0s autopkgtest [22:00:39]: starting date and time: 2024-03-17 22:00:39+0000 0s autopkgtest [22:00:39]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [22:00:39]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xqbl2eel/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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-2@bos02-s390x-15.secgroup --name adt-noble-s390x-microbiomeutil-20240317-220039-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 115s autopkgtest [22:02:34]: testbed dpkg architecture: s390x 116s autopkgtest [22:02:35]: testbed apt version: 2.7.12 116s autopkgtest [22:02:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 116s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 117s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3676 kB] 117s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [484 kB] 117s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 117s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [639 kB] 117s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 117s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 117s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 117s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3877 kB] 117s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 117s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [33.2 kB] 117s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 119s Fetched 8895 kB in 2s (3859 kB/s) 119s Reading package lists... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 123s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 123s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 123s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 124s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s autopkgtest [22:02:47]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 128s autopkgtest [22:02:47]: @@@@@@@@@@@@@@@@@@@@ apt-source microbiomeutil 132s Get:1 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (dsc) [2409 B] 132s Get:2 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (tar) [1610 kB] 132s Get:3 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (diff) [10.4 kB] 132s gpgv: Signature made Mon Jan 10 17:50:05 2022 UTC 132s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 132s gpgv: issuer "tille@debian.org" 132s gpgv: Can't check signature: No public key 132s dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-5.dsc: no acceptable signature found 132s autopkgtest [22:02:51]: testing package microbiomeutil version 20101212+dfsg1-5 133s autopkgtest [22:02:52]: build not needed 137s autopkgtest [22:02:56]: test run-unit-test: preparing testbed 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Starting pkgProblemResolver with broken count: 0 140s Starting 2 pkgProblemResolver with broken count: 0 141s Done 141s The following additional packages will be installed: 141s cdbfasta chimeraslayer libgclib3 libgomp1 libmbedcrypto7t64 libmbedtls14t64 141s libmbedx509-1t64 microbiomeutil microbiomeutil-data nast-ier ncbi-blast+ 141s ncbi-blast+-legacy ncbi-data wigeon 141s The following NEW packages will be installed: 141s autopkgtest-satdep cdbfasta chimeraslayer libgclib3 libgomp1 141s libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 microbiomeutil 141s microbiomeutil-data nast-ier ncbi-blast+ ncbi-blast+-legacy ncbi-data wigeon 141s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 19.5 MB/19.5 MB of archives. 141s After this operation, 126 MB of additional disk space will be used. 141s Get:1 /tmp/autopkgtest.rCpQvQ/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [740 B] 141s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libgclib3 s390x 0.12.7+ds-5 [152 kB] 141s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x cdbfasta s390x 1.00+git20230710.da8f5ba+dfsg-1 [130 kB] 141s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x microbiomeutil-data all 20101212+dfsg1-5 [1487 kB] 142s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 143s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 143s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedcrypto7t64 s390x 2.28.7-1.1ubuntu1 [216 kB] 143s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedx509-1t64 s390x 2.28.7-1.1ubuntu1 [46.2 kB] 143s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedtls14t64 s390x 2.28.7-1.1ubuntu1 [84.7 kB] 143s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x ncbi-blast+ s390x 2.12.0+ds-4build1 [12.8 MB] 144s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x ncbi-blast+-legacy all 2.12.0+ds-4build1 [4990 B] 144s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x chimeraslayer all 20101212+dfsg1-5 [32.8 kB] 144s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x nast-ier s390x 20101212+dfsg1-5 [21.7 kB] 144s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x wigeon all 20101212+dfsg1-5 [32.0 kB] 144s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x microbiomeutil all 20101212+dfsg1-5 [18.2 kB] 144s Fetched 19.5 MB in 3s (5681 kB/s) 144s Selecting previously unselected package libgclib3:s390x. 145s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52171 files and directories currently installed.) 145s Preparing to unpack .../00-libgclib3_0.12.7+ds-5_s390x.deb ... 145s Unpacking libgclib3:s390x (0.12.7+ds-5) ... 145s Selecting previously unselected package cdbfasta. 145s Preparing to unpack .../01-cdbfasta_1.00+git20230710.da8f5ba+dfsg-1_s390x.deb ... 145s Unpacking cdbfasta (1.00+git20230710.da8f5ba+dfsg-1) ... 145s Selecting previously unselected package microbiomeutil-data. 145s Preparing to unpack .../02-microbiomeutil-data_20101212+dfsg1-5_all.deb ... 145s Unpacking microbiomeutil-data (20101212+dfsg1-5) ... 145s Selecting previously unselected package ncbi-data. 145s Preparing to unpack .../03-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 145s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 145s Selecting previously unselected package libgomp1:s390x. 145s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 145s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 145s Selecting previously unselected package libmbedcrypto7t64:s390x. 145s Preparing to unpack .../05-libmbedcrypto7t64_2.28.7-1.1ubuntu1_s390x.deb ... 145s Unpacking libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ... 145s Selecting previously unselected package libmbedx509-1t64:s390x. 145s Preparing to unpack .../06-libmbedx509-1t64_2.28.7-1.1ubuntu1_s390x.deb ... 145s Unpacking libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ... 145s Selecting previously unselected package libmbedtls14t64:s390x. 145s Preparing to unpack .../07-libmbedtls14t64_2.28.7-1.1ubuntu1_s390x.deb ... 145s Unpacking libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ... 145s Selecting previously unselected package ncbi-blast+. 145s Preparing to unpack .../08-ncbi-blast+_2.12.0+ds-4build1_s390x.deb ... 145s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ... 145s Selecting previously unselected package ncbi-blast+-legacy. 145s Preparing to unpack .../09-ncbi-blast+-legacy_2.12.0+ds-4build1_all.deb ... 145s Unpacking ncbi-blast+-legacy (2.12.0+ds-4build1) ... 145s Selecting previously unselected package chimeraslayer. 145s Preparing to unpack .../10-chimeraslayer_20101212+dfsg1-5_all.deb ... 145s Unpacking chimeraslayer (20101212+dfsg1-5) ... 145s Selecting previously unselected package nast-ier. 145s Preparing to unpack .../11-nast-ier_20101212+dfsg1-5_s390x.deb ... 145s Unpacking nast-ier (20101212+dfsg1-5) ... 145s Selecting previously unselected package wigeon. 145s Preparing to unpack .../12-wigeon_20101212+dfsg1-5_all.deb ... 145s Unpacking wigeon (20101212+dfsg1-5) ... 145s Selecting previously unselected package microbiomeutil. 145s Preparing to unpack .../13-microbiomeutil_20101212+dfsg1-5_all.deb ... 145s Unpacking microbiomeutil (20101212+dfsg1-5) ... 145s Selecting previously unselected package autopkgtest-satdep. 145s Preparing to unpack .../14-1-autopkgtest-satdep.deb ... 145s Unpacking autopkgtest-satdep (0) ... 145s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 145s Setting up libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ... 145s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 145s Setting up microbiomeutil-data (20101212+dfsg1-5) ... 145s Setting up libgclib3:s390x (0.12.7+ds-5) ... 145s Setting up libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ... 145s Setting up wigeon (20101212+dfsg1-5) ... 145s Setting up cdbfasta (1.00+git20230710.da8f5ba+dfsg-1) ... 145s Setting up nast-ier (20101212+dfsg1-5) ... 145s Setting up libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ... 145s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 145s Setting up ncbi-blast+-legacy (2.12.0+ds-4build1) ... 145s Setting up chimeraslayer (20101212+dfsg1-5) ... 145s Setting up microbiomeutil (20101212+dfsg1-5) ... 145s Setting up autopkgtest-satdep (0) ... 145s Processing triggers for man-db (2.12.0-3) ... 146s Processing triggers for libc-bin (2.39-0ubuntu2) ... 148s (Reading database ... 52590 files and directories currently installed.) 148s Removing autopkgtest-satdep (0) ... 149s autopkgtest [22:03:08]: test run-unit-test: [----------------------- 149s CMD: formatdb -i /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta -p F 2>/dev/null 149s 149s 149s Building a new DB, current time: 03/17/2024 22:03:08 149s New DB name: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta 149s New DB title: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta 149s Sequence type: Nucleotide 149s Keep MBits: T 149s Maximum file size: 1000000000B 149s Adding sequences from FASTA; added 5181 sequences in 0.172613 seconds. 149s 149s 149s 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 150s 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 150s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 151s T(1)=1 s 151s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds 152s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 153s T(1)=1 s 153s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds 153s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 154s T(1)=0 s 154s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds 155s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 156s T(1)=1 s 156s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds 156s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 156s T(1)=0 s 156s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds 157s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 158s T(1)=1 s 158s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds 159s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 160s T(1)=1 s 160s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds 160s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 161s T(1)=1 s 161s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds 161s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 162s T(1)=0 s 162s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds 163s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2437.query --db_NAST /tmp/tmp.2437.db -R 1.007 164s T(1)=1 s 164s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 seconds 164s 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 164s 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)] 164s 10 entries from file chims.NAST were indexed in file chims.NAST.cidx 164s Alignment parameters: 164s MATCH: 5 164s MISMATCH: -4 164s GAP: -4 164s 164s Highest score: 10945 164s 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)] 164s Alignment parameters: 164s MATCH: 5 164s MISMATCH: -4 164s GAP: -4 164s 164s Highest score: 12151 164s 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)] 164s Alignment parameters: 164s MATCH: 5 164s MISMATCH: -4 164s GAP: -4 164s 164s Highest score: 12852 164s 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)] 164s Alignment parameters: 164s MATCH: 5 164s MISMATCH: -4 164s GAP: -4 164s 165s Highest score: 12579 165s 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)] 165s Alignment parameters: 165s MATCH: 5 165s MISMATCH: -4 165s GAP: -4 165s 165s Highest score: 13167 165s 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)] 165s Alignment parameters: 165s MATCH: 5 165s MISMATCH: -4 165s GAP: -4 165s 165s Highest score: 11650 165s 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)] 165s Alignment parameters: 165s MATCH: 5 165s MISMATCH: -4 165s GAP: -4 165s 165s Highest score: 11807 165s 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)] 165s Alignment parameters: 165s MATCH: 5 165s MISMATCH: -4 165s GAP: -4 165s 165s Highest score: 13234 165s 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)] 165s Alignment parameters: 165s MATCH: 5 165s MISMATCH: -4 165s GAP: -4 165s 165s Highest score: 12609 165s 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)] 165s Alignment parameters: 165s MATCH: 5 165s MISMATCH: -4 165s GAP: -4 165s 166s Highest score: 11227 166s 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 166s 10 entries from file chims.NAST.CPS_RENAST were indexed in file chims.NAST.CPS_RENAST.cidx 166s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 172s examined parents (7000004128191580, S000428666) or (0, 1) took 2 seconds 172s ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 6 seconds 172s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 178s examined parents (S000378387, S000016146) or (0, 1) took 3 seconds 178s ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 6 seconds 178s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 182s examined parents (7000004131500344, S000127669) or (0, 1) took 2 seconds 182s ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 4 seconds 182s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 188s examined parents (S000004801, S000437365) or (0, 1) took 2 seconds 188s ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 5 seconds 188s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 192s examined parents (S000437007, S000437299) or (0, 1) took 2 seconds 192s ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 4 seconds 192s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 197s examined parents (S000414109, S000253432) or (0, 1) took 2 seconds 197s ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 5 seconds 197s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 204s examined parents (7000004131502379, 7000004128198963) or (0, 1) took 2 seconds 204s ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 7 seconds 204s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 208s examined parents (S000503167, S000004272) or (0, 1) took 2 seconds 208s ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 4 seconds 208s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 211s examined parents (S000436014, 7000004128189973) or (0, 1) took 1 seconds 211s ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 3 seconds 211s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3147.query --db_NAST /tmp/tmp.3147.db -P 90 -R 1.007 --minBS 90 --printAlignments 216s examined parents (S000009720, S000437236) or (0, 1) took 2 seconds 216s ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 5 seconds 216s CMD: /usr/lib/ChimeraSlayer/util/CS_add_taxonomy.pl < chims.NAST.CPS.CPC > chims.NAST.CPS.CPC.wTaxons 217s 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 217s T(1)=0 s 217s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 0 seconds 217s T(1)=0 s 217s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds 217s T(1)=0 s 217s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds 218s T(1)=1 s 218s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds 218s T(1)=0 s 218s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds 218s T(1)=0 s 218s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds 218s T(1)=0 s 218s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds 219s T(1)=0 s 219s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds 219s T(1)=0 s 219s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds 219s T(1)=0 s 219s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 0 seconds 219s 219s 219s query to NAST format 219s NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST 219s 219s 219s query and template (profile) to query NAST and template consensus NAST 219s NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST 219s 219s 219s converting NAST mfasta to multi-alignment output highlighting differences 219s ../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign 219s 219s 219s Use of uninitialized value $accs[0] in hash element at /usr/lib/NAST-iEr/util/show_malign_no_gap.pl line 75. 219s Can't use an undefined value as an ARRAY reference at /usr/lib/NAST-iEr/util/show_malign_no_gap.pl line 75. 219s Run via the megablast wrapper 219s Num template seqs to align to: 2 219s Alignment parameters: 219s MATCH: 5 219s MISMATCH: -4 219s GAP: -4 219s 219s Highest score: 11681 219s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 219s Warning: [blastn] Examining 5 or more matches is recommended 220s chmraD24_7000004128191580_1-4580:4581-7682_S000428666 7000004128191580 div: 9.37 stDev: 10.66 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 220s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 220s Warning: [blastn] Examining 5 or more matches is recommended 220s chmraD19_S000378387_1-5075:5076-7682_S000016146 7000004128191204 div: 4.85 stDev: 6.36 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 220s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 220s Warning: [blastn] Examining 5 or more matches is recommended 221s chmraD12_7000004131500344_1-4694:4695-7682_S000127669 7000004131500344 div: 3.75 stDev: 4.32 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 221s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 221s Warning: [blastn] Examining 5 or more matches is recommended 221s chmraD13_S000004801_1-4690:4691-7682_S000437365 S000004801 div: 3.89 stDev: 4.96 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 221s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 221s Warning: [blastn] Examining 5 or more matches is recommended 222s chmraD9_S000437007_1-4525:4526-7682_S000437299 S000437007 div: 3.73 stDev: 5.10 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 222s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 222s Warning: [blastn] Examining 5 or more matches is recommended 222s chmraD17_S000414109_1-4650:4651-7682_S000253432 S000414109 div: 5.56 stDev: 6.73 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 222s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 222s Warning: [blastn] Examining 5 or more matches is recommended 223s chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963 7000004131502379 div: 7.66 stDev: 9.74 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 223s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 223s Warning: [blastn] Examining 5 or more matches is recommended 223s chmraD8_S000004272_1-3794:3795-7682_S000503167 S000503167 div: 3.88 stDev: 3.27 Quant95:Yes Quant99:YES Quant99.9:No Quant99.99:No 223s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 223s Warning: [blastn] Examining 5 or more matches is recommended 223s chmraD11_S000436014_1-5755:5756-7682_7000004128189973 S000436014 div: 2.18 stDev: 2.89 Quant95:Yes Quant99:YES Quant99.9:No Quant99.99:No 224s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 224s Warning: [blastn] Examining 5 or more matches is recommended 224s chmraD23_S000009720_1-5056:5057-7682_S000437236 S000009720 div: 5.00 stDev: 6.17 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 224s autopkgtest [22:04:23]: test run-unit-test: -----------------------] 225s autopkgtest [22:04:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 225s run-unit-test PASS 225s autopkgtest [22:04:24]: @@@@@@@@@@@@@@@@@@@@ summary 225s run-unit-test PASS 244s Creating nova instance adt-noble-s390x-microbiomeutil-20240317-220039-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240316.img (UUID 7afe023c-7cb8-41b6-91a7-c69e7d1e7c0d)...