0s autopkgtest [20:01:56]: starting date and time: 2024-03-24 20:01:56+0000 0s autopkgtest [20:01:56]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [20:01:56]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.71z72kc6/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-ppc64el-25.secgroup --name adt-noble-ppc64el-velvetoptimiser-20240324-200156-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-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/ 94s autopkgtest [20:03:30]: testbed dpkg architecture: ppc64el 94s autopkgtest [20:03:30]: testbed apt version: 2.7.12 94s autopkgtest [20:03:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 95s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 95s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 95s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 95s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 95s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 96s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 96s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 96s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 96s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4263 kB] 96s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 96s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.1 kB] 96s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 99s Fetched 9694 kB in 2s (3967 kB/s) 99s Reading package lists... 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Calculating upgrade... 102s The following packages will be upgraded: 102s libproc2-0 procps 102s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 804 kB of archives. 102s After this operation, 4096 B of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu2 [68.8 kB] 103s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el procps ppc64el 2:4.0.4-4ubuntu2 [736 kB] 103s Fetched 804 kB in 1s (1153 kB/s) 103s (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 ... 70156 files and directories currently installed.) 103s Preparing to unpack .../libproc2-0_2%3a4.0.4-4ubuntu2_ppc64el.deb ... 103s Unpacking libproc2-0:ppc64el (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 103s Preparing to unpack .../procps_2%3a4.0.4-4ubuntu2_ppc64el.deb ... 103s Unpacking procps (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 103s Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu2) ... 103s Setting up procps (2:4.0.4-4ubuntu2) ... 104s Processing triggers for man-db (2.12.0-3) ... 105s Processing triggers for libc-bin (2.39-0ubuntu6) ... 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s sh: Attempting to set up Debian/Ubuntu apt sources automatically 106s sh: Distribution appears to be Ubuntu 107s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s eatmydata is already the newest version (131-1). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s dbus is already the newest version (1.14.10-4ubuntu1). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s rng-tools-debian is already the newest version (2.4). 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s The following packages will be REMOVED: 109s cloud-init* python3-configobj* python3-debconf* 110s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 110s After this operation, 3256 kB disk space will be freed. 110s (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 ... 70157 files and directories currently installed.) 110s Removing cloud-init (24.1.2-0ubuntu1) ... 110s Removing python3-configobj (5.0.8-3) ... 110s Removing python3-debconf (1.5.86) ... 110s Processing triggers for man-db (2.12.0-3) ... 111s (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 ... 69768 files and directories currently installed.) 111s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 111s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 111s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 111s invoke-rc.d: policy-rc.d denied execution of try-restart. 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s linux-generic is already the newest version (6.8.0-11.11+1). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 112s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 112s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 115s Reading package lists... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [20:03:52]: rebooting testbed after setup commands that affected boot 151s autopkgtest [20:04:27]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 154s autopkgtest [20:04:30]: @@@@@@@@@@@@@@@@@@@@ apt-source velvetoptimiser 157s Get:1 http://ftpmaster.internal/ubuntu noble/universe velvetoptimiser 2.2.6-5 (dsc) [2106 B] 157s Get:2 http://ftpmaster.internal/ubuntu noble/universe velvetoptimiser 2.2.6-5 (tar) [5886 kB] 157s Get:3 http://ftpmaster.internal/ubuntu noble/universe velvetoptimiser 2.2.6-5 (diff) [4080 B] 157s gpgv: Signature made Tue Dec 6 15:26:05 2022 UTC 157s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 157s gpgv: issuer "tille@debian.org" 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./velvetoptimiser_2.2.6-5.dsc: no acceptable signature found 157s autopkgtest [20:04:33]: testing package velvetoptimiser version 2.2.6-5 157s autopkgtest [20:04:33]: build not needed 158s autopkgtest [20:04:34]: test run-unit-test: preparing testbed 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 162s The following additional packages will be installed: 162s bioperl libalgorithm-diff-perl libbio-perl-perl libcapture-tiny-perl 162s libclass-data-inheritable-perl libdata-stag-perl libdevel-stacktrace-perl 162s libexception-class-perl libgomp1 libio-string-perl libsub-uplevel-perl 162s libtest-deep-perl libtest-differences-perl libtest-exception-perl 162s libtest-most-perl libtest-warn-perl libtext-diff-perl velvet velvetoptimiser 162s Suggested packages: 162s libxml-sax-expatxs-perl velvet-example 162s Recommended packages: 162s bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl 162s libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl 162s liburi-perl libxml-simple-perl libyaml-perl libace-perl 162s liblist-moreutils-perl libxml-twig-perl libset-scalar-perl 162s libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl 162s libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl 162s libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl 162s libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl 162s libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl 162s libsort-naturally-perl libspreadsheet-parseexcel-perl 162s libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl 162s libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl 162s libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk 162s libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl 162s libxml-perl 162s The following NEW packages will be installed: 162s autopkgtest-satdep bioperl libalgorithm-diff-perl libbio-perl-perl 162s libcapture-tiny-perl libclass-data-inheritable-perl libdata-stag-perl 162s libdevel-stacktrace-perl libexception-class-perl libgomp1 libio-string-perl 162s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 162s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 162s velvet velvetoptimiser 162s 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 4333 kB/4334 kB of archives. 162s After this operation, 13.1 MB of additional disk space will be used. 162s Get:1 /tmp/autopkgtest.z490qn/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 162s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libio-string-perl all 1.08-4 [11.1 kB] 163s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libdata-stag-perl all 0.14-3 [372 kB] 163s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbio-perl-perl all 1.7.8-1 [2580 kB] 163s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libclass-data-inheritable-perl all 0.08-3 [8084 B] 163s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 163s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libexception-class-perl all 1.45-1 [28.6 kB] 163s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtest-deep-perl all 1.204-1 [47.1 kB] 163s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libcapture-tiny-perl all 0.48-2 [20.2 kB] 163s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libalgorithm-diff-perl all 1.201-1 [41.8 kB] 163s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtext-diff-perl all 1.45-2 [25.6 kB] 163s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtest-differences-perl all 0.71-1 [15.8 kB] 163s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsub-uplevel-perl all 0.2800-3 [11.6 kB] 163s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtest-exception-perl all 0.43-3 [13.4 kB] 163s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtest-warn-perl all 0.37-2 [12.6 kB] 163s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libtest-most-perl all 0.38-1 [21.5 kB] 163s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el bioperl all 1.7.8-1 [216 kB] 164s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 164s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el velvet ppc64el 1.2.10+dfsg1-8 [699 kB] 164s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el velvetoptimiser all 2.2.6-5 [25.2 kB] 164s Fetched 4333 kB in 1s (3143 kB/s) 164s Selecting previously unselected package libio-string-perl. 164s (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 ... 69713 files and directories currently installed.) 164s Preparing to unpack .../00-libio-string-perl_1.08-4_all.deb ... 164s Unpacking libio-string-perl (1.08-4) ... 164s Selecting previously unselected package libdata-stag-perl. 164s Preparing to unpack .../01-libdata-stag-perl_0.14-3_all.deb ... 164s Unpacking libdata-stag-perl (0.14-3) ... 164s Selecting previously unselected package libbio-perl-perl. 164s Preparing to unpack .../02-libbio-perl-perl_1.7.8-1_all.deb ... 164s Unpacking libbio-perl-perl (1.7.8-1) ... 164s Selecting previously unselected package libclass-data-inheritable-perl. 164s Preparing to unpack .../03-libclass-data-inheritable-perl_0.08-3_all.deb ... 164s Unpacking libclass-data-inheritable-perl (0.08-3) ... 164s Selecting previously unselected package libdevel-stacktrace-perl. 164s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 164s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 164s Selecting previously unselected package libexception-class-perl. 164s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 164s Unpacking libexception-class-perl (1.45-1) ... 164s Selecting previously unselected package libtest-deep-perl. 164s Preparing to unpack .../06-libtest-deep-perl_1.204-1_all.deb ... 164s Unpacking libtest-deep-perl (1.204-1) ... 164s Selecting previously unselected package libcapture-tiny-perl. 164s Preparing to unpack .../07-libcapture-tiny-perl_0.48-2_all.deb ... 164s Unpacking libcapture-tiny-perl (0.48-2) ... 164s Selecting previously unselected package libalgorithm-diff-perl. 164s Preparing to unpack .../08-libalgorithm-diff-perl_1.201-1_all.deb ... 164s Unpacking libalgorithm-diff-perl (1.201-1) ... 164s Selecting previously unselected package libtext-diff-perl. 164s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 164s Unpacking libtext-diff-perl (1.45-2) ... 164s Selecting previously unselected package libtest-differences-perl. 164s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 164s Unpacking libtest-differences-perl (0.71-1) ... 164s Selecting previously unselected package libsub-uplevel-perl. 164s Preparing to unpack .../11-libsub-uplevel-perl_0.2800-3_all.deb ... 164s Unpacking libsub-uplevel-perl (0.2800-3) ... 164s Selecting previously unselected package libtest-exception-perl. 164s Preparing to unpack .../12-libtest-exception-perl_0.43-3_all.deb ... 164s Unpacking libtest-exception-perl (0.43-3) ... 164s Selecting previously unselected package libtest-warn-perl. 164s Preparing to unpack .../13-libtest-warn-perl_0.37-2_all.deb ... 164s Unpacking libtest-warn-perl (0.37-2) ... 164s Selecting previously unselected package libtest-most-perl. 164s Preparing to unpack .../14-libtest-most-perl_0.38-1_all.deb ... 164s Unpacking libtest-most-perl (0.38-1) ... 164s Selecting previously unselected package bioperl. 164s Preparing to unpack .../15-bioperl_1.7.8-1_all.deb ... 164s Unpacking bioperl (1.7.8-1) ... 164s Selecting previously unselected package libgomp1:ppc64el. 164s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 164s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 164s Selecting previously unselected package velvet. 164s Preparing to unpack .../17-velvet_1.2.10+dfsg1-8_ppc64el.deb ... 164s Unpacking velvet (1.2.10+dfsg1-8) ... 165s Selecting previously unselected package velvetoptimiser. 165s Preparing to unpack .../18-velvetoptimiser_2.2.6-5_all.deb ... 165s Unpacking velvetoptimiser (2.2.6-5) ... 165s Selecting previously unselected package autopkgtest-satdep. 165s Preparing to unpack .../19-1-autopkgtest-satdep.deb ... 165s Unpacking autopkgtest-satdep (0) ... 165s Setting up libtest-deep-perl (1.204-1) ... 165s Setting up libalgorithm-diff-perl (1.201-1) ... 165s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 165s Setting up libio-string-perl (1.08-4) ... 165s Setting up libclass-data-inheritable-perl (0.08-3) ... 165s Setting up libtext-diff-perl (1.45-2) ... 165s Setting up libcapture-tiny-perl (0.48-2) ... 165s Setting up libdata-stag-perl (0.14-3) ... 165s Setting up libsub-uplevel-perl (0.2800-3) ... 165s Setting up libdevel-stacktrace-perl (2.0500-1) ... 165s Setting up libbio-perl-perl (1.7.8-1) ... 165s Setting up velvet (1.2.10+dfsg1-8) ... 165s Setting up libtest-warn-perl (0.37-2) ... 165s Setting up libtest-differences-perl (0.71-1) ... 165s Setting up libexception-class-perl (1.45-1) ... 165s Setting up libtest-exception-perl (0.43-3) ... 165s Setting up libtest-most-perl (0.38-1) ... 165s Setting up bioperl (1.7.8-1) ... 165s Setting up velvetoptimiser (2.2.6-5) ... 165s Setting up autopkgtest-satdep (0) ... 165s Processing triggers for man-db (2.12.0-3) ... 165s Processing triggers for libc-bin (2.39-0ubuntu6) ... 167s (Reading database ... 71202 files and directories currently installed.) 167s Removing autopkgtest-satdep (0) ... 168s autopkgtest [20:04:44]: test run-unit-test: [----------------------- 168s Running VelvetOptimiser on short test data. 168s 168s **************************************************** 168s VelvetOptimiser.pl Version 2.2.6 168s **************************************************** 168s Number of CPUs available: 1 168s Current free RAM: 1.390GB 168s Velvet OMP compiler setting: 1 168s Mar 24 20:04:44 Starting to check input parameters. 168s Start hash value too high. New start hash value is 31. 168s End hash value not in workable range. New end hash value is 31. 168s Velveth parameter string OK. 168s Mar 24 20:04:44 Finished checking input parameters. 168s Velvet details: 168s Velvet version: 1.2.09 168s Compiled categories: 2 168s Compiled max kmer length: 31 168s Maximum number of velvetinstances to run: 1 168s Will run velvet optimiser with the following paramters: 168s Velveth parameter string: 168s -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz 168s Velveth start hash values: 31 168s Velveth end hash value: 31 168s Velveth hash step value: 2 168s Velvetg minimum coverage cutoff to use: 0 168s 168s Read tracking for final assembly off. 168s Mar 24 20:04:44 Beginning velveth runs. 168s Logfile name: 24-03-2024-20-04-44_Logfile.txt 168s Mar 24 20:04:44 Running velveth with hash value: 31. 169s Mar 24 20:04:44 Velveth with hash value 31 finished. 170s Mar 24 20:04:46 Finished velveth runs. 170s Mar 24 20:04:46 Beginning vanilla velvetg runs. 170s Mar 24 20:04:46 Running vanilla velvetg on hash value: 31 172s Mar 24 20:04:47 Velvetg on hash value: 31 finished. 172s Mar 24 20:04:48 Hash value of best assembly by assembly score: 31 172s Mar 24 20:04:48 Optimisation routine chosen for best assembly: shortPaired 172s Mar 24 20:04:48 Looking for the expected coverage 172s Mar 24 20:04:48 Expected coverage set to 14 172s Mar 24 20:04:48 Setting assembly short insert length(s) to auto 172s Mar 24 20:04:48 Beginning coverage cutoff optimisation 172s Mar 24 20:04:48 Setting cov_cutoff to 6.922. 173s Mar 24 20:04:49 Setting cov_cutoff to 4.278. 174s Looking for best cutoff score between 0.000 and 11.200 174s Max cutoff lies between 0.000 & 6.922 174s fc = 177101 fd = 177349 abs diff = 248 174s Mar 24 20:04:49 Setting cov_cutoff to 2.644. 174s Max cutoff lies between 0.000 & 4.278 174s fc = 177349 fd = 177349 abs diff = 0 174s Mar 24 20:04:49 Setting cov_cutoff to 1.634. 174s Max cutoff lies between 0.000 & 2.644 174s fc = 177349 fd = 177380 abs diff = 31 174s Mar 24 20:04:49 Setting cov_cutoff to 1.010. 174s Max cutoff lies between 0.000 & 1.634 174s fc = 177380 fd = 177380 abs diff = 0 174s Mar 24 20:04:50 Setting cov_cutoff to 0.624. 174s Max cutoff lies between 0.624 & 1.634 174s fc = 177380 fd = 177314 abs diff = 66 174s Mar 24 20:04:50 Setting cov_cutoff to 1.249. 174s Max cutoff lies between 0.624 & 1.249 174s fc = 177380 fd = 177380 abs diff = 0 174s Mar 24 20:04:50 Setting cov_cutoff to 0.863. 174s Optimum value of cutoff is 1.25 174s Took 7 iterations 174s Mar 24 20:04:50 174s 174s 174s Final optimised assembly details: 174s ******************************************************** 174s Assembly id: 1 174s Assembly score: 177314 174s Velveth timestamp: Mar 24 2024 20:04:44 174s Velvetg timestamp: Mar 24 2024 20:04:50 174s Velveth version: 1.2.09 174s Velvetg version: 1.2.09 174s Readfile(s): -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz 174s Velveth parameter string: auto_data_31 31 -shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz 174s Velvetg parameter string: auto_data_31 -clean yes -exp_cov 14 -cov_cutoff 0.862764507476839 174s Assembly directory: /tmp/autopkgtest.z490qn/autopkgtest_tmp/auto_data_31 174s Velvet hash value: 31 174s Roadmap file size: 1496358 174s Total number of contigs: 121 174s n50: 131988 174s length of longest contig: 131988 174s Total bases in contigs: 187506 174s Number of contigs > 1k: 5 174s Total bases in contigs > 1k: 177314 174s Paired Library insert stats: 174s Paired-end library 1 has length: 399, sample standard deviation: 39 174s Paired-end library 1 has length: 399, sample standard deviation: 40 174s ********************************************************** 174s 174s 174s Assembly output files are in the following directory: 174s test_out 174s 174s Number of contigs in final assembly: 174s 121 174s Running VelvetOptimiser on short and long test data. 174s 174s **************************************************** 174s VelvetOptimiser.pl Version 2.2.6 174s **************************************************** 174s Number of CPUs available: 1 174s Current free RAM: 1.433GB 174s Velvet OMP compiler setting: 1 174s Mar 24 20:04:50 Starting to check input parameters. 174s Start hash value too high. New start hash value is 31. 174s End hash value not in workable range. New end hash value is 31. 174s Velveth parameter string OK. 174s Mar 24 20:04:50 Finished checking input parameters. 174s Velvet details: 174s Velvet version: 1.2.09 174s Compiled categories: 2 174s Compiled max kmer length: 31 174s Maximum number of velvetinstances to run: 1 174s Will run velvet optimiser with the following paramters: 174s Velveth parameter string: 174s -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 174s Velveth start hash values: 31 174s Velveth end hash value: 31 174s Velveth hash step value: 4 174s Velvetg minimum coverage cutoff to use: 0 174s 174s Read tracking for final assembly off. 174s Mar 24 20:04:50 Beginning velveth runs. 174s Mar 24 20:04:50 Running velveth with hash value: 31. 174s Logfile name: 24-03-2024-20-04-50_Logfile.txt 176s Mar 24 20:04:51 Velveth with hash value 31 finished. 176s Mar 24 20:04:52 Finished velveth runs. 176s Mar 24 20:04:52 Beginning vanilla velvetg runs. 176s Mar 24 20:04:52 Running vanilla velvetg on hash value: 31 180s Mar 24 20:04:55 Velvetg on hash value: 31 finished. 180s Mar 24 20:04:55 Hash value of best assembly by assembly score: 31 180s Mar 24 20:04:55 Optimisation routine chosen for best assembly: shortLongPaired 180s Mar 24 20:04:55 Looking for the expected coverage 180s Mar 24 20:04:55 Expected coverage set to 2235 180s Mar 24 20:04:55 Setting assembly short insert length(s) to auto 180s Mar 24 20:04:55 Setting assembly long insert length auto 180s Mar 24 20:04:55 Beginning coverage cutoff optimisation 180s Mar 24 20:04:55 Setting cov_cutoff to 1104.984. 182s ********** 182s Warning: Assembly score for assembly_id 1 is 0 182s You may want to consider choosing a different optimisation variable or function. 182s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 182s ********** 182s Mar 24 20:04:58 Setting cov_cutoff to 683.016. 182s ********** 182s Warning: Assembly score for assembly_id 1 is 0 182s You may want to consider choosing a different optimisation variable or function. 182s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 182s ********** 182s Looking for best cutoff score between 0.000 and 1788.000 182s Max cutoff lies between 0.000 & 1104.984 182s fc = 0 fd = 0 abs diff = 0 182s Mar 24 20:04:58 Setting cov_cutoff to 422.104. 183s ********** 183s Warning: Assembly score for assembly_id 1 is 0 183s You may want to consider choosing a different optimisation variable or function. 183s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 183s ********** 183s Max cutoff lies between 0.000 & 683.016 183s fc = 0 fd = 0 abs diff = 0 183s Mar 24 20:04:58 Setting cov_cutoff to 260.912. 183s ********** 183s Warning: Assembly score for assembly_id 1 is 0 183s You may want to consider choosing a different optimisation variable or function. 183s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 183s ********** 183s Max cutoff lies between 0.000 & 422.104 183s fc = 0 fd = 0 abs diff = 0 183s Mar 24 20:04:59 Setting cov_cutoff to 161.244. 184s ********** 184s Warning: Assembly score for assembly_id 1 is 0 184s You may want to consider choosing a different optimisation variable or function. 184s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 184s ********** 184s Max cutoff lies between 0.000 & 260.912 184s fc = 0 fd = 0 abs diff = 0 184s Mar 24 20:04:59 Setting cov_cutoff to 99.668. 184s ********** 184s Warning: Assembly score for assembly_id 1 is 0 184s You may want to consider choosing a different optimisation variable or function. 184s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 184s ********** 184s Max cutoff lies between 0.000 & 161.244 184s fc = 0 fd = 0 abs diff = 0 184s Mar 24 20:04:59 Setting cov_cutoff to 61.595. 184s ********** 184s Warning: Assembly score for assembly_id 1 is 0 184s You may want to consider choosing a different optimisation variable or function. 184s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 184s ********** 184s Max cutoff lies between 0.000 & 99.668 184s fc = 0 fd = 0 abs diff = 0 184s Mar 24 20:04:59 Setting cov_cutoff to 38.073. 184s ********** 184s Warning: Assembly score for assembly_id 1 is 0 184s You may want to consider choosing a different optimisation variable or function. 184s Current optimisation functions are n50 for k value and Lbp for cov_cutoff 184s ********** 184s Max cutoff lies between 0.000 & 61.595 184s fc = 0 fd = 0 abs diff = 0 184s Mar 24 20:04:59 Setting cov_cutoff to 23.529. 184s Max cutoff lies between 0.000 & 38.073 184s fc = 0 fd = 5376 abs diff = 5376 184s Mar 24 20:04:59 Setting cov_cutoff to 14.544. 184s Max cutoff lies between 0.000 & 23.529 184s fc = 5376 fd = 110154 abs diff = 104778 184s Mar 24 20:05:00 Setting cov_cutoff to 8.988. 184s Max cutoff lies between 0.000 & 14.544 184s fc = 110154 fd = 179893 abs diff = 69739 184s Mar 24 20:05:00 Setting cov_cutoff to 5.556. 184s Max cutoff lies between 0.000 & 8.988 184s fc = 179893 fd = 180411 abs diff = 518 184s Mar 24 20:05:00 Setting cov_cutoff to 3.433. 185s Max cutoff lies between 0.000 & 5.556 185s fc = 180411 fd = 180659 abs diff = 248 185s Mar 24 20:05:00 Setting cov_cutoff to 2.122. 185s Max cutoff lies between 0.000 & 3.433 185s fc = 180659 fd = 180659 abs diff = 0 185s Mar 24 20:05:01 Setting cov_cutoff to 1.312. 185s Max cutoff lies between 0.000 & 2.122 185s fc = 180659 fd = 180659 abs diff = 0 185s Mar 24 20:05:01 Setting cov_cutoff to 0.811. 185s Max cutoff lies between 0.811 & 2.122 185s fc = 180659 fd = 179182 abs diff = 1477 185s Mar 24 20:05:01 Setting cov_cutoff to 1.621. 186s Max cutoff lies between 0.811 & 1.621 186s fc = 180659 fd = 180659 abs diff = 0 186s Mar 24 20:05:02 Setting cov_cutoff to 1.120. 186s Optimum value of cutoff is 1.62 186s Took 17 iterations 186s Mar 24 20:05:02 186s 186s 186s Final optimised assembly details: 186s ******************************************************** 186s Assembly id: 1 186s Assembly score: 180659 186s Velveth timestamp: Mar 24 2024 20:04:51 186s Velvetg timestamp: Mar 24 2024 20:05:02 186s Velveth version: 1.2.09 186s Velvetg version: 1.2.09 186s 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 186s 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 186s Velvetg parameter string: auto_data_31 -long_mult_cutoff 3 -clean yes -exp_cov 2235 -cov_cutoff 1.12036253377189 186s Assembly directory: /tmp/autopkgtest.z490qn/autopkgtest_tmp/auto_data_31 186s Velvet hash value: 31 186s Roadmap file size: 3225258 186s Total number of contigs: 6 186s n50: 180659 186s length of longest contig: 180659 186s Total bases in contigs: 181888 186s Number of contigs > 1k: 1 186s Total bases in contigs > 1k: 180659 186s Paired Library insert stats: 186s Paired-end library 1 has length: 399, sample standard deviation: 39 186s Paired-end library 3 has length: -2744, sample standard deviation: 1397 186s Paired-end library 1 has length: 399, sample standard deviation: 39 186s Paired-end library 3 has length: -39747, sample standard deviation: 42590 186s Paired-end library 1 has length: 399, sample standard deviation: 39 186s Paired-end library 3 has length: -76924, sample standard deviation: 51129 186s ********************************************************** 186s 186s 186s Assembly output files are in the following directory: 186s test_out_2 186s 186s Number of contigs in final assembly: 186s 6 186s Estimation of memory test: 186s 186s **************************************************** 186s VelvetOptimiser.pl Version 2.2.6 186s **************************************************** 186s Number of CPUs available: 1 186s Current free RAM: 1.477GB 186s Velvet OMP compiler setting: 1 186s Mar 24 20:05:02 Starting to check input parameters. 186s Start hash value too high. New start hash value is 31. 186s End hash value not in workable range. New end hash value is 31. 186s Velveth parameter string OK. 186s Mar 24 20:05:02 Finished checking input parameters. 186s 186s Memory use estimation only! Script will terminate after showing results. 186s 186s Velvet details: 186s Velvet version: 1.2.09 186s Compiled categories: 2 186s Compiled max kmer length: 31 186s Maximum number of velvetinstances to run: 1 186s Will run velvet optimiser with the following paramters: 186s Velveth parameter string: 186s -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 186s Velveth start hash values: 31 186s Velveth end hash value: 31 186s Velveth hash step value: 2 186s Velvetg minimum coverage cutoff to use: 0 186s 186s Read tracking for final assembly off. 186s Logfile name: 24-03-2024-20-05-02_Logfile.txt 186s File: data/test_long_R1.fq.gz has 13150 reads of length 150 186s File: data/test_long_R2.fq.gz has 13150 reads of length 150 186s Total reads: 0.0 million. Avg length: 150.0 186s 186s Memory use estimated to be: 1.1GB for 1 threads. 186s 186s You should have enough memory to complete this job. (Though this estimate is no guarantee..) 186s autopkgtest [20:05:02]: test run-unit-test: -----------------------] 187s autopkgtest [20:05:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 187s run-unit-test PASS 187s autopkgtest [20:05:03]: @@@@@@@@@@@@@@@@@@@@ summary 187s run-unit-test PASS 200s Creating nova instance adt-noble-ppc64el-velvetoptimiser-20240324-200156-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240324.img (UUID 456c38b1-f024-4aa9-9fc9-7cea731b220e)...