0s autopkgtest [02:02:48]: starting date: 2024-03-18 0s autopkgtest [02:02:48]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt 0s autopkgtest [02:02:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3nya_2m5/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@bos03-arm64-4.secgroup --name adt-noble-arm64-microbiomeutil-20240318-020248-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 155s autopkgtest [02:05:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 156s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 156s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 156s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 156s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 156s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 156s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 156s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 156s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 156s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 156s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 156s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 156s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 158s Fetched 9189 kB in 2s (5185 kB/s) 158s Reading package lists... 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Calculating upgrade... 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 163s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 163s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 163s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 164s Reading package lists... 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Calculating upgrade... 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s autopkgtest [02:05:35]: testbed dpkg architecture: arm64 169s autopkgtest [02:05:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 169s autopkgtest [02:05:37]: @@@@@@@@@@@@@@@@@@@@ apt-source microbiomeutil 171s Get:1 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (dsc) [2409 B] 171s Get:2 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (tar) [1610 kB] 171s Get:3 http://ftpmaster.internal/ubuntu noble/universe microbiomeutil 20101212+dfsg1-5 (diff) [10.4 kB] 172s gpgv: Signature made Mon Jan 10 17:50:05 2022 UTC 172s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 172s gpgv: issuer "tille@debian.org" 172s gpgv: Can't check signature: No public key 172s dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-5.dsc: no acceptable signature found 172s autopkgtest [02:05:40]: testing package microbiomeutil version 20101212+dfsg1-5 172s autopkgtest [02:05:40]: build not needed 176s autopkgtest [02:05:44]: test run-unit-test: preparing testbed 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 179s Done 179s Starting pkgProblemResolver with broken count: 0 179s Starting 2 pkgProblemResolver with broken count: 0 179s Done 180s The following additional packages will be installed: 180s cdbfasta chimeraslayer libgclib3 libgomp1 libmbedcrypto7t64 libmbedtls14t64 180s libmbedx509-1t64 microbiomeutil microbiomeutil-data nast-ier ncbi-blast+ 180s ncbi-blast+-legacy ncbi-data wigeon 180s The following NEW packages will be installed: 180s cdbfasta chimeraslayer libgclib3 libgomp1 libmbedcrypto7t64 libmbedtls14t64 180s libmbedx509-1t64 microbiomeutil microbiomeutil-data nast-ier ncbi-blast+ 180s ncbi-blast+-legacy ncbi-data wigeon 180s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 180s 1 not fully installed or removed. 180s Need to get 18.8 MB of archives. 180s After this operation, 128 MB of additional disk space will be used. 180s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 microbiomeutil-data all 20101212+dfsg1-5 [1487 kB] 181s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libgclib3 arm64 0.12.7+ds-5 [148 kB] 181s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 cdbfasta arm64 1.00+git20230710.da8f5ba+dfsg-1 [128 kB] 181s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 181s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 181s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB] 181s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB] 181s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB] 181s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB] 182s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+-legacy all 2.12.0+ds-4build1 [4990 B] 182s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 chimeraslayer all 20101212+dfsg1-5 [32.8 kB] 182s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 nast-ier arm64 20101212+dfsg1-5 [21.3 kB] 182s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 wigeon all 20101212+dfsg1-5 [32.0 kB] 182s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 microbiomeutil all 20101212+dfsg1-5 [18.2 kB] 183s Fetched 18.8 MB in 2s (11.5 MB/s) 183s Selecting previously unselected package microbiomeutil-data. 183s (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 ... 74758 files and directories currently installed.) 183s Preparing to unpack .../00-microbiomeutil-data_20101212+dfsg1-5_all.deb ... 183s Unpacking microbiomeutil-data (20101212+dfsg1-5) ... 183s Selecting previously unselected package libgclib3:arm64. 183s Preparing to unpack .../01-libgclib3_0.12.7+ds-5_arm64.deb ... 183s Unpacking libgclib3:arm64 (0.12.7+ds-5) ... 183s Selecting previously unselected package cdbfasta. 183s Preparing to unpack .../02-cdbfasta_1.00+git20230710.da8f5ba+dfsg-1_arm64.deb ... 183s Unpacking cdbfasta (1.00+git20230710.da8f5ba+dfsg-1) ... 184s Selecting previously unselected package ncbi-data. 184s Preparing to unpack .../03-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 184s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 184s Selecting previously unselected package libgomp1:arm64. 184s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 184s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 184s Selecting previously unselected package libmbedcrypto7t64:arm64. 184s Preparing to unpack .../05-libmbedcrypto7t64_2.28.7-1.1ubuntu1_arm64.deb ... 184s Unpacking libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 184s Selecting previously unselected package libmbedx509-1t64:arm64. 184s Preparing to unpack .../06-libmbedx509-1t64_2.28.7-1.1ubuntu1_arm64.deb ... 184s Unpacking libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 184s Selecting previously unselected package libmbedtls14t64:arm64. 184s Preparing to unpack .../07-libmbedtls14t64_2.28.7-1.1ubuntu1_arm64.deb ... 184s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 184s Selecting previously unselected package ncbi-blast+. 184s Preparing to unpack .../08-ncbi-blast+_2.12.0+ds-4build1_arm64.deb ... 184s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ... 185s Selecting previously unselected package ncbi-blast+-legacy. 185s Preparing to unpack .../09-ncbi-blast+-legacy_2.12.0+ds-4build1_all.deb ... 185s Unpacking ncbi-blast+-legacy (2.12.0+ds-4build1) ... 185s Selecting previously unselected package chimeraslayer. 185s Preparing to unpack .../10-chimeraslayer_20101212+dfsg1-5_all.deb ... 185s Unpacking chimeraslayer (20101212+dfsg1-5) ... 185s Selecting previously unselected package nast-ier. 185s Preparing to unpack .../11-nast-ier_20101212+dfsg1-5_arm64.deb ... 185s Unpacking nast-ier (20101212+dfsg1-5) ... 185s Selecting previously unselected package wigeon. 185s Preparing to unpack .../12-wigeon_20101212+dfsg1-5_all.deb ... 185s Unpacking wigeon (20101212+dfsg1-5) ... 185s Selecting previously unselected package microbiomeutil. 185s Preparing to unpack .../13-microbiomeutil_20101212+dfsg1-5_all.deb ... 185s Unpacking microbiomeutil (20101212+dfsg1-5) ... 185s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 185s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 185s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 185s Setting up microbiomeutil-data (20101212+dfsg1-5) ... 185s Setting up libgclib3:arm64 (0.12.7+ds-5) ... 185s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 185s Setting up wigeon (20101212+dfsg1-5) ... 185s Setting up cdbfasta (1.00+git20230710.da8f5ba+dfsg-1) ... 185s Setting up nast-ier (20101212+dfsg1-5) ... 185s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 185s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 185s Setting up ncbi-blast+-legacy (2.12.0+ds-4build1) ... 185s Setting up chimeraslayer (20101212+dfsg1-5) ... 185s Setting up microbiomeutil (20101212+dfsg1-5) ... 185s Setting up autopkgtest-satdep (0) ... 185s Processing triggers for man-db (2.12.0-3) ... 186s Processing triggers for libc-bin (2.39-0ubuntu2) ... 190s (Reading database ... 75177 files and directories currently installed.) 190s Removing autopkgtest-satdep (0) ... 191s autopkgtest [02:05:59]: test run-unit-test: [----------------------- 191s 191s 191s query to NAST format 191s NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST 191s 191s 192s query and template (profile) to query NAST and template consensus NAST 192s NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST 192s 192s 192s converting NAST mfasta to multi-alignment output highlighting differences 192s ../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign 192s 192s 192s Use of uninitialized value $accs[0] in hash element at /usr/lib/NAST-iEr/util/show_malign_no_gap.pl line 75. 192s Can't use an undefined value as an ARRAY reference at /usr/lib/NAST-iEr/util/show_malign_no_gap.pl line 75. 192s Run via the megablast wrapper 193s 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 193s Num template seqs to align to: 2 193s Alignment parameters: 193s MATCH: 5 193s MISMATCH: -4 193s GAP: -4 193s 193s Highest score: 11681 193s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 193s Warning: [blastn] Examining 5 or more matches is recommended 193s chmraD24_7000004128191580_1-4580:4581-7682_S000428666 7000004128191580 div: 9.37 stDev: 10.66 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 193s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 193s Warning: [blastn] Examining 5 or more matches is recommended 194s chmraD19_S000378387_1-5075:5076-7682_S000016146 7000004128191204 div: 4.85 stDev: 6.36 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 194s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 194s Warning: [blastn] Examining 5 or more matches is recommended 194s chmraD12_7000004131500344_1-4694:4695-7682_S000127669 7000004131500344 div: 3.75 stDev: 4.32 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 194s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 194s Warning: [blastn] Examining 5 or more matches is recommended 195s chmraD13_S000004801_1-4690:4691-7682_S000437365 S000004801 div: 3.89 stDev: 4.96 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 195s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 195s Warning: [blastn] Examining 5 or more matches is recommended 195s chmraD9_S000437007_1-4525:4526-7682_S000437299 S000437007 div: 3.73 stDev: 5.10 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 195s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 195s Warning: [blastn] Examining 5 or more matches is recommended 195s chmraD17_S000414109_1-4650:4651-7682_S000253432 S000414109 div: 5.56 stDev: 6.73 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 196s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 196s Warning: [blastn] Examining 5 or more matches is recommended 196s chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963 7000004131502379 div: 7.66 stDev: 9.74 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 196s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 196s Warning: [blastn] Examining 5 or more matches is recommended 196s chmraD8_S000004272_1-3794:3795-7682_S000503167 S000503167 div: 3.88 stDev: 3.27 Quant95:Yes Quant99:YES Quant99.9:No Quant99.99:No 196s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 196s Warning: [blastn] Examining 5 or more matches is recommended 197s chmraD11_S000436014_1-5755:5756-7682_7000004128189973 S000436014 div: 2.18 stDev: 2.89 Quant95:Yes Quant99:YES Quant99.9:No Quant99.99:No 197s Warning: [blastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output 197s Warning: [blastn] Examining 5 or more matches is recommended 197s chmraD23_S000009720_1-5056:5057-7682_S000437236 S000009720 div: 5.00 stDev: 6.17 Quant95:Yes Quant99:YES Quant99.9:YES Quant99.99:YES 197s 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 198s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 199s T(1)=1 s 199s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds 200s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 201s T(1)=1 s 201s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds 202s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 203s T(1)=1 s 203s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds 203s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 204s T(1)=0 s 204s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds 204s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 205s T(1)=0 s 205s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds 205s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 207s T(1)=0 s 207s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds 207s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 208s T(1)=1 s 208s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds 208s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 209s T(1)=0 s 209s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds 210s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 210s T(1)=0 s 210s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds 211s /usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2312.query --db_NAST /tmp/tmp.2312.db -R 1.007 212s T(1)=1 s 212s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 seconds 212s 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 212s 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)] 212s 10 entries from file chims.NAST were indexed in file chims.NAST.cidx 212s Alignment parameters: 212s MATCH: 5 212s MISMATCH: -4 212s GAP: -4 212s 212s Highest score: 10945 212s 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)] 212s Alignment parameters: 212s MATCH: 5 212s MISMATCH: -4 212s GAP: -4 212s 212s Highest score: 12151 212s 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)] 212s Alignment parameters: 212s MATCH: 5 212s MISMATCH: -4 212s GAP: -4 212s 212s Highest score: 12852 213s 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)] 213s Alignment parameters: 213s MATCH: 5 213s MISMATCH: -4 213s GAP: -4 213s 213s Highest score: 12579 213s 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)] 213s Alignment parameters: 213s MATCH: 5 213s MISMATCH: -4 213s GAP: -4 213s 213s Highest score: 13167 213s 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)] 213s Alignment parameters: 213s MATCH: 5 213s MISMATCH: -4 213s GAP: -4 213s 213s Highest score: 11650 213s 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)] 213s Alignment parameters: 213s MATCH: 5 213s MISMATCH: -4 213s GAP: -4 213s 213s Highest score: 11807 213s 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)] 213s Alignment parameters: 213s MATCH: 5 213s MISMATCH: -4 213s GAP: -4 213s 213s Highest score: 13234 213s 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)] 213s Alignment parameters: 213s MATCH: 5 213s MISMATCH: -4 213s GAP: -4 213s 213s Highest score: 12609 213s 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)] 213s Alignment parameters: 213s MATCH: 5 213s MISMATCH: -4 213s GAP: -4 213s 213s Highest score: 11227 213s 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 213s 10 entries from file chims.NAST.CPS_RENAST were indexed in file chims.NAST.CPS_RENAST.cidx 213s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 219s examined parents (7000004128191580, S000428666) or (0, 1) took 2 seconds 219s ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 6 seconds 219s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 224s examined parents (S000378387, S000016146) or (0, 1) took 2 seconds 224s ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 5 seconds 224s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 229s examined parents (7000004131500344, S000127669) or (0, 1) took 2 seconds 229s ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 5 seconds 229s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 234s examined parents (S000004801, S000437365) or (0, 1) took 2 seconds 234s ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 5 seconds 234s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 238s examined parents (S000437007, S000437299) or (0, 1) took 2 seconds 238s ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 4 seconds 238s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 242s examined parents (S000414109, S000253432) or (0, 1) took 2 seconds 242s ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 4 seconds 242s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 250s examined parents (7000004131502379, 7000004128198963) or (0, 1) took 3 seconds 250s ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 8 seconds 250s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 253s examined parents (S000503167, S000004272) or (0, 1) took 2 seconds 253s ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 3 seconds 253s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 256s examined parents (S000436014, 7000004128189973) or (0, 1) took 2 seconds 256s ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 3 seconds 257s /usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3021.query --db_NAST /tmp/tmp.3021.db -P 90 -R 1.007 --minBS 90 --printAlignments 261s examined parents (S000009720, S000437236) or (0, 1) took 2 seconds 261s ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 4 seconds 261s CMD: /usr/lib/ChimeraSlayer/util/CS_add_taxonomy.pl < chims.NAST.CPS.CPC > chims.NAST.CPS.CPC.wTaxons 262s 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 262s T(1)=0 s 262s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 0 seconds 262s T(1)=0 s 262s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds 262s T(1)=0 s 262s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds 263s T(1)=1 s 263s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds 263s T(1)=0 s 263s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds 263s T(1)=0 s 263s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds 263s T(1)=0 s 263s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds 263s T(1)=0 s 263s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds 263s T(1)=0 s 263s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds 264s T(1)=1 s 264s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 seconds 264s autopkgtest [02:07:12]: test run-unit-test: -----------------------] 265s run-unit-test PASS 265s autopkgtest [02:07:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 265s autopkgtest [02:07:13]: @@@@@@@@@@@@@@@@@@@@ summary 265s run-unit-test PASS 276s Creating nova instance adt-noble-arm64-microbiomeutil-20240318-020248-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...