0s autopkgtest [20:06:48]: starting date and time: 2024-03-24 20:06:48+0000 0s autopkgtest [20:06:48]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [20:06:48]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jis3gfeu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:procps --apt-upgrade velvetoptimiser --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=procps/2:4.0.4-4ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-11.secgroup --name adt-noble-s390x-velvetoptimiser-20240324-200648-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 101s autopkgtest [20:08:29]: testbed dpkg architecture: s390x 101s autopkgtest [20:08:29]: testbed apt version: 2.7.12 101s autopkgtest [20:08:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 103s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 104s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 104s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 104s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 104s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 104s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 104s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 104s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 104s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4195 kB] 104s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 104s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.2 kB] 104s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 107s Fetched 9603 kB in 3s (2780 kB/s) 108s Reading package lists... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade... 113s The following packages will be upgraded: 113s libproc2-0 procps 114s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 784 kB of archives. 114s After this operation, 4096 B of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu2 [60.1 kB] 114s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x procps s390x 2:4.0.4-4ubuntu2 [724 kB] 115s Fetched 784 kB in 1s (981 kB/s) 115s (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 ... 52170 files and directories currently installed.) 115s Preparing to unpack .../libproc2-0_2%3a4.0.4-4ubuntu2_s390x.deb ... 115s Unpacking libproc2-0:s390x (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 115s Preparing to unpack .../procps_2%3a4.0.4-4ubuntu2_s390x.deb ... 115s Unpacking procps (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 115s Setting up libproc2-0:s390x (2:4.0.4-4ubuntu2) ... 115s Setting up procps (2:4.0.4-4ubuntu2) ... 116s Processing triggers for man-db (2.12.0-3) ... 117s Processing triggers for libc-bin (2.39-0ubuntu6) ... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Unknown architecture, assuming PC-style ttyS0 119s sh: Attempting to set up Debian/Ubuntu apt sources automatically 119s sh: Distribution appears to be Ubuntu 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s eatmydata is already the newest version (131-1). 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s dbus is already the newest version (1.14.10-4ubuntu1). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s rng-tools-debian is already the newest version (2.4). 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s The following packages will be REMOVED: 123s cloud-init* python3-configobj* python3-debconf* 124s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 124s After this operation, 3256 kB disk space will be freed. 124s (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 ... 52171 files and directories currently installed.) 124s Removing cloud-init (24.1.2-0ubuntu1) ... 124s Removing python3-configobj (5.0.8-3) ... 124s Removing python3-debconf (1.5.86) ... 125s Processing triggers for man-db (2.12.0-3) ... 125s (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 ... 51782 files and directories currently installed.) 125s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 126s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 126s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 126s invoke-rc.d: policy-rc.d denied execution of try-restart. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s linux-generic is already the newest version (6.8.0-11.11+1). 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 128s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 128s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 131s Reading package lists... 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Calculating upgrade... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s autopkgtest [20:09:02]: rebooting testbed after setup commands that affected boot 153s autopkgtest [20:09:21]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 156s autopkgtest [20:09:24]: @@@@@@@@@@@@@@@@@@@@ apt-source velvetoptimiser 160s Get:1 http://ftpmaster.internal/ubuntu noble/universe velvetoptimiser 2.2.6-5 (dsc) [2106 B] 160s Get:2 http://ftpmaster.internal/ubuntu noble/universe velvetoptimiser 2.2.6-5 (tar) [5886 kB] 160s Get:3 http://ftpmaster.internal/ubuntu noble/universe velvetoptimiser 2.2.6-5 (diff) [4080 B] 161s gpgv: Signature made Tue Dec 6 15:26:05 2022 UTC 161s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 161s gpgv: issuer "tille@debian.org" 161s gpgv: Can't check signature: No public key 161s dpkg-source: warning: cannot verify inline signature for ./velvetoptimiser_2.2.6-5.dsc: no acceptable signature found 161s autopkgtest [20:09:29]: testing package velvetoptimiser version 2.2.6-5 161s autopkgtest [20:09:29]: build not needed 162s autopkgtest [20:09:30]: test run-unit-test: preparing testbed 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 164s Done 165s The following additional packages will be installed: 165s bioperl libalgorithm-diff-perl libbio-perl-perl libcapture-tiny-perl 165s libclass-data-inheritable-perl libdata-stag-perl libdevel-stacktrace-perl 165s libexception-class-perl libgomp1 libio-string-perl libsub-uplevel-perl 165s libtest-deep-perl libtest-differences-perl libtest-exception-perl 165s libtest-most-perl libtest-warn-perl libtext-diff-perl velvet velvetoptimiser 165s Suggested packages: 165s libxml-sax-expatxs-perl velvet-example 165s Recommended packages: 165s bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl 165s libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl 165s liburi-perl libxml-simple-perl libyaml-perl libace-perl 165s liblist-moreutils-perl libxml-twig-perl libset-scalar-perl 165s libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl 165s libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl 165s libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl 165s libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl 165s libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl 165s libsort-naturally-perl libspreadsheet-parseexcel-perl 165s libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl 165s libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl 165s libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk 165s libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl 165s libxml-perl 165s The following NEW packages will be installed: 165s autopkgtest-satdep bioperl libalgorithm-diff-perl libbio-perl-perl 165s libcapture-tiny-perl libclass-data-inheritable-perl libdata-stag-perl 165s libdevel-stacktrace-perl libexception-class-perl libgomp1 libio-string-perl 165s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 165s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 165s velvet velvetoptimiser 165s 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 4314 kB/4315 kB of archives. 165s After this operation, 12.8 MB of additional disk space will be used. 165s Get:1 /tmp/autopkgtest.GogJoX/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B] 165s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libio-string-perl all 1.08-4 [11.1 kB] 165s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libdata-stag-perl all 0.14-3 [372 kB] 165s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libbio-perl-perl all 1.7.8-1 [2580 kB] 166s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libclass-data-inheritable-perl all 0.08-3 [8084 B] 166s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 166s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libexception-class-perl all 1.45-1 [28.6 kB] 166s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libtest-deep-perl all 1.204-1 [47.1 kB] 166s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libcapture-tiny-perl all 0.48-2 [20.2 kB] 166s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libalgorithm-diff-perl all 1.201-1 [41.8 kB] 166s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x libtext-diff-perl all 1.45-2 [25.6 kB] 166s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x libtest-differences-perl all 0.71-1 [15.8 kB] 166s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x libsub-uplevel-perl all 0.2800-3 [11.6 kB] 166s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x libtest-exception-perl all 0.43-3 [13.4 kB] 166s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x libtest-warn-perl all 0.37-2 [12.6 kB] 166s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x libtest-most-perl all 0.38-1 [21.5 kB] 166s Get:17 http://ftpmaster.internal/ubuntu noble/universe s390x bioperl all 1.7.8-1 [216 kB] 166s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 166s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x velvet s390x 1.2.10+dfsg1-8 [689 kB] 166s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x velvetoptimiser all 2.2.6-5 [25.2 kB] 167s Fetched 4314 kB in 2s (2874 kB/s) 167s Selecting previously unselected package libio-string-perl. 167s (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 ... 51727 files and directories currently installed.) 167s Preparing to unpack .../00-libio-string-perl_1.08-4_all.deb ... 167s Unpacking libio-string-perl (1.08-4) ... 167s Selecting previously unselected package libdata-stag-perl. 167s Preparing to unpack .../01-libdata-stag-perl_0.14-3_all.deb ... 167s Unpacking libdata-stag-perl (0.14-3) ... 167s Selecting previously unselected package libbio-perl-perl. 167s Preparing to unpack .../02-libbio-perl-perl_1.7.8-1_all.deb ... 167s Unpacking libbio-perl-perl (1.7.8-1) ... 167s Selecting previously unselected package libclass-data-inheritable-perl. 167s Preparing to unpack .../03-libclass-data-inheritable-perl_0.08-3_all.deb ... 167s Unpacking libclass-data-inheritable-perl (0.08-3) ... 167s Selecting previously unselected package libdevel-stacktrace-perl. 167s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 167s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 167s Selecting previously unselected package libexception-class-perl. 167s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 167s Unpacking libexception-class-perl (1.45-1) ... 167s Selecting previously unselected package libtest-deep-perl. 167s Preparing to unpack .../06-libtest-deep-perl_1.204-1_all.deb ... 167s Unpacking libtest-deep-perl (1.204-1) ... 167s Selecting previously unselected package libcapture-tiny-perl. 167s Preparing to unpack .../07-libcapture-tiny-perl_0.48-2_all.deb ... 167s Unpacking libcapture-tiny-perl (0.48-2) ... 167s Selecting previously unselected package libalgorithm-diff-perl. 167s Preparing to unpack .../08-libalgorithm-diff-perl_1.201-1_all.deb ... 167s Unpacking libalgorithm-diff-perl (1.201-1) ... 167s Selecting previously unselected package libtext-diff-perl. 167s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 167s Unpacking libtext-diff-perl (1.45-2) ... 168s Selecting previously unselected package libtest-differences-perl. 168s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 168s Unpacking libtest-differences-perl (0.71-1) ... 168s Selecting previously unselected package libsub-uplevel-perl. 168s Preparing to unpack .../11-libsub-uplevel-perl_0.2800-3_all.deb ... 168s Unpacking libsub-uplevel-perl (0.2800-3) ... 168s Selecting previously unselected package libtest-exception-perl. 168s Preparing to unpack .../12-libtest-exception-perl_0.43-3_all.deb ... 168s Unpacking libtest-exception-perl (0.43-3) ... 168s Selecting previously unselected package libtest-warn-perl. 168s Preparing to unpack .../13-libtest-warn-perl_0.37-2_all.deb ... 168s Unpacking libtest-warn-perl (0.37-2) ... 168s Selecting previously unselected package libtest-most-perl. 168s Preparing to unpack .../14-libtest-most-perl_0.38-1_all.deb ... 168s Unpacking libtest-most-perl (0.38-1) ... 168s Selecting previously unselected package bioperl. 168s Preparing to unpack .../15-bioperl_1.7.8-1_all.deb ... 168s Unpacking bioperl (1.7.8-1) ... 168s Selecting previously unselected package libgomp1:s390x. 168s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 168s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 168s Selecting previously unselected package velvet. 168s Preparing to unpack .../17-velvet_1.2.10+dfsg1-8_s390x.deb ... 168s Unpacking velvet (1.2.10+dfsg1-8) ... 168s Selecting previously unselected package velvetoptimiser. 168s Preparing to unpack .../18-velvetoptimiser_2.2.6-5_all.deb ... 168s Unpacking velvetoptimiser (2.2.6-5) ... 168s Selecting previously unselected package autopkgtest-satdep. 168s Preparing to unpack .../19-1-autopkgtest-satdep.deb ... 168s Unpacking autopkgtest-satdep (0) ... 168s Setting up libtest-deep-perl (1.204-1) ... 168s Setting up libalgorithm-diff-perl (1.201-1) ... 168s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 168s Setting up libio-string-perl (1.08-4) ... 168s Setting up libclass-data-inheritable-perl (0.08-3) ... 168s Setting up libtext-diff-perl (1.45-2) ... 168s Setting up libcapture-tiny-perl (0.48-2) ... 168s Setting up libdata-stag-perl (0.14-3) ... 168s Setting up libsub-uplevel-perl (0.2800-3) ... 168s Setting up libdevel-stacktrace-perl (2.0500-1) ... 168s Setting up libbio-perl-perl (1.7.8-1) ... 168s Setting up velvet (1.2.10+dfsg1-8) ... 168s Setting up libtest-warn-perl (0.37-2) ... 168s Setting up libtest-differences-perl (0.71-1) ... 168s Setting up libexception-class-perl (1.45-1) ... 168s Setting up libtest-exception-perl (0.43-3) ... 168s Setting up libtest-most-perl (0.38-1) ... 168s Setting up bioperl (1.7.8-1) ... 168s Setting up velvetoptimiser (2.2.6-5) ... 168s Setting up autopkgtest-satdep (0) ... 168s Processing triggers for man-db (2.12.0-3) ... 169s Processing triggers for libc-bin (2.39-0ubuntu6) ... 172s (Reading database ... 53216 files and directories currently installed.) 172s Removing autopkgtest-satdep (0) ... 172s autopkgtest [20:09:40]: test run-unit-test: [----------------------- 173s Running VelvetOptimiser on short test data. 173s 173s **************************************************** 173s VelvetOptimiser.pl Version 2.2.6 173s **************************************************** 173s Number of CPUs available: 1 173s Current free RAM: 2.245GB 173s Velvet OMP compiler setting: 1 173s Mar 24 20:09:39 Starting to check input parameters. 173s Start hash value too high. New start hash value is 31. 173s End hash value not in workable range. New end hash value is 31. 173s Velveth parameter string OK. 173s Mar 24 20:09:39 Finished checking input parameters. 173s Velvet details: 173s Velvet version: 1.2.09 173s Compiled categories: 2 173s Compiled max kmer length: 31 173s Maximum number of velvetinstances to run: 1 173s Will run velvet optimiser with the following paramters: 173s Velveth parameter string: 173s -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz 173s Velveth start hash values: 31 173s Velveth end hash value: 31 173s Velveth hash step value: 2 173s Velvetg minimum coverage cutoff to use: 0 173s 173s Read tracking for final assembly off. 173s Mar 24 20:09:39 Beginning velveth runs. 173s Mar 24 20:09:39 Running velveth with hash value: 31. 173s Logfile name: 24-03-2024-20-09-39_Logfile.txt 174s Mar 24 20:09:41 Velveth with hash value 31 finished. 175s Mar 24 20:09:41 Finished velveth runs. 175s Mar 24 20:09:41 Beginning vanilla velvetg runs. 175s Mar 24 20:09:41 Running vanilla velvetg on hash value: 31 178s Mar 24 20:09:44 Velvetg on hash value: 31 finished. 178s Mar 24 20:09:44 Hash value of best assembly by assembly score: 31 178s Mar 24 20:09:44 Optimisation routine chosen for best assembly: shortPaired 178s Mar 24 20:09:44 Looking for the expected coverage 178s Mar 24 20:09:44 Expected coverage set to 14 178s Mar 24 20:09:44 Setting assembly short insert length(s) to auto 178s Mar 24 20:09:44 Beginning coverage cutoff optimisation 178s Mar 24 20:09:44 Setting cov_cutoff to 6.922. 181s Mar 24 20:09:48 Setting cov_cutoff to 4.278. 181s Looking for best cutoff score between 0.000 and 11.200 181s Max cutoff lies between 0.000 & 6.922 181s fc = 177101 fd = 177349 abs diff = 248 181s Mar 24 20:09:49 Setting cov_cutoff to 2.644. 181s Max cutoff lies between 0.000 & 4.278 181s fc = 177349 fd = 177349 abs diff = 0 181s Mar 24 20:09:49 Setting cov_cutoff to 1.634. 181s Max cutoff lies between 0.000 & 2.644 181s fc = 177349 fd = 177380 abs diff = 31 181s Mar 24 20:09:49 Setting cov_cutoff to 1.010. 181s Max cutoff lies between 0.000 & 1.634 181s fc = 177380 fd = 177380 abs diff = 0 181s Mar 24 20:09:49 Setting cov_cutoff to 0.624. 182s Max cutoff lies between 0.624 & 1.634 182s fc = 177380 fd = 177314 abs diff = 66 182s Mar 24 20:09:50 Setting cov_cutoff to 1.249. 182s Max cutoff lies between 0.624 & 1.249 182s fc = 177380 fd = 177380 abs diff = 0 182s Mar 24 20:09:50 Setting cov_cutoff to 0.863. 182s Optimum value of cutoff is 1.25 182s Took 7 iterations 182s Mar 24 20:09:50 182s 182s 182s Final optimised assembly details: 182s ******************************************************** 182s Assembly id: 1 182s Assembly score: 177314 182s Velveth timestamp: Mar 24 2024 20:09:41 182s Velvetg timestamp: Mar 24 2024 20:09:50 182s Velveth version: 1.2.09 182s Velvetg version: 1.2.09 182s Readfile(s): -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz 182s Velveth parameter string: auto_data_31 31 -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz 182s Velvetg parameter string: auto_data_31 -clean yes -exp_cov 14 -cov_cutoff 0.862764507476839 182s Assembly directory: /tmp/autopkgtest.GogJoX/autopkgtest_tmp/auto_data_31 182s Velvet hash value: 31 182s Roadmap file size: 1496358 182s Total number of contigs: 121 182s n50: 131988 182s length of longest contig: 131988 182s Total bases in contigs: 187506 182s Number of contigs > 1k: 5 182s Total bases in contigs > 1k: 177314 182s Paired Library insert stats: 182s Paired-end library 1 has length: 399, sample standard deviation: 39 182s Paired-end library 1 has length: 399, sample standard deviation: 40 182s ********************************************************** 182s 182s 182s Assembly output files are in the following directory: 182s test_out 182s 182s Number of contigs in final assembly: 182s 182s **************************************************** 182s VelvetOptimiser.pl Version 2.2.6 182s **************************************************** 182s Number of CPUs available: 1 182s Current free RAM: 2.227GB 182s Velvet OMP compiler setting: 1 182s Mar 24 20:09:50 Starting to check input parameters. 182s Start hash value too high. New start hash value is 31. 182s End hash value not in workable range. New end hash value is 31. 182s Velveth parameter string OK. 182s Mar 24 20:09:50 Finished checking input parameters. 182s Velvet details: 182s Velvet version: 1.2.09 182s Compiled categories: 2 182s Compiled max kmer length: 31 182s Maximum number of velvetinstances to run: 1 182s Will run velvet optimiser with the following paramters: 182s Velveth parameter string: 182s -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz -longPaired -fastq.gz -separate data/test_long_R1.fq.gz data/test_long_R2.fq.gz 182s Velveth start hash values: 31 182s Velveth end hash value: 31 182s Velveth hash step value: 4 182s Velvetg minimum coverage cutoff to use: 0 182s 182s Read tracking for final assembly off. 182s Mar 24 20:09:50 Beginning velveth runs. 182s Mar 24 20:09:50 Running velveth with hash value: 31. 182s 121 182s Running VelvetOptimiser on short and long test data. 182s Logfile name: 24-03-2024-20-09-50_Logfile.txt 185s Mar 24 20:09:53 Velveth with hash value 31 finished. 185s Mar 24 20:09:53 Finished velveth runs. 185s Mar 24 20:09:53 Beginning vanilla velvetg runs. 185s Mar 24 20:09:53 Running vanilla velvetg on hash value: 31 190s Mar 24 20:09:58 Velvetg on hash value: 31 finished. 190s Mar 24 20:09:58 Hash value of best assembly by assembly score: 31 190s Mar 24 20:09:58 Optimisation routine chosen for best assembly: shortLongPaired 190s Mar 24 20:09:58 Looking for the expected coverage 190s Mar 24 20:09:58 Expected coverage set to 2235 190s Mar 24 20:09:58 Setting assembly short insert length(s) to auto 190s Mar 24 20:09:58 Setting assembly long insert length auto 190s Mar 24 20:09:58 Beginning coverage cutoff optimisation 190s Mar 24 20:09:58 Setting cov_cutoff to 1104.984. 195s ********** 195s Warning: Assembly score for assembly_id 1 is 0 195s You may want to consider choosing a different optimisation variable or function. 195s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 195s ********** 195s Mar 24 20:10:03 Setting cov_cutoff to 683.016. 195s ********** 195s Warning: Assembly score for assembly_id 1 is 0 195s You may want to consider choosing a different optimisation variable or function. 195s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 195s ********** 195s Looking for best cutoff score between 0.000 and 1788.000 195s Max cutoff lies between 0.000 & 1104.984 195s fc = 0 fd = 0 abs diff = 0 195s Mar 24 20:10:03 Setting cov_cutoff to 422.104. 196s ********** 196s Warning: Assembly score for assembly_id 1 is 0 196s You may want to consider choosing a different optimisation variable or function. 196s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 196s ********** 196s Max cutoff lies between 0.000 & 683.016 196s fc = 0 fd = 0 abs diff = 0 196s Mar 24 20:10:04 Setting cov_cutoff to 260.912. 196s ********** 196s Warning: Assembly score for assembly_id 1 is 0 196s You may want to consider choosing a different optimisation variable or function. 196s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 196s ********** 196s Max cutoff lies between 0.000 & 422.104 196s fc = 0 fd = 0 abs diff = 0 196s Mar 24 20:10:04 Setting cov_cutoff to 161.244. 196s ********** 196s Warning: Assembly score for assembly_id 1 is 0 196s You may want to consider choosing a different optimisation variable or function. 196s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 196s ********** 196s Max cutoff lies between 0.000 & 260.912 196s fc = 0 fd = 0 abs diff = 0 196s Mar 24 20:10:04 Setting cov_cutoff to 99.668. 197s ********** 197s Warning: Assembly score for assembly_id 1 is 0 197s You may want to consider choosing a different optimisation variable or function. 197s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 197s ********** 197s Max cutoff lies between 0.000 & 161.244 197s fc = 0 fd = 0 abs diff = 0 197s Mar 24 20:10:05 Setting cov_cutoff to 61.595. 197s ********** 197s Warning: Assembly score for assembly_id 1 is 0 197s You may want to consider choosing a different optimisation variable or function. 197s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 197s ********** 197s Max cutoff lies between 0.000 & 99.668 197s fc = 0 fd = 0 abs diff = 0 197s Mar 24 20:10:05 Setting cov_cutoff to 38.073. 197s ********** 197s Warning: Assembly score for assembly_id 1 is 0 197s You may want to consider choosing a different optimisation variable or function. 197s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 197s ********** 197s Max cutoff lies between 0.000 & 61.595 197s fc = 0 fd = 0 abs diff = 0 197s Mar 24 20:10:05 Setting cov_cutoff to 23.529. 198s Max cutoff lies between 0.000 & 38.073 198s fc = 0 fd = 5376 abs diff = 5376 198s Mar 24 20:10:06 Setting cov_cutoff to 14.544. 198s Max cutoff lies between 0.000 & 23.529 198s fc = 5376 fd = 110154 abs diff = 104778 198s Mar 24 20:10:06 Setting cov_cutoff to 8.988. 199s Max cutoff lies between 0.000 & 14.544 199s fc = 110154 fd = 179893 abs diff = 69739 199s Mar 24 20:10:07 Setting cov_cutoff to 5.556. 199s Max cutoff lies between 0.000 & 8.988 199s fc = 179893 fd = 180411 abs diff = 518 199s Mar 24 20:10:07 Setting cov_cutoff to 3.433. 200s Max cutoff lies between 0.000 & 5.556 200s fc = 180411 fd = 180659 abs diff = 248 200s Mar 24 20:10:08 Setting cov_cutoff to 2.122. 200s Max cutoff lies between 0.000 & 3.433 200s fc = 180659 fd = 180659 abs diff = 0 200s Mar 24 20:10:08 Setting cov_cutoff to 1.312. 201s Max cutoff lies between 0.000 & 2.122 201s fc = 180659 fd = 180659 abs diff = 0 201s Mar 24 20:10:09 Setting cov_cutoff to 0.811. 202s Max cutoff lies between 0.811 & 2.122 202s fc = 180659 fd = 179182 abs diff = 1477 202s Mar 24 20:10:09 Setting cov_cutoff to 1.621. 202s Max cutoff lies between 0.811 & 1.621 202s fc = 180659 fd = 180659 abs diff = 0 202s Mar 24 20:10:10 Setting cov_cutoff to 1.120. 202s Optimum value of cutoff is 1.62 202s Took 17 iterations 202s Mar 24 20:10:10 202s 202s 202s Final optimised assembly details: 202s ******************************************************** 202s Assembly id: 1 202s Assembly score: 180659 202s Velveth timestamp: Mar 24 2024 20:09:53 202s Velvetg timestamp: Mar 24 2024 20:10:10 202s Velveth version: 1.2.09 202s Velvetg version: 1.2.09 202s Readfile(s): -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz -longPaired -fastq.gz -separate data/test_long_R1.fq.gz data/test_long_R2.fq.gz 202s Velveth parameter string: auto_data_31 31 -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz -longPaired -fastq.gz -separate data/test_long_R1.fq.gz data/test_long_R2.fq.gz 202s Velvetg parameter string: auto_data_31 -long_mult_cutoff 3 -clean yes -exp_cov 2235 -cov_cutoff 1.12036253377189 202s Assembly directory: /tmp/autopkgtest.GogJoX/autopkgtest_tmp/auto_data_31 202s Velvet hash value: 31 202s Roadmap file size: 3225258 202s Total number of contigs: 6 202s n50: 180659 202s length of longest contig: 180659 202s Total bases in contigs: 181888 202s Number of contigs > 1k: 1 202s Total bases in contigs > 1k: 180659 202s Paired Library insert stats: 202s Paired-end library 1 has length: 399, sample standard deviation: 39 202s Paired-end library 3 has length: -2744, sample standard deviation: 1397 202s Paired-end library 1 has length: 399, sample standard deviation: 39 202s Paired-end library 3 has length: -39747, sample standard deviation: 42590 202s Paired-end library 1 has length: 399, sample standard deviation: 39 202s Paired-end library 3 has length: -76924, sample standard deviation: 51129 202s ********************************************************** 202s 202s 202s Assembly output files are in the following directory: 202s test_out_2 202s 202s Number of contigs in final assembly: 202s 6 202s Estimation of memory test: 202s 202s **************************************************** 202s VelvetOptimiser.pl Version 2.2.6 202s **************************************************** 202s Number of CPUs available: 1 202s Current free RAM: 2.267GB 202s Velvet OMP compiler setting: 1 202s Mar 24 20:10:10 Starting to check input parameters. 202s Start hash value too high. New start hash value is 31. 202s End hash value not in workable range. New end hash value is 31. 202s Velveth parameter string OK. 202s Mar 24 20:10:10 Finished checking input parameters. 202s 202s Memory use estimation only! Script will terminate after showing results. 202s 202s Velvet details: 202s Velvet version: 1.2.09 202s Compiled categories: 2 202s Compiled max kmer length: 31 202s Maximum number of velvetinstances to run: 1 202s Will run velvet optimiser with the following paramters: 202s Velveth parameter string: 202s -shortPaired -fastq.gz -separate mutant_R1.fq.gz mutant_R2.fq.gz -longPaired -fastq.gz -separate data/test_long_R1.fq.gz data/test_long_R2.fq.gz 202s Velveth start hash values: 31 202s Velveth end hash value: 31 202s Velveth hash step value: 2 202s Logfile name: 24-03-2024-20-10-10_Logfile.txt 202s Velvetg minimum coverage cutoff to use: 0 202s 202s Read tracking for final assembly off. 202s File: data/test_long_R1.fq.gz has 13150 reads of length 150 202s File: data/test_long_R2.fq.gz has 13150 reads of length 150 202s Total reads: 0.0 million. Avg length: 150.0 202s 202s Memory use estimated to be: 1.1GB for 1 threads. 202s 202s You should have enough memory to complete this job. (Though this estimate is no guarantee..) 203s autopkgtest [20:10:11]: test run-unit-test: -----------------------] 203s autopkgtest [20:10:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 203s run-unit-test PASS 204s autopkgtest [20:10:12]: @@@@@@@@@@@@@@@@@@@@ summary 204s run-unit-test PASS 215s Creating nova instance adt-noble-s390x-velvetoptimiser-20240324-200648-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240324.img (UUID e13d5247-1289-46d4-b3a9-3aa9fa45fdc9)...