0s autopkgtest [18:36:36]: starting date and time: 2024-03-18 18:36:36+0000 0s autopkgtest [18:36:36]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [18:36:36]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fhpqy1o8/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:ncbi-blast+,src:mbedtls --apt-upgrade microbiomeutil --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-8.secgroup --name adt-noble-ppc64el-microbiomeutil-20240318-183635-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/ 253s autopkgtest [18:40:49]: testbed dpkg architecture: ppc64el 253s autopkgtest [18:40:49]: testbed apt version: 2.7.12 253s autopkgtest [18:40:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 254s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 255s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 255s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 255s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 255s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3720 kB] 256s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [643 kB] 256s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 256s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 256s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 256s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4012 kB] 257s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 257s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [48.4 kB] 257s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 260s Fetched 9098 kB in 3s (2711 kB/s) 260s Reading package lists... 263s Reading package lists... 263s Building dependency tree... 263s Reading state information... 263s Calculating upgrade... 263s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 263s Reading package lists... 263s Building dependency tree... 263s Reading state information... 264s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 264s sh: Attempting to set up Debian/Ubuntu apt sources automatically 264s sh: Distribution appears to be Ubuntu 265s Reading package lists... 265s Building dependency tree... 265s Reading state information... 265s eatmydata is already the newest version (131-1). 265s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 265s Reading package lists... 266s Building dependency tree... 266s Reading state information... 266s dbus is already the newest version (1.14.10-4ubuntu1). 266s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 266s Reading package lists... 266s Building dependency tree... 266s Reading state information... 266s rng-tools-debian is already the newest version (2.4). 266s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 266s Reading package lists... 266s Building dependency tree... 266s Reading state information... 267s The following packages will be REMOVED: 267s cloud-init* python3-configobj* python3-debconf* 267s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 267s After this operation, 3252 kB disk space will be freed. 267s (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 ... 70095 files and directories currently installed.) 267s Removing cloud-init (24.1.1-0ubuntu1) ... 267s Removing python3-configobj (5.0.8-3) ... 268s Removing python3-debconf (1.5.86) ... 268s Processing triggers for man-db (2.12.0-3) ... 268s (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 ... 69706 files and directories currently installed.) 268s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 269s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 269s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 269s invoke-rc.d: policy-rc.d denied execution of try-restart. 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 269s linux-generic is already the newest version (6.8.0-11.11+1). 269s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 270s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 270s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 270s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 272s Reading package lists... 272s Reading package lists... 273s Building dependency tree... 273s Reading state information... 273s Calculating upgrade... 273s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 273s Reading package lists... 273s Building dependency tree... 273s Reading state information... 273s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 274s autopkgtest [18:41:10]: rebooting testbed after setup commands that affected boot 441s autopkgtest [18:43:57]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 444s autopkgtest [18:44:00]: @@@@@@@@@@@@@@@@@@@@ apt-source microbiomeutil 447s Get:1 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (dsc) [2409 B] 447s Get:2 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (tar) [1610 kB] 447s Get:3 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (diff) [10.4 kB] 448s gpgv: Signature made Mon Jan 10 17:50:05 2022 UTC 448s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 448s gpgv: issuer "tille@debian.org" 448s gpgv: Can't check signature: No public key 448s dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-5.dsc: no acceptable signature found 448s autopkgtest [18:44:04]: testing package microbiomeutil version 20101212+dfsg1-5 448s autopkgtest [18:44:04]: build not needed 562s autopkgtest [18:45:58]: test run-unit-test: preparing testbed 565s Reading package lists... 565s Building dependency tree... 565s Reading state information... 565s Starting pkgProblemResolver with broken count: 0 565s Starting 2 pkgProblemResolver with broken count: 0 565s Done 565s The following additional packages will be installed: 565s cdbfasta chimeraslayer libgclib3 libgomp1 libmbedcrypto7 libmbedtls14 565s libmbedx509-1 microbiomeutil microbiomeutil-data nast-ier ncbi-blast+ 565s ncbi-blast+-legacy ncbi-data wigeon 565s The following NEW packages will be installed: 565s autopkgtest-satdep cdbfasta chimeraslayer libgclib3 libgomp1 libmbedcrypto7 565s libmbedtls14 libmbedx509-1 microbiomeutil microbiomeutil-data nast-ier 565s ncbi-blast+ ncbi-blast+-legacy ncbi-data wigeon 565s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 565s Need to get 20.2 MB/20.2 MB of archives. 565s After this operation, 136 MB of additional disk space will be used. 565s Get:1 /tmp/autopkgtest.JC5ql8/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [748 B] 565s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgclib3 ppc64el 0.12.7+ds-5 [193 kB] 566s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el cdbfasta ppc64el 1.00+git20230710.da8f5ba+dfsg-1 [132 kB] 566s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el microbiomeutil-data all 20101212+dfsg1-5 [1487 kB] 566s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 567s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 567s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedcrypto7 ppc64el 2.28.7-1ubuntu1 [262 kB] 567s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedx509-1 ppc64el 2.28.7-1ubuntu1 [51.4 kB] 567s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedtls14 ppc64el 2.28.7-1ubuntu1 [89.7 kB] 567s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-blast+ ppc64el 2.12.0+ds-4 [13.4 MB] 568s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-blast+-legacy all 2.12.0+ds-4 [4984 B] 568s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el chimeraslayer all 20101212+dfsg1-5 [32.8 kB] 568s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el nast-ier ppc64el 20101212+dfsg1-5 [22.2 kB] 568s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el wigeon all 20101212+dfsg1-5 [32.0 kB] 568s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el microbiomeutil all 20101212+dfsg1-5 [18.2 kB] 568s Fetched 20.2 MB in 2s (8301 kB/s) 568s Selecting previously unselected package libgclib3:ppc64el. 568s (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 ... 69651 files and directories currently installed.) 568s Preparing to unpack .../00-libgclib3_0.12.7+ds-5_ppc64el.deb ... 568s Unpacking libgclib3:ppc64el (0.12.7+ds-5) ... 568s Selecting previously unselected package cdbfasta. 568s Preparing to unpack .../01-cdbfasta_1.00+git20230710.da8f5ba+dfsg-1_ppc64el.deb ... 568s Unpacking cdbfasta (1.00+git20230710.da8f5ba+dfsg-1) ... 568s Selecting previously unselected package microbiomeutil-data. 568s Preparing to unpack .../02-microbiomeutil-data_20101212+dfsg1-5_all.deb ... 568s Unpacking microbiomeutil-data (20101212+dfsg1-5) ... 568s Selecting previously unselected package ncbi-data. 568s Preparing to unpack .../03-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 568s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 569s Selecting previously unselected package libgomp1:ppc64el. 569s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 569s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 569s Selecting previously unselected package libmbedcrypto7:ppc64el. 569s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_ppc64el.deb ... 569s Unpacking libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 569s Selecting previously unselected package libmbedx509-1:ppc64el. 569s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_ppc64el.deb ... 569s Unpacking libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 569s Selecting previously unselected package libmbedtls14:ppc64el. 569s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_ppc64el.deb ... 569s Unpacking libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 569s Selecting previously unselected package ncbi-blast+. 569s Preparing to unpack .../08-ncbi-blast+_2.12.0+ds-4_ppc64el.deb ... 569s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 569s Selecting previously unselected package ncbi-blast+-legacy. 569s Preparing to unpack .../09-ncbi-blast+-legacy_2.12.0+ds-4_all.deb ... 569s Unpacking ncbi-blast+-legacy (2.12.0+ds-4) ... 569s Selecting previously unselected package chimeraslayer. 569s Preparing to unpack .../10-chimeraslayer_20101212+dfsg1-5_all.deb ... 569s Unpacking chimeraslayer (20101212+dfsg1-5) ... 569s Selecting previously unselected package nast-ier. 569s Preparing to unpack .../11-nast-ier_20101212+dfsg1-5_ppc64el.deb ... 569s Unpacking nast-ier (20101212+dfsg1-5) ... 569s Selecting previously unselected package wigeon. 569s Preparing to unpack .../12-wigeon_20101212+dfsg1-5_all.deb ... 569s Unpacking wigeon (20101212+dfsg1-5) ... 569s Selecting previously unselected package microbiomeutil. 569s Preparing to unpack .../13-microbiomeutil_20101212+dfsg1-5_all.deb ... 569s Unpacking microbiomeutil (20101212+dfsg1-5) ... 569s Selecting previously unselected package autopkgtest-satdep. 569s Preparing to unpack .../14-1-autopkgtest-satdep.deb ... 569s Unpacking autopkgtest-satdep (0) ... 569s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 569s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 569s Setting up libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 569s Setting up microbiomeutil-data (20101212+dfsg1-5) ... 569s Setting up libgclib3:ppc64el (0.12.7+ds-5) ... 569s Setting up libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 569s Setting up libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 569s Setting up ncbi-blast+ (2.12.0+ds-4) ... 569s Setting up wigeon (20101212+dfsg1-5) ... 569s Setting up cdbfasta (1.00+git20230710.da8f5ba+dfsg-1) ... 569s Setting up nast-ier (20101212+dfsg1-5) ... 569s Setting up ncbi-blast+-legacy (2.12.0+ds-4) ... 569s Setting up chimeraslayer (20101212+dfsg1-5) ... 569s Setting up microbiomeutil (20101212+dfsg1-5) ... 569s Setting up autopkgtest-satdep (0) ... 569s Processing triggers for man-db (2.12.0-3) ... 570s Processing triggers for libc-bin (2.39-0ubuntu2) ... 572s (Reading database ... 70067 files and directories currently installed.) 572s Removing autopkgtest-satdep (0) ... 573s autopkgtest [18:46:09]: test run-unit-test: [----------------------- 573s 573s 573s query to NAST format 573s NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST 573s 573s 573s query and template (profile) to query NAST and template consensus NAST 573s NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST 573s 573s 573s converting NAST mfasta to multi-alignment output highlighting differences 573s ../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign 573s 573s 573s Run via the megablast wrapper 573s Use of uninitialized value $accs[0] in hash element at /usr/lib/NAST-iEr/util/show_malign_no_gap.pl line 75. 573s Can't use an undefined value as an ARRAY reference at /usr/lib/NAST-iEr/util/show_malign_no_gap.pl line 75. 574s 5181 entries from file /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta were indexed in file /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta.cidx 574s Num template seqs to align to: 2 574s Alignment parameters: 574s MATCH: 5 574s MISMATCH: -4 574s GAP: -4 574s 574s Highest score: 11681 574s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 574s Warning: [blastn] Examining 5 or more matches is recommended 575s chmraD24_7000004128191580_1-4580:4581-7682_S000428666 7000004128191580 div: 9.37 stDev: 10.66 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 575s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 575s Warning: [blastn] Examining 5 or more matches is recommended 575s chmraD19_S000378387_1-5075:5076-7682_S000016146 7000004128191204 div: 4.85 stDev: 6.36 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 575s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 575s Warning: [blastn] Examining 5 or more matches is recommended 576s chmraD12_7000004131500344_1-4694:4695-7682_S000127669 7000004131500344 div: 3.75 stDev: 4.32 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 576s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 576s Warning: [blastn] Examining 5 or more matches is recommended 576s chmraD13_S000004801_1-4690:4691-7682_S000437365 S000004801 div: 3.89 stDev: 4.96 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 576s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 576s Warning: [blastn] Examining 5 or more matches is recommended 577s chmraD9_S000437007_1-4525:4526-7682_S000437299 S000437007 div: 3.73 stDev: 5.10 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 577s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 577s Warning: [blastn] Examining 5 or more matches is recommended 577s chmraD17_S000414109_1-4650:4651-7682_S000253432 S000414109 div: 5.56 stDev: 6.73 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 577s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 577s Warning: [blastn] Examining 5 or more matches is recommended 578s chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963 7000004131502379 div: 7.66 stDev: 9.74 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 578s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 578s Warning: [blastn] Examining 5 or more matches is recommended 578s chmraD8_S000004272_1-3794:3795-7682_S000503167 S000503167 div: 3.88 stDev: 3.27 Quant95:Yes Quant99:YES Quant99.9:No Quant99.99:No 578s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 578s Warning: [blastn] Examining 5 or more matches is recommended 578s chmraD11_S000436014_1-5755:5756-7682_7000004128189973 S000436014 div: 2.18 stDev: 2.89 Quant95:Yes Quant99:YES Quant99.9:No Quant99.99:No 579s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 579s Warning: [blastn] Examining 5 or more matches is recommended 579s chmraD23_S000009720_1-5056:5057-7682_S000437236 S000009720 div: 5.00 stDev: 6.17 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 579s CMD: /usr/lib/ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl --query_NAST chims.NAST --db_NAST /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta --db_FASTA /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta -n 15 -P 90 -R 1.007 > chims.NAST.CPS 579s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 581s T(1)=1 s 581s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds 582s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 583s T(1)=1 s 583s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds 584s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 585s T(1)=1 s 585s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds 586s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 587s T(1)=1 s 587s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds 587s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 588s T(1)=1 s 588s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 1 seconds 588s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 590s T(1)=1 s 590s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds 590s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 592s T(1)=1 s 592s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds 592s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 594s T(1)=1 s 594s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds 594s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 595s T(1)=1 s 595s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds 596s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1617.query --db_NAST /tmp/tmp.1617.db -R 1.007 597s T(1)=1 s 597s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 seconds 597s CMD: /usr/lib/ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST --db_NAST /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS_RENAST 597s processing: ChimeraParentSelector chmraD24_7000004128191580_1-4580:4581-7682_S000428666 YES 100.00[(7000004128191580, NAST:164-4593, ECO:36-940, RawLen:876, G:90.90, L:100.00, 1.100);(S000428666, NAST:4594-6747, ECO:940-1470, RawLen:531, G:84.36, L:100.00, 1.185)] 597s 10 entries from file chims.NAST were indexed in file chims.NAST.cidx 597s Alignment parameters: 597s MATCH: 5 597s MISMATCH: -4 597s GAP: -4 597s 597s Highest score: 10945 597s processing: ChimeraParentSelector chmraD19_S000378387_1-5075:5076-7682_S000016146 YES 100.00[(S000378387, NAST:443-5077, ECO:94-1125, RawLen:1041, G:96.08, L:100.00, 1.041);(S000016146, NAST:5079-6498, ECO:1126-1424, RawLen:301, G:85.08, L:100.00, 1.175)] 597s Alignment parameters: 597s MATCH: 5 597s MISMATCH: -4 597s GAP: -4 597s 598s Highest score: 12151 598s processing: ChimeraParentSelector chmraD12_7000004131500344_1-4694:4695-7682_S000127669 YES 100.00[(7000004131500344, NAST:426-4710, ECO:86-999, RawLen:914, G:96.38, L:100.00, 1.038);(S000127669, NAST:4711-6711, ECO:999-1451, RawLen:453, G:92.52, L:100.00, 1.081)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 598s Highest score: 12852 598s processing: ChimeraParentSelector chmraD13_S000004801_1-4690:4691-7682_S000437365 YES 100.00[(S000004801, NAST:455-4707, ECO:101-997, RawLen:913, G:96.34, L:100.00, 1.038);(S000437365, NAST:4708-6424, ECO:997-1382, RawLen:391, G:90.85, L:100.00, 1.101)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 598s Highest score: 12579 598s processing: ChimeraParentSelector chmraD9_S000437007_1-4525:4526-7682_S000437299 YES 100.00[(S000437007, NAST:164-4657, ECO:36-982, RawLen:903, G:96.21, L:100.00, 1.039);(S000437299, NAST:4658-6422, ECO:983-1380, RawLen:401, G:94.45, L:100.00, 1.059)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 598s Highest score: 13167 598s processing: ChimeraParentSelector chmraD17_S000414109_1-4650:4651-7682_S000253432 YES 100.00[(S000414109, NAST:153-4671, ECO:31-990, RawLen:907, G:94.16, L:100.00, 1.062);(S000253432, NAST:4673-6716, ECO:991-1453, RawLen:462, G:88.62, L:100.00, 1.128)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 598s Highest score: 11650 598s processing: ChimeraParentSelector chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963 YES 100.00[(7000004131502379, NAST:489-4623, ECO:115-959, RawLen:851, G:92.66, L:100.00, 1.079);(7000004128198963, NAST:4625-6422, ECO:961-1380, RawLen:422, G:84.94, L:100.00, 1.177)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 598s Highest score: 11807 598s processing: ChimeraParentSelector chmraD8_S000004272_1-3794:3795-7682_S000503167 YES 100.00[(S000004272, NAST:162-3829, ECO:35-701, RawLen:668, G:95.64, L:100.00, 1.046);(S000503167, NAST:3831-6464, ECO:702-1405, RawLen:705, G:95.81, L:100.00, 1.044)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 598s Highest score: 13234 598s processing: ChimeraParentSelector chmraD11_S000436014_1-5755:5756-7682_7000004128189973 YES 100.00[(S000436014, NAST:428-5920, ECO:88-1237, RawLen:1122, G:97.80, L:100.00, 1.022);(7000004128189973, NAST:5921-6521, ECO:1238-1435, RawLen:200, G:91.75, L:100.00, 1.090)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 598s Highest score: 12609 598s processing: ChimeraParentSelector chmraD23_S000009720_1-5056:5057-7682_S000437236 YES 100.00[(S000009720, NAST:184-5057, ECO:47-1116, RawLen:1079, G:96.18, L:100.00, 1.040);(S000437236, NAST:5058-6474, ECO:1117-1411, RawLen:296, G:81.53, L:100.00, 1.227)] 598s Alignment parameters: 598s MATCH: 5 598s MISMATCH: -4 598s GAP: -4 598s 599s Highest score: 11227 599s CMD: /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/CPS_to_CPC.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST.CPS_RENAST --db_NAST /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta -P 90 -R 1.007 --minBS 90 --printAlignments > chims.NAST.CPS.CPC 599s 10 entries from file chims.NAST.CPS_RENAST were indexed in file chims.NAST.CPS_RENAST.cidx 599s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 608s examined parents (7000004128191580, S000428666) or (0, 1) took 3 seconds 608s ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 9 seconds 608s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 614s examined parents (S000378387, S000016146) or (0, 1) took 3 seconds 614s ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 6 seconds 614s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 621s examined parents (7000004131500344, S000127669) or (0, 1) took 3 seconds 621s ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 7 seconds 621s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 628s examined parents (S000004801, S000437365) or (0, 1) took 3 seconds 628s ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 7 seconds 628s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 634s examined parents (S000437007, S000437299) or (0, 1) took 3 seconds 634s ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 6 seconds 634s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 640s examined parents (S000414109, S000253432) or (0, 1) took 2 seconds 640s ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 6 seconds 640s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 650s examined parents (7000004131502379, 7000004128198963) or (0, 1) took 3 seconds 650s ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 10 seconds 650s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 654s examined parents (S000503167, S000004272) or (0, 1) took 2 seconds 654s ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 4 seconds 654s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 659s examined parents (S000436014, 7000004128189973) or (0, 1) took 3 seconds 659s ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 5 seconds 659s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2326.query --db_NAST /tmp/tmp.2326.db -P 90 -R 1.007 --minBS 90 --printAlignments 665s examined parents (S000009720, S000437236) or (0, 1) took 3 seconds 665s ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 6 seconds 665s CMD: /usr/lib/ChimeraSlayer/util/CS_add_taxonomy.pl < chims.NAST.CPS.CPC > chims.NAST.CPS.CPC.wTaxons 666s CMD: /usr/lib/ChimeraSlayer/ChimeraParentSelector/CPC_to_CPS.pl --CPC_output chims.NAST.CPS.CPC --query_NAST chims.NAST.CPS_RENAST --db_NAST /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS.CPC.align 666s T(1)=0 s 666s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 0 seconds 666s T(1)=0 s 666s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds 667s T(1)=0 s 667s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds 667s T(1)=0 s 667s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds 667s T(1)=0 s 667s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds 667s T(1)=0 s 667s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds 667s T(1)=0 s 667s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds 668s T(1)=0 s 668s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds 668s T(1)=0 s 668s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds 668s T(1)=0 s 668s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 0 seconds 668s autopkgtest [18:47:44]: test run-unit-test: -----------------------] 669s autopkgtest [18:47:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 669s run-unit-test PASS 670s autopkgtest [18:47:46]: @@@@@@@@@@@@@@@@@@@@ summary 670s run-unit-test PASS 693s Creating nova instance adt-noble-ppc64el-microbiomeutil-20240318-183635-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240318.img (UUID 290ce4c5-ca44-4691-9a55-79589f8700e4)...