0s autopkgtest [13:41:48]: starting date and time: 2025-03-15 13:41:48+0000 0s autopkgtest [13:41:48]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:41:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rw_p8bfq/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-31.secgroup --name adt-plucky-arm64-obitools-20250315-134147-juju-7f2275-prod-proposed-migration-environment-2-5aebf411-32e3-4913-a522-ce08644e149d --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 167s autopkgtest [13:44:35]: testbed dpkg architecture: arm64 167s autopkgtest [13:44:35]: testbed apt version: 2.9.33 167s autopkgtest [13:44:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 167s autopkgtest [13:44:35]: testbed release detected to be: None 168s autopkgtest [13:44:36]: updating testbed package index (apt update) 169s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 169s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 169s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 169s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 169s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 170s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 170s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 170s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 170s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 170s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 170s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 170s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 170s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 170s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 171s Fetched 1094 kB in 2s (634 kB/s) 172s Reading package lists... 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Calculating upgrade... 175s Calculating upgrade... 175s The following packages will be upgraded: 175s python3-jinja2 strace 175s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 608 kB of archives. 175s After this operation, 11.3 kB of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 176s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 177s Fetched 608 kB in 1s (479 kB/s) 177s (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 ... 117701 files and directories currently installed.) 177s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 177s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 178s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 178s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 178s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 178s Setting up strace (6.13+ds-1ubuntu1) ... 178s Processing triggers for man-db (2.13.0-1) ... 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s Solving dependencies... 180s The following packages will be REMOVED: 180s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 180s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 180s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 180s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 181s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 181s After this operation, 267 MB disk space will be freed. 181s (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 ... 117701 files and directories currently installed.) 181s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 181s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 181s Removing libpython3.12t64:arm64 (3.12.9-1) ... 181s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 181s Removing libnsl2:arm64 (1.3.0-3build3) ... 181s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 181s Removing libunwind8:arm64 (1.6.2-3.1) ... 181s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 182s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 184s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 184s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 184s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 184s /etc/kernel/postrm.d/initramfs-tools: 184s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 184s /etc/kernel/postrm.d/zz-flash-kernel: 184s flash-kernel: Kernel 6.11.0-8-generic has been removed. 184s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 185s /etc/kernel/postrm.d/zz-update-grub: 185s Sourcing file `/etc/default/grub' 185s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 185s Generating grub configuration file ... 185s Found linux image: /boot/vmlinuz-6.14.0-10-generic 185s Found initrd image: /boot/initrd.img-6.14.0-10-generic 186s Warning: os-prober will not be executed to detect other bootable partitions. 186s Systems on them will not be added to the GRUB boot configuration. 186s Check GRUB_DISABLE_OS_PROBER documentation entry. 186s Adding boot menu entry for UEFI Firmware Settings ... 186s done 186s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 186s Processing triggers for libc-bin (2.41-1ubuntu1) ... 186s (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 ... 81650 files and directories currently installed.) 186s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 186s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 186s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 187s autopkgtest [13:44:55]: upgrading testbed (apt dist-upgrade and autopurge) 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 189s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 190s Entering ResolveByKeep 191s 191s Calculating upgrade... 192s The following packages will be upgraded: 192s libc-bin libc-dev-bin libc6 libc6-dev locales 193s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Need to get 9530 kB of archives. 193s After this operation, 0 B of additional disk space will be used. 193s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 195s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 199s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 199s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 205s Preconfiguring packages ... 205s Fetched 9530 kB in 12s (808 kB/s) 205s (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 ... 81647 files and directories currently installed.) 205s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 205s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 205s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 206s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 206s Setting up libc6:arm64 (2.41-1ubuntu2) ... 206s (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 ... 81647 files and directories currently installed.) 206s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 206s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 206s Setting up libc-bin (2.41-1ubuntu2) ... 207s (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 ... 81647 files and directories currently installed.) 207s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 207s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 207s Setting up locales (2.41-1ubuntu2) ... 208s Generating locales (this might take a while)... 211s en_US.UTF-8... done 211s Generation complete. 211s Setting up libc-dev-bin (2.41-1ubuntu2) ... 211s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 211s Processing triggers for man-db (2.13.0-1) ... 212s Processing triggers for systemd (257.3-1ubuntu3) ... 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 214s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 215s Solving dependencies... 215s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 216s autopkgtest [13:45:24]: rebooting testbed after setup commands that affected boot 240s autopkgtest [13:45:48]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 243s autopkgtest [13:45:51]: @@@@@@@@@@@@@@@@@@@@ apt-source obitools 249s Get:1 http://ftpmaster.internal/ubuntu plucky/universe obitools 3.0.1~b26+dfsg-4 (dsc) [2186 B] 249s Get:2 http://ftpmaster.internal/ubuntu plucky/universe obitools 3.0.1~b26+dfsg-4 (tar) [255 kB] 249s Get:3 http://ftpmaster.internal/ubuntu plucky/universe obitools 3.0.1~b26+dfsg-4 (diff) [3556 kB] 249s gpgv: Signature made Fri Jan 10 12:57:35 2025 UTC 249s gpgv: using RSA key 90E2D2C1AD146A1B7EBB891DBBC17EBB1396F2F7 249s gpgv: Can't check signature: No public key 249s dpkg-source: warning: cannot verify inline signature for ./obitools_3.0.1~b26+dfsg-4.dsc: no acceptable signature found 250s autopkgtest [13:45:58]: testing package obitools version 3.0.1~b26+dfsg-4 251s autopkgtest [13:45:59]: build not needed 253s autopkgtest [13:46:01]: test command1: preparing testbed 253s Reading package lists... 254s Building dependency tree... 254s Reading state information... 255s Starting pkgProblemResolver with broken count: 0 255s Starting 2 pkgProblemResolver with broken count: 0 255s Done 257s The following NEW packages will be installed: 257s libgomp1 obitools 257s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 257s Need to get 5974 kB of archives. 257s After this operation, 36.9 MB of additional disk space will be used. 257s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 257s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 obitools arm64 3.0.1~b26+dfsg-4 [5828 kB] 264s Fetched 5974 kB in 6s (963 kB/s) 264s Selecting previously unselected package libgomp1:arm64. 264s (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 ... 81647 files and directories currently installed.) 264s Preparing to unpack .../libgomp1_15-20250222-0ubuntu1_arm64.deb ... 264s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 264s Selecting previously unselected package obitools. 264s Preparing to unpack .../obitools_3.0.1~b26+dfsg-4_arm64.deb ... 264s Unpacking obitools (3.0.1~b26+dfsg-4) ... 265s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 265s Setting up obitools (3.0.1~b26+dfsg-4) ... 265s Processing triggers for libc-bin (2.41-1ubuntu2) ... 267s autopkgtest [13:46:15]: test command1: obi --help 267s autopkgtest [13:46:15]: test command1: [----------------------- 267s usage: obi [-h] [--version] [--log OBI:LOG] 267s {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} ... 267s 267s options: 267s -h, --help show this help message and exit 267s --version Print the version of The OBITools 3 267s --log OBI:LOG Create a logfile 267s 267s subcommands: 267s valid subcommands 267s 267s {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} 267s additional help 267s addtaxids Annotate sequences with their corresponding NCBI taxid 267s found from the taxon scientific name 267s align Align one sequence column with itself or two sequence 267s columns 267s alignpairedend Align paired-ended reads 267s annotate Annotate views with new tags and edit existing 267s annotations 267s build_ref_db Build a reference database for ecotag 267s cat Concatenate views 267s clean Tag a set of sequences for PCR and sequencing errors 267s identification 267s clean_dms Clean a DMS from unfinished views and columns 267s count Count sequence records 267s ecopcr in silico PCR 267s ecotag Taxonomic assignment of sequences 267s export Export a view to a different file format 267s grep Grep view lines that match the given predicates 267s head Keep the N first lines of a view 267s history Command line histories and view history graphs 267s import Import sequences from different formats into a DMS 267s less Less equivalent 267s ls Print a preview of a DMS, view, column.... 267s ngsfilter Assign sequence records to the corresponding 267s experiment/sample based on DNA tags and primers 267s rm Delete a view 267s sort Sort view lines according to the value of a given 267s attribute 267s split Split 267s stats Compute basic statistics for attribute values 267s tail Keep the N last lines of a view 267s taxonomy Add taxa with a new generated taxid to an NCBI 267s taxonomy database 267s test Test if the obitools are working properly 267s uniq Group sequence records together 268s autopkgtest [13:46:16]: test command1: -----------------------] 268s command1 PASS (superficial) 268s autopkgtest [13:46:16]: test command1: - - - - - - - - - - results - - - - - - - - - - 269s autopkgtest [13:46:17]: test wolf-tutorial: preparing testbed 269s Reading package lists... 270s Building dependency tree... 270s Reading state information... 270s Starting pkgProblemResolver with broken count: 0 271s Starting 2 pkgProblemResolver with broken count: 0 271s Done 272s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 273s autopkgtest [13:46:21]: test wolf-tutorial: [----------------------- 274s + pkg=obitools 274s + export LC_ALL=C.UTF-8 274s + LC_ALL=C.UTF-8 274s + '[' /tmp/autopkgtest.fFxeUa/autopkgtest_tmp = '' ']' 274s + cp -a /usr/share/doc/obitools/examples/wolf_tutorial /tmp/autopkgtest.fFxeUa/autopkgtest_tmp 274s + cd /tmp/autopkgtest.fFxeUa/autopkgtest_tmp 274s + obi import --quality-solexa wolf_tutorial/wolf_F.fastq wolf/reads1 274s 2025-03-15 13:46:22,474 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 274s 2025-03-15 13:46:22,488 [import : INFO ] Opened file: wolf_tutorial/wolf_F.fastq 274s 2025-03-15 13:46:22,541 [import : INFO ] Importing 45276 entries 275s 275s 2025-03-15 13:46:23,931 [import : INFO ] Imported 45276 entries 275s 2025-03-15 13:46:23,954 [import : INFO ] Done. 276s + obi import --quality-solexa wolf_tutorial/wolf_R.fastq wolf/reads2 276s 2025-03-15 13:46:24,301 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 276s 2025-03-15 13:46:24,315 [import : INFO ] Opened file: wolf_tutorial/wolf_R.fastq 276s 2025-03-15 13:46:24,372 [import : INFO ] Importing 45276 entries 278s 278s 2025-03-15 13:46:26,070 [import : INFO ] Imported 45276 entries 278s 2025-03-15 13:46:26,094 [import : INFO ] Done. 278s + obi import --ngsfilter-input wolf_tutorial/wolf_diet_ngsfilter.txt wolf/ngsfile 278s 2025-03-15 13:46:26,445 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 278s 2025-03-15 13:46:26,458 [import : INFO ] Opened file: wolf_tutorial/wolf_diet_ngsfilter.txt 278s 2025-03-15 13:46:26,459 [import : INFO ] Importing 4 entries 278s 278s 2025-03-15 13:46:26,514 [import : INFO ] Imported 4 entries 278s 2025-03-15 13:46:26,521 [import : INFO ] Done. 278s + obi ls wolf 278s 2025-03-15 13:46:26,872 [ls : INFO ] obi ls 278s # DMS name: wolf 278s # Views: 278s # ngsfile: Date created: Sat Mar 15 13:46:26 2025 ; Line count: 4 278s # reads2: Date created: Sat Mar 15 13:46:24 2025 ; Line count: 45276 278s # reads1: Date created: Sat Mar 15 13:46:22 2025 ; Line count: 45276 278s # Taxonomies: 278s 278s + obi ls -l wolf 279s 2025-03-15 13:46:27,222 [ls : INFO ] obi ls 279s # DMS name: wolf 279s # Views: 279s # View name: 279s ngsfile 279s # Date created: 279s Sat Mar 15 13:46:26 2025 279s # Line count: 279s 4 279s # Columns: 279s experiment, data type: OBI_STR 279s sample, data type: OBI_STR 279s forward_tag, data type: OBI_SEQ 279s reverse_tag, data type: OBI_SEQ 279s forward_primer, data type: OBI_SEQ 279s reverse_primer, data type: OBI_SEQ 279s # Comments: 279s { 279s "obi": { 279s "software": "The OBITools 3", 279s "inputURI": "wolf_tutorial/wolf_diet_ngsfilter.txt", 279s "outputURI": "wolf/ngsfile", 279s "skip": 0, 279s "skiperror": true, 279s "qualityformat": "sanger", 279s "offset": -1, 279s "noquality": false, 279s "header": true, 279s "sep": "\t", 279s "quote": ["'", "\""], 279s "dec": ".", 279s "nastring": "NA", 279s "stripwhite": true, 279s "blanklineskip": true, 279s "commentchar": "#", 279s "version": false, 279s "inputformat": "ngsfilter", 279s "inputnastring": "NA", 279s "taxdump": false, 279s "noprogressbar": false, 279s "modulename": "import" 279s }, 279s "import": { 279s "skip": 0, 279s "skiperror": false, 279s "moltype": "nuc", 279s "preread": false, 279s "space_priority": false 279s }, 279s "command_line": "import --ngsfilter-input wolf_tutorial/wolf_diet_ngsfilter.txt wolf/ngsfile", 279s "input_dms_name": null, 279s "input_view_name": null, 279s "input_str": ["/tmp/autopkgtest.fFxeUa/autopkgtest_tmp/wolf_tutorial/wolf_diet_ngsfilter.txt"], 279s "version": "3.0.1b26", 279s "Date created": "Sat Mar 15 13:46:26 2025" 279s } 279s 279s # View name: 279s reads2 279s # Date created: 279s Sat Mar 15 13:46:24 2025 279s # Line count: 279s 45276 279s # Columns: 279s NUC_SEQ, data type: OBI_SEQ 279s ID, data type: OBI_STR 279s DEFINITION, data type: OBI_STR 279s QUALITY, data type: OBI_QUAL 279s COUNT, data type: OBI_INT 279s # Comments: 279s { 279s "obi": { 279s "software": "The OBITools 3", 279s "inputURI": "wolf_tutorial/wolf_R.fastq", 279s "outputURI": "wolf/reads2", 279s "skip": 0, 279s "skiperror": true, 279s "qualityformat": "solexa", 279s "offset": -1, 279s "noquality": false, 279s "seqtype": "nuc", 279s "header": true, 279s "sep": "\t", 279s "quote": ["'", "\""], 279s "dec": ".", 279s "nastring": "NA", 279s "stripwhite": true, 279s "blanklineskip": true, 279s "commentchar": "#", 279s "version": false, 279s "inputnastring": "NA", 279s "taxdump": false, 279s "noprogressbar": false, 279s "modulename": "import" 279s }, 279s "import": { 279s "skip": 0, 279s "skiperror": false, 279s "moltype": "nuc", 279s "preread": false, 279s "space_priority": false 279s }, 279s "command_line": "import --quality-solexa wolf_tutorial/wolf_R.fastq wolf/reads2", 279s "input_dms_name": null, 279s "input_view_name": null, 279s "input_str": ["/tmp/autopkgtest.fFxeUa/autopkgtest_tmp/wolf_tutorial/wolf_R.fastq"], 279s "version": "3.0.1b26", 279s "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."], 279s "Date created": "Sat Mar 15 13:46:26 2025" 279s } 279s 279s # View name: 279s reads1 279s # Date created: 279s Sat Mar 15 13:46:22 2025 279s # Line count: 279s 45276 279s # Columns: 279s NUC_SEQ, data type: OBI_SEQ 279s ID, data type: OBI_STR 279s DEFINITION, data type: OBI_STR 279s QUALITY, data type: OBI_QUAL 279s COUNT, data type: OBI_INT 279s # Comments: 279s { 279s "obi": { 279s "software": "The OBITools 3", 279s "inputURI": "wolf_tutorial/wolf_F.fastq", 279s "outputURI": "wolf/reads1", 279s "skip": 0, 279s "skiperror": true, 279s "qualityformat": "solexa", 279s "offset": -1, 279s "noquality": false, 279s "seqtype": "nuc", 279s "header": true, 279s "sep": "\t", 279s "quote": ["'", "\""], 279s "dec": ".", 279s "nastring": "NA", 279s "stripwhite": true, 279s "blanklineskip": true, 279s "commentchar": "#", 279s "version": false, 279s "inputnastring": "NA", 279s "taxdump": false, 279s "noprogressbar": false, 279s "modulename": "import" 279s }, 279s "import": { 279s "skip": 0, 279s "skiperror": false, 279s "moltype": "nuc", 279s "preread": false, 279s "space_priority": false 279s }, 279s "command_line": "import --quality-solexa wolf_tutorial/wolf_F.fastq wolf/reads1", 279s "input_dms_name": null, 279s "input_view_name": null, 279s "input_str": ["/tmp/autopkgtest.fFxeUa/autopkgtest_tmp/wolf_tutorial/wolf_F.fastq"], 279s "version": "3.0.1b26", 279s "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."], 279s "Date created": "Sat Mar 15 13:46:23 2025" 279s } 279s 279s # Taxonomies: 279s 279s + obi ls wolf/reads1 279s 2025-03-15 13:46:27,563 [ls : INFO ] obi ls 279s # View name: 279s reads1 279s # Date created: 279s Sat Mar 15 13:46:22 2025 279s # Line count: 279s 45276 279s # Columns: 279s NUC_SEQ, data type: OBI_SEQ 279s ID, data type: OBI_STR 279s DEFINITION, data type: OBI_STR 279s QUALITY, data type: OBI_QUAL 279s COUNT, data type: OBI_INT 279s 279s + obi ls wolf/ngsfile/sample 279s 2025-03-15 13:46:27,879 [ls : INFO ] obi ls 279s data type: OBI_STR 279s + obi less wolf/reads1 281s + obi alignpairedend -R wolf/reads2 wolf/reads1 wolf/aligned_reads 281s 2025-03-15 13:46:29,549 [alignpairedend : INFO ] obi alignpairedend 287s 287s 2025-03-15 13:46:35,336 [alignpairedend : INFO ] Done. 287s + obi alignpairedend -R wolf/reads2 wolf/reads1 - 287s 2025-03-15 13:46:35,660 [alignpairedend : INFO ] obi alignpairedend 293s 293s 2025-03-15 13:46:41,016 [alignpairedend : INFO ] Printing to output... 295s 295s 2025-03-15 13:46:43,256 [alignpairedend : INFO ] Done. 295s + obi stats -a score_norm wolf/aligned_reads 295s 2025-03-15 13:46:43,562 [stats : INFO ] obi stats 295s 295s 2025-03-15 13:46:43,886 [stats : INFO ] Done. 295s mean_score_norm count total 295s 0.888201 45276 45276 295s + obi grep -p 'sequence['\''score_norm'\''] > 0.8' wolf/aligned_reads wolf/good_sequences 296s 2025-03-15 13:46:44,203 [grep : INFO ] obi grep 296s 296s 2025-03-15 13:46:44,360 [grep : INFO ] Grepped 38562 entries 296s 2025-03-15 13:46:44,382 [grep : INFO ] Done. 296s + obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences wolf/good_sequences wolf/identified_sequences 296s 2025-03-15 13:46:44,685 [ngsfilter : INFO ] obi ngsfilter 320s 320s 2025-03-15 13:47:08,204 [ngsfilter : INFO ] Done. 320s + obi uniq -m sample wolf/identified_sequences wolf/dereplicated_sequences 320s 2025-03-15 13:47:08,505 [uniq : INFO ] obi uniq 320s 2025-03-15 13:47:08,514 [uniq : INFO ] First browsing through the input 320s 2025-03-15 13:47:08,815 [uniq : INFO ] Second browsing through the input 331s 331s 331s 2025-03-15 13:47:19,083 [uniq : INFO ] Done. 331s + obi annotate -k COUNT -k MERGED_sample wolf/dereplicated_sequences wolf/cleaned_metadata_sequences 331s 2025-03-15 13:47:19,343 [annotate : INFO ] obi annotate 331s 331s 2025-03-15 13:47:19,362 [annotate : INFO ] Done. 331s + obi grep -p 'len(sequence)>=80 and sequence['\''COUNT'\'']>=10' wolf/cleaned_metadata_sequences wolf/denoised_sequences 331s 2025-03-15 13:47:19,606 [grep : INFO ] obi grep 331s 331s 2025-03-15 13:47:19,630 [grep : INFO ] Grepped 190 entries 331s 2025-03-15 13:47:19,632 [grep : INFO ] Done. 331s + obi clean -s MERGED_sample -r 0.05 -H wolf/denoised_sequences wolf/cleaned_sequences 331s 2025-03-15 13:47:19,877 [clean : INFO ] obi clean 331s Running on 2 thread(s) 331s Building kmer tables... : Done 331s Done : 0.000000 % 331s Annotating : 0.000000 % Done : 100 % 331s 2025-03-15 13:47:19,895 [clean : INFO ] Done. 331s + tar cJf /tmp/autopkgtest.fFxeUa/wolf-tutorial-artifacts/wolf.obidms.tar.xz wolf.obidms 436s autopkgtest [13:49:04]: test wolf-tutorial: -----------------------] 437s wolf-tutorial PASS 437s autopkgtest [13:49:05]: test wolf-tutorial: - - - - - - - - - - results - - - - - - - - - - 440s autopkgtest [13:49:08]: @@@@@@@@@@@@@@@@@@@@ summary 440s command1 PASS (superficial) 440s wolf-tutorial PASS 458s nova [W] Using flock in prodstack6-arm64 458s Creating nova instance adt-plucky-arm64-obitools-20250315-134147-juju-7f2275-prod-proposed-migration-environment-2-5aebf411-32e3-4913-a522-ce08644e149d from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 458s nova [W] Timed out waiting for 0f42bd5c-d117-4753-aecb-1432775ea60f to get deleted.