0s autopkgtest [13:35:26]: starting date and time: 2025-03-15 13:35:26+0000 0s autopkgtest [13:35:26]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:35:26]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5hu2wh9m/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade obitools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-27.secgroup --name adt-plucky-s390x-obitools-20250315-133525-juju-7f2275-prod-proposed-migration-environment-20-a507bc94-3111-4f53-93bc-263b4050d6e3 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 113s autopkgtest [13:37:19]: testbed dpkg architecture: s390x 113s autopkgtest [13:37:19]: testbed apt version: 2.9.33 114s autopkgtest [13:37:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s autopkgtest [13:37:20]: testbed release detected to be: None 115s autopkgtest [13:37:21]: updating testbed package index (apt update) 115s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 115s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 115s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 115s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [80.6 kB] 116s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1940 B] 116s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 116s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [342 kB] 116s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [14.4 kB] 116s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 116s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [328 B] 117s Fetched 1090 kB in 2s (674 kB/s) 117s Reading package lists... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s Calculating upgrade... 119s The following packages were automatically installed and are no longer required: 119s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 119s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 119s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 119s linux-tools-6.11.0-8-generic 119s Use 'sudo apt autoremove' to remove them. 119s The following packages will be upgraded: 119s python3-jinja2 strace 119s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 609 kB of archives. 119s After this operation, 27.6 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 119s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 120s Fetched 609 kB in 1s (734 kB/s) 120s (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 ... 81428 files and directories currently installed.) 120s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 120s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 120s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 120s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 120s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 120s Setting up strace (6.13+ds-1ubuntu1) ... 120s Processing triggers for man-db (2.13.0-1) ... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Solving dependencies... 121s The following packages will be REMOVED: 121s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 121s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 121s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 121s linux-tools-6.11.0-8-generic* 121s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 121s After this operation, 167 MB disk space will be freed. 121s (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 ... 81428 files and directories currently installed.) 121s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 121s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 121s Removing libpython3.12t64:s390x (3.12.9-1) ... 121s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 121s Removing libnsl2:s390x (1.3.0-3build3) ... 121s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 121s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 121s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 122s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 122s Processing triggers for libc-bin (2.41-1ubuntu1) ... 122s (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 ... 56328 files and directories currently installed.) 122s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 122s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 122s autopkgtest [13:37:28]: upgrading testbed (apt dist-upgrade and autopurge) 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 123s Starting 2 pkgProblemResolver with broken count: 0 123s Done 123s Entering ResolveByKeep 123s 123s Calculating upgrade... 123s The following packages will be upgraded: 123s libc-bin libc-dev-bin libc6 libc6-dev locales 124s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 9512 kB of archives. 124s After this operation, 8192 B of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 125s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 128s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 129s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 133s Preconfiguring packages ... 133s Fetched 9512 kB in 10s (998 kB/s) 133s (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 ... 56326 files and directories currently installed.) 133s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 133s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 133s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 133s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 133s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 133s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 133s Setting up libc6:s390x (2.41-1ubuntu2) ... 134s (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 ... 56326 files and directories currently installed.) 134s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 134s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 134s Setting up libc-bin (2.41-1ubuntu2) ... 134s (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 ... 56326 files and directories currently installed.) 134s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 134s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 134s Setting up locales (2.41-1ubuntu2) ... 134s Generating locales (this might take a while)... 135s en_US.UTF-8... done 135s Generation complete. 135s Setting up libc-dev-bin (2.41-1ubuntu2) ... 135s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 135s Processing triggers for man-db (2.13.0-1) ... 136s Processing triggers for systemd (257.3-1ubuntu3) ... 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 137s Solving dependencies... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s autopkgtest [13:37:43]: rebooting testbed after setup commands that affected boot 158s autopkgtest [13:38:04]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 160s autopkgtest [13:38:06]: @@@@@@@@@@@@@@@@@@@@ apt-source obitools 166s Get:1 http://ftpmaster.internal/ubuntu plucky/universe obitools 3.0.1~b26+dfsg-4 (dsc) [2186 B] 166s Get:2 http://ftpmaster.internal/ubuntu plucky/universe obitools 3.0.1~b26+dfsg-4 (tar) [255 kB] 166s Get:3 http://ftpmaster.internal/ubuntu plucky/universe obitools 3.0.1~b26+dfsg-4 (diff) [3556 kB] 166s gpgv: Signature made Fri Jan 10 12:57:35 2025 UTC 166s gpgv: using RSA key 90E2D2C1AD146A1B7EBB891DBBC17EBB1396F2F7 166s gpgv: Can't check signature: No public key 166s dpkg-source: warning: cannot verify inline signature for ./obitools_3.0.1~b26+dfsg-4.dsc: no acceptable signature found 166s autopkgtest [13:38:12]: testing package obitools version 3.0.1~b26+dfsg-4 168s autopkgtest [13:38:14]: build not needed 169s autopkgtest [13:38:15]: test command1: preparing testbed 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s Starting pkgProblemResolver with broken count: 0 170s Starting 2 pkgProblemResolver with broken count: 0 170s Done 170s The following NEW packages will be installed: 170s libgomp1 obitools 170s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 170s Need to get 6268 kB of archives. 170s After this operation, 36.2 MB of additional disk space will be used. 170s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 171s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x obitools s390x 3.0.1~b26+dfsg-4 [6117 kB] 178s Fetched 6268 kB in 7s (844 kB/s) 178s Selecting previously unselected package libgomp1:s390x. 178s (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 ... 56326 files and directories currently installed.) 178s Preparing to unpack .../libgomp1_15-20250222-0ubuntu1_s390x.deb ... 178s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 178s Selecting previously unselected package obitools. 178s Preparing to unpack .../obitools_3.0.1~b26+dfsg-4_s390x.deb ... 178s Unpacking obitools (3.0.1~b26+dfsg-4) ... 178s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 178s Setting up obitools (3.0.1~b26+dfsg-4) ... 178s Processing triggers for libc-bin (2.41-1ubuntu2) ... 179s autopkgtest [13:38:25]: test command1: obi --help 179s autopkgtest [13:38:25]: test command1: [----------------------- 179s usage: obi [-h] [--version] [--log OBI:LOG] 179s {addtaxids,align,alignpairedend,annotate,build_ref_db,cat,clean,clean_dms,count,ecopcr,ecotag,export,grep,head,history,import,less,ls,ngsfilter,rm,sort,split,stats,tail,taxonomy,test,uniq} ... 179s 179s options: 179s -h, --help show this help message and exit 179s --version Print the version of The OBITools 3 179s --log OBI:LOG Create a logfile 179s 179s subcommands: 179s valid subcommands 179s 179s {addtaxids,align,alignpairedend,annotate,build_ref_db,cat,clean,clean_dms,count,ecopcr,ecotag,export,grep,head,history,import,less,ls,ngsfilter,rm,sort,split,stats,tail,taxonomy,test,uniq} 179s additional help 179s addtaxids Annotate sequences with their corresponding NCBI taxid 179s found from the taxon scientific name 179s align Align one sequence column with itself or two sequence 179s columns 179s alignpairedend Align paired-ended reads 179s annotate Annotate views with new tags and edit existing 179s annotations 179s build_ref_db Build a reference database for ecotag 179s cat Concatenate views 179s clean Tag a set of sequences for PCR and sequencing errors 179s identification 179s clean_dms Clean a DMS from unfinished views and columns 179s count Count sequence records 179s ecopcr in silico PCR 179s ecotag Taxonomic assignment of sequences 179s export Export a view to a different file format 179s grep Grep view lines that match the given predicates 179s head Keep the N first lines of a view 179s history Command line histories and view history graphs 179s import Import sequences from different formats into a DMS 179s less Less equivalent 179s ls Print a preview of a DMS, view, column.... 179s ngsfilter Assign sequence records to the corresponding 179s experiment/sample based on DNA tags and primers 179s rm Delete a view 179s sort Sort view lines according to the value of a given 179s attribute 179s split Split 179s stats Compute basic statistics for attribute values 179s tail Keep the N last lines of a view 179s taxonomy Add taxa with a new generated taxid to an NCBI 179s taxonomy database 179s test Test if the obitools are working properly 179s uniq Group sequence records together 179s autopkgtest [13:38:25]: test command1: -----------------------] 180s command1 PASS (superficial) 180s autopkgtest [13:38:26]: test command1: - - - - - - - - - - results - - - - - - - - - - 180s autopkgtest [13:38:26]: test wolf-tutorial: preparing testbed 180s Reading package lists... 181s Building dependency tree... 181s Reading state information... 181s Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 181s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 182s autopkgtest [13:38:28]: test wolf-tutorial: [----------------------- 182s + pkg=obitools 182s + export LC_ALL=C.UTF-8 182s + LC_ALL=C.UTF-8 182s + '[' /tmp/autopkgtest.YjkdRJ/autopkgtest_tmp = '' ']' 182s + cp -a /usr/share/doc/obitools/examples/wolf_tutorial /tmp/autopkgtest.YjkdRJ/autopkgtest_tmp 182s + cd /tmp/autopkgtest.YjkdRJ/autopkgtest_tmp 182s + obi import --quality-solexa wolf_tutorial/wolf_F.fastq wolf/reads1 182s 2025-03-15 13:38:28,307 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 182s 2025-03-15 13:38:28,316 [import : INFO ] Opened file: wolf_tutorial/wolf_F.fastq 182s 2025-03-15 13:38:28,348 [import : INFO ] Importing 45276 entries 183s 183s 2025-03-15 13:38:29,059 [import : INFO ] Imported 45276 entries 183s 2025-03-15 13:38:29,101 [import : INFO ] Done. 183s + obi import --quality-solexa wolf_tutorial/wolf_R.fastq wolf/reads2 183s 2025-03-15 13:38:29,200 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 183s 2025-03-15 13:38:29,209 [import : INFO ] Opened file: wolf_tutorial/wolf_R.fastq 183s 2025-03-15 13:38:29,243 [import : INFO ] Importing 45276 entries 184s 184s 2025-03-15 13:38:30,012 [import : INFO ] Imported 45276 entries 184s 2025-03-15 13:38:30,053 [import : INFO ] Done. 184s + obi import --ngsfilter-input wolf_tutorial/wolf_diet_ngsfilter.txt wolf/ngsfile 184s 2025-03-15 13:38:30,158 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 184s 2025-03-15 13:38:30,168 [import : INFO ] Opened file: wolf_tutorial/wolf_diet_ngsfilter.txt 184s 2025-03-15 13:38:30,168 [import : INFO ] Importing 4 entries 184s 184s 2025-03-15 13:38:30,193 [import : INFO ] Imported 4 entries 184s 2025-03-15 13:38:30,195 [import : INFO ] Done. 184s + obi ls wolf 184s 2025-03-15 13:38:30,299 [ls : INFO ] obi ls 184s # DMS name: wolf 184s # Views: 184s # ngsfile: Date created: Sat Mar 15 13:38:30 2025 ; Line count: 4 184s # reads1: Date created: Sat Mar 15 13:38:28 2025 ; Line count: 45276 184s # reads2: Date created: Sat Mar 15 13:38:29 2025 ; Line count: 45276 184s # Taxonomies: 184s 184s + obi ls -l wolf 184s 2025-03-15 13:38:30,399 [ls : INFO ] obi ls 184s # DMS name: wolf 184s # Views: 184s # View name: 184s ngsfile 184s # Date created: 184s Sat Mar 15 13:38:30 2025 184s # Line count: 184s 4 184s # Columns: 184s experiment, data type: OBI_STR 184s sample, data type: OBI_STR 184s forward_tag, data type: OBI_SEQ 184s reverse_tag, data type: OBI_SEQ 184s forward_primer, data type: OBI_SEQ 184s reverse_primer, data type: OBI_SEQ 184s # Comments: 184s { 184s "obi": { 184s "software": "The OBITools 3", 184s "inputURI": "wolf_tutorial/wolf_diet_ngsfilter.txt", 184s "outputURI": "wolf/ngsfile", 184s "skip": 0, 184s "skiperror": true, 184s "qualityformat": "sanger", 184s "offset": -1, 184s "noquality": false, 184s "header": true, 184s "sep": "\t", 184s "quote": ["'", "\""], 184s "dec": ".", 184s "nastring": "NA", 184s "stripwhite": true, 184s "blanklineskip": true, 184s "commentchar": "#", 184s "version": false, 184s "inputformat": "ngsfilter", 184s "inputnastring": "NA", 184s "taxdump": false, 184s "noprogressbar": false, 184s "modulename": "import" 184s }, 184s "import": { 184s "skip": 0, 184s "skiperror": false, 184s "moltype": "nuc", 184s "preread": false, 184s "space_priority": false 184s }, 184s "command_line": "import --ngsfilter-input wolf_tutorial/wolf_diet_ngsfilter.txt wolf/ngsfile", 184s "input_dms_name": null, 184s "input_view_name": null, 184s "input_str": ["/tmp/autopkgtest.YjkdRJ/autopkgtest_tmp/wolf_tutorial/wolf_diet_ngsfilter.txt"], 184s "version": "3.0.1b26", 184s "Date created": "Sat Mar 15 13:38:30 2025" 184s } 184s 184s # View name: 184s reads1 184s # Date created: 184s Sat Mar 15 13:38:28 2025 184s # Line count: 184s 45276 184s # Columns: 184s NUC_SEQ, data type: OBI_SEQ 184s ID, data type: OBI_STR 184s DEFINITION, data type: OBI_STR 184s QUALITY, data type: OBI_QUAL 184s COUNT, data type: OBI_INT 184s # Comments: 184s { 184s "obi": { 184s "software": "The OBITools 3", 184s "inputURI": "wolf_tutorial/wolf_F.fastq", 184s "outputURI": "wolf/reads1", 184s "skip": 0, 184s "skiperror": true, 184s "qualityformat": "solexa", 184s "offset": -1, 184s "noquality": false, 184s "seqtype": "nuc", 184s "header": true, 184s "sep": "\t", 184s "quote": ["'", "\""], 184s "dec": ".", 184s "nastring": "NA", 184s "stripwhite": true, 184s "blanklineskip": true, 184s "commentchar": "#", 184s "version": false, 184s "inputnastring": "NA", 184s "taxdump": false, 184s "noprogressbar": false, 184s "modulename": "import" 184s }, 184s "import": { 184s "skip": 0, 184s "skiperror": false, 184s "moltype": "nuc", 184s "preread": false, 184s "space_priority": false 184s }, 184s "command_line": "import --quality-solexa wolf_tutorial/wolf_F.fastq wolf/reads1", 184s "input_dms_name": null, 184s "input_view_name": null, 184s "input_str": ["/tmp/autopkgtest.YjkdRJ/autopkgtest_tmp/wolf_tutorial/wolf_F.fastq"], 184s "version": "3.0.1b26", 184s "predicates": ["The sequences and sequence quality arrays match.", "The view has an associated nucleotide sequence column.", "The view has an associated identifier column.", "The view has an associated definition column."], 184s "Date created": "Sat Mar 15 13:38:29 2025" 184s } 184s 184s # View name: 184s reads2 184s # Date created: 184s Sat Mar 15 13:38:29 2025 184s # Line count: 184s 45276 184s # Columns: 184s NUC_SEQ, data type: OBI_SEQ 184s ID, data type: OBI_STR 184s DEFINITION, data type: OBI_STR 184s QUALITY, data type: OBI_QUAL 184s COUNT, data type: OBI_INT 184s # Comments: 184s { 184s "obi": { 184s "software": "The OBITools 3", 184s "inputURI": "wolf_tutorial/wolf_R.fastq", 184s "outputURI": "wolf/reads2", 184s "skip": 0, 184s "skiperror": true, 184s "qualityformat": "solexa", 184s "offset": -1, 184s "noquality": false, 184s "seqtype": "nuc", 184s "header": true, 184s "sep": "\t", 184s "quote": ["'", "\""], 184s "dec": ".", 184s "nastring": "NA", 184s "stripwhite": true, 184s "blanklineskip": true, 184s "commentchar": "#", 184s "version": false, 184s "inputnastring": "NA", 184s "taxdump": false, 184s "noprogressbar": false, 184s "modulename": "import" 184s }, 184s "import": { 184s "skip": 0, 184s "skiperror": false, 184s "moltype": "nuc", 184s "preread": false, 184s "space_priority": false 184s }, 184s "command_line": "import --quality-solexa wolf_tutorial/wolf_R.fastq wolf/reads2", 184s "input_dms_name": null, 184s "input_view_name": null, 184s "input_str": ["/tmp/autopkgtest.YjkdRJ/autopkgtest_tmp/wolf_tutorial/wolf_R.fastq"], 184s "version": "3.0.1b26", 184s "predicates": ["The sequences and sequence quality arrays match.", "The view has an associated nucleotide sequence column.", "The view has an associated identifier column.", "The view has an associated definition column."], 184s "Date created": "Sat Mar 15 13:38:30 2025" 184s } 184s 184s # Taxonomies: 184s 184s + obi ls wolf/reads1 184s 2025-03-15 13:38:30,490 [ls : INFO ] obi ls 184s # View name: 184s reads1 184s # Date created: 184s Sat Mar 15 13:38:28 2025 184s # Line count: 184s 45276 184s # Columns: 184s NUC_SEQ, data type: OBI_SEQ 184s ID, data type: OBI_STR 184s DEFINITION, data type: OBI_STR 184s QUALITY, data type: OBI_QUAL 184s COUNT, data type: OBI_INT 184s 184s + obi ls wolf/ngsfile/sample 184s data type: OBI_STR 184s 2025-03-15 13:38:30,579 [ls : INFO ] obi ls 184s + obi less wolf/reads1 185s + obi alignpairedend -R wolf/reads2 wolf/reads1 wolf/aligned_reads 185s 2025-03-15 13:38:31,421 [alignpairedend : INFO ] obi alignpairedend 188s 188s 2025-03-15 13:38:34,541 [alignpairedend : INFO ] Done. 188s + obi alignpairedend -R wolf/reads2 wolf/reads1 - 188s 2025-03-15 13:38:34,639 [alignpairedend : INFO ] obi alignpairedend 191s 191s 2025-03-15 13:38:37,796 [alignpairedend : INFO ] Printing to output... 193s 193s 2025-03-15 13:38:39,299 [alignpairedend : INFO ] Done. 193s + obi stats -a score_norm wolf/aligned_reads 193s 2025-03-15 13:38:39,403 [stats : INFO ] obi stats 193s 193s 2025-03-15 13:38:39,608 [stats : INFO ] Done. 193s mean_score_norm count total 193s 0.888201 45276 45276 193s + obi grep -p 'sequence['\''score_norm'\''] > 0.8' wolf/aligned_reads wolf/good_sequences 193s 2025-03-15 13:38:39,705 [grep : INFO ] obi grep 193s 193s 2025-03-15 13:38:39,795 [grep : INFO ] Grepped 38562 entries 193s 2025-03-15 13:38:39,843 [grep : INFO ] Done. 193s + obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences wolf/good_sequences wolf/identified_sequences 193s 2025-03-15 13:38:39,937 [ngsfilter : INFO ] obi ngsfilter 208s 208s 2025-03-15 13:38:54,650 [ngsfilter : INFO ] Done. 208s + obi uniq -m sample wolf/identified_sequences wolf/dereplicated_sequences 208s 2025-03-15 13:38:54,748 [uniq : INFO ] obi uniq 208s 2025-03-15 13:38:54,751 [uniq : INFO ] First browsing through the input 208s 2025-03-15 13:38:54,955 [uniq : INFO ] Second browsing through the input 216s 216s 2025-03-15 13:39:02,583 [uniq : INFO ] Done. 216s 216s + obi annotate -k COUNT -k MERGED_sample wolf/dereplicated_sequences wolf/cleaned_metadata_sequences 216s 2025-03-15 13:39:02,714 [annotate : INFO ] obi annotate 216s 216s 2025-03-15 13:39:02,721 [annotate : INFO ] Done. 216s + obi grep -p 'len(sequence)>=80 and sequence['\''COUNT'\'']>=10' wolf/cleaned_metadata_sequences wolf/denoised_sequences 216s 2025-03-15 13:39:02,826 [grep : INFO ] obi grep 216s 216s 2025-03-15 13:39:02,841 [grep : INFO ] Grepped 190 entries 216s 2025-03-15 13:39:02,842 [grep : INFO ] Done. 216s + obi clean -s MERGED_sample -r 0.05 -H wolf/denoised_sequences wolf/cleaned_sequences 216s 2025-03-15 13:39:02,952 [clean : INFO ] obi clean 216s Running on 2 thread(s) 216s Building kmer tables... : Done 216s Done : 0.000000 % 216s Annotating : 0.000000 % Done : 100 % 216s 2025-03-15 13:39:02,960 [clean : INFO ] Done. 217s + tar cJf /tmp/autopkgtest.YjkdRJ/wolf-tutorial-artifacts/wolf.obidms.tar.xz wolf.obidms 333s autopkgtest [13:40:59]: test wolf-tutorial: -----------------------] 334s wolf-tutorial PASS 334s autopkgtest [13:41:00]: test wolf-tutorial: - - - - - - - - - - results - - - - - - - - - - 336s autopkgtest [13:41:02]: @@@@@@@@@@@@@@@@@@@@ summary 336s command1 PASS (superficial) 336s wolf-tutorial PASS 342s nova [W] Using flock in prodstack6-s390x 342s Creating nova instance adt-plucky-s390x-obitools-20250315-133525-juju-7f2275-prod-proposed-migration-environment-20-a507bc94-3111-4f53-93bc-263b4050d6e3 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 342s nova [W] Timed out waiting for a40505e9-9cb4-4dc6-b89b-50640c489724 to get deleted.