988s --sam BOOL Optional Output SAM alignment for aligned reads. 988s 988s 988s --SQ BOOL Optional Add SQ tags to the SAM file 988s 988s 988s --blast STR Optional output alignments in various Blast-like formats 988s 988s Sample values: '0' - pairwise 988s '1' - tabular (Blast - m 8 format) 988s '1 cigar' - tabular + column for CIGAR 988s '1 cigar qcov' - tabular + columns for CIGAR and query coverage 988s '1 cigar qcov qstrand' - tabular + columns for CIGAR, query coverage, 988s and strand 988s 988s 988s --aligned STR/BOOL Optional Aligned reads file prefix [dir/][pfx] WORKDIR/out/aligned 988s 988s Directory and file prefix for aligned output i.e. each 988s output file goes into the specified directory with the given prefix. 988s The appropriate extension: (fasta|fastq|blast|sam|etc) is automatically added. 988s Both 'dir' and 'pfx' are optional. 988s The 'dir' can be a relative or an absolute path. 988s If 'dir' is not specified, the output is created in the WORKDIR/out/ 988s If 'pfx' is not specified, the prefix 'aligned' is used 988s Examples: 988s '-aligned $MYDIR/dir_1/dir_2/1' -> $MYDIR/dir_1/dir_2/1.fasta 988s '-aligned dir_1/apfx' -> $PWD/dir_1/apfx.fasta 988s '-aligned dir_1/' -> $PWD/aligned.fasta 988s '-aligned apfx' -> $PWD/apfx.fasta 988s '-aligned (no argument)' -> WORKDIR/out/aligned.fasta 988s 988s 988s --other STR/BOOL Optional Non-aligned reads file prefix [dir/][pfx] WORKDIR/out/other 988s 988s Directory and file prefix for non-aligned output i.e. each 988s output file goes into the specified directory with the given prefix. 988s The appropriate extension: (fasta|fastq|blast|sam|etc) is automatically added. 988s Must be used with 'fastx'. 988s Both 'dir' and 'pfx' are optional. 988s The 'dir' can be a relative or an absolute path. 988s If 'dir' is not specified, the output is created in the WORKDIR/out/ 988s If 'pfx' is not specified, the prefix 'other' is used 988s Examples: 988s '-other $MYDIR/dir_1/dir_2/1' -> $MYDIR/dir_1/dir_2/1.fasta 988s '-other dir_1/apfx' -> $PWD/dir_1/apfx.fasta 988s '-other dir_1/' -> $PWD/dir_1/other.fasta 988s '-other apfx' -> $PWD/apfx.fasta 988s '-other (no argument)' -> aligned_out/other.fasta 988s i.e. the same output directory 988s as used for aligned output 988s 988s 988s --num_alignments INT Optional Positive integer (INT >=0). 988s 988s If used with '-no-best' reports first INT alignments per read reaching 988s E-value threshold, which allows to lower the CPU time and memory use. 988s Otherwise outputs INT best alignments. 988s If INT = 0, all alignments are output 988s 988s 988s --no-best BOOL Optional Disable best alignments search False 988s 988s The 'best' alignment is the highest scoring alignment out of All alignments of a read, 988s and the read can potentially be aligned (reaching E-value threshold) to multiple reference 988s sequences. 988s By default the program searches for best alignments i.e. performs an exhaustive search 988s over all references. Using '-no-best' will make the program to search just 988s the first N alignments, where N is set using '-num_alignments' i.e. 1 by default. 988s 988s 988s --min_lis INT Optional Search only alignments that have the LIS 2 988s of at least N seeds long 988s 988s LIS stands for Longest Increasing Subsequence. It is computed using seeds, which 988s are k-mers common to the read and the reference sequence. Sorted sequences of such seeds 988s are used to filter the candidate references prior performing the Smith-Waterman alignment. 988s 988s 988s --print_all_reads BOOL Optional Output null alignment strings for non-aligned reads False 988s to SAM and/or BLAST tabular files 988s 988s --paired BOOL Optional Flags paired reads False 988s 988s If a single reads file is provided, use this option to indicate 988s the file contains interleaved paired reads when neither 988s 'paired_in' | 'paired_out' | 'out2' | 'sout' are specified. 988s 988s 988s --paired_in BOOL Optional Flags the paired-end reads as Aligned, False 988s when either of them is Aligned. 988s 988s With this option both reads are output into Aligned FASTA/Q file 988s Must be used with 'fastx'. 988s Mutually exclusive with 'paired_out'. 988s 988s 988s --paired_out BOOL Optional Flags the paired-end reads as Non-aligned, False 988s when either of them is non-aligned. 988s 988s With this option both reads are output into Non-Aligned FASTA/Q file 988s Must be used with 'fastx'. 988s Mutually exclusive with 'paired_in'. 988s 988s 988s --out2 BOOL Optional Output paired reads into separate files. False 988s 988s Must be used with 'fastx'. 988s If a single reads file is provided, this options implies interleaved paired reads 988s When used with 'sout', four (4) output files for aligned reads will be generated: 988s 'aligned-paired-fwd, aligned-paired-rev, aligned-singleton-fwd, aligned-singleton-rev'. 988s If 'other' option is also used, eight (8) output files will be generated. 988s 988s 988s --sout BOOL Optional Separate paired and singleton aligned reads. False 988s 988s To be used with 'fastx'. 988s If a single reads file is provided, this options implies interleaved paired reads 988s Cannot be used with 'paired_in' | 'paired_out' 988s 988s 988s --zip-out STR/BOOL Optional Controls the output compression '-1' 988s 988s By default the report files are produced in the same format as the input i.e. 988s if the reads files are compressed (gz), the output is also compressed. 988s The default behaviour can be overriden by using '-zip-out'. 988s The possible values: '1/true/t/yes/y' 988s '0/false/f/no/n' 988s '-1' (the same format as input - default) 988s The values are Not case sensitive i.e. 'Yes, YES, yEs, Y, y' are all OK 988s Examples: 988s '-reads freads.gz -zip-out n' : generate flat output when the input is compressed 988s '-reads freads.flat -zip-out' : compress the output when the input files are flat 988s 988s 988s --match INT Optional SW score (positive integer) for a match. 2 988s 988s --mismatch INT Optional SW penalty (negative integer) for a mismatch. -3 988s 988s --gap_open INT Optional SW penalty (positive integer) for introducing a gap. 5 988s 988s --gap_ext INT Optional SW penalty (positive integer) for extending a gap. 2 988s 988s -e DOUBLE Optional E-value threshold. 1 988s 988s Defines the 'statistical significance' of a local alignment. 988s Exponentially correllates with the Minimal Alignment score. 988s Higher E-values (100, 1000, ...) cause More reads to Pass the alignment threshold 988s 988s 988s -F BOOL Optional Search only the forward strand. False 988s 988s -N BOOL Optional SW penalty for ambiguous letters (N's) scored 988s as --mismatch 988s 988s -R BOOL Optional Search only the reverse-complementary strand. False 988s 988s 988s [OTU_PICKING] 988s --id INT Optional %%id similarity threshold (the alignment 0.97 988s must still pass the E-value threshold). 988s 988s --coverage INT Optional %%query coverage threshold (the alignment must 0.97 988s still pass the E-value threshold) 988s 988s --de_novo_otu BOOL Optional Output FASTA file with 'de novo' reads False 988s 988s Read is 'de novo' if its alignment score passes E-value threshold, but both the identity 988s '-id', and the '-coverage' are below their corresponding thresholds 988s i.e. ID < %%id and COV < %%cov 988s 988s 988s --otu_map BOOL Optional Output OTU map (input to QIIME's make_otu_table.py). False 988s Cannot be used with 'no-best because 988s the grouping is done around the best alignment' 988s 988s 988s [ADVANCED] 988s --passes INT,INT,INT Optional Three intervals at which to place the seed on L,L/2,3 988s the read (L is the seed length) 988s 988s --edges INT Optional Number (or percent if INT followed by %% sign) of 4 988s nucleotides to add to each edge of the read 988s prior to SW local alignment 988s 988s --num_seeds BOOL Optional Number of seeds matched before searching 2 988s for candidate LIS 988s 988s --full_search INT Optional Search for all 0-error and 1-error seed False 988s matches in the index rather than stopping 988s after finding a 0-error match (<1%% gain in 988s sensitivity with up four-fold decrease in speed) 988s 988s --pid BOOL Optional Add pid to output file names. False 988s 988s -a INT Optional DEPRECATED in favour of '-threads'. Number of numCores 988s processing threads to use. 988s Automatically redirects to '-threads' 988s 988s --threads INT Optional Number of Processing threads to use 2 988s 988s 988s [INDEXING] 988s --index INT Optional Build reference database index 2 988s 988s By default when this option is not used, the program checks the reference index and 988s builds it if not already existing. 988s This can be changed by using '-index' as follows: 988s '-index 0' - skip indexing. If the index does not exist, the program will terminate 988s and warn to build the index prior performing the alignment 988s '-index 1' - only perform the indexing and terminate 988s '-index 2' - the default behaviour, the same as when not using this option at all 988s 988s 988s -L DOUBLE Optional Indexing: seed length. 18 988s 988s -m DOUBLE Optional Indexing: the amount of memory (in Mbytes) for 3072 988s building the index. 988s 988s -v BOOL Optional Produce verbose output when building the index True 988s 988s --interval INT Optional Indexing: Positive integer: index every Nth L-mer in 1 988s the reference database e.g. '-interval 2'. 988s 988s --max_pos INT Optional Indexing: maximum (integer) number of positions to 1000 988s store for each unique L-mer. 988s If 0 - all positions are stored. 988s 988s 988s [HELP] 988s -h BOOL Optional Print help information 988s 988s --version BOOL Optional Print SortMeRNA version number 988s 988s 988s [DEVELOPER] 988s --dbg_put_db BOOL Optional 988s --cmd BOOL Optional Launch an interactive session (command prompt) False 988s 988s --task INT Optional Processing Task 4 988s 988s Possible values: 0 - align. Only perform alignment 988s 1 - post-processing (log writing) 988s 2 - generate reports 988s 3 - align and post-process 988s 4 - all 988s 988s 988s --dbg-level INT Optional Debug level 0 988s 988s Controls verbosity of the execution trace. Default value of 0 corresponds to 988s the least verbose output. 988s The highest value currently is 2. 988s 988s 988s autopkgtest [14:19:56]: test run-unit-test: -----------------------] 997s autopkgtest [14:20:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 997s run-unit-test PASS (superficial) 1001s autopkgtest [14:20:09]: @@@@@@@@@@@@@@@@@@@@ summary 1001s run-unit-test PASS (superficial) 1042s nova [W] Skipping flock for amd64 1042s Creating nova instance adt-oracular-amd64-sortmerna-20240712-140327-juju-7f2275-prod-proposed-migration-environment-2-9b24dcc4-7a04-46fc-9bfb-12c855dd690e from image adt/ubuntu-oracular-amd64-server-20240711.img (UUID 4d65b1cc-a829-44fc-a8ac-cdd52093f9db)...