0s autopkgtest [02:06:45]: starting date: 2024-03-18 0s autopkgtest [02:06:45]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt 0s autopkgtest [02:06:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f5wqmcbc/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 proteinortho --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-arm64-20.secgroup --name adt-noble-arm64-proteinortho-20240318-020645-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/ 69s autopkgtest [02:07:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 69s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 69s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 69s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 69s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 69s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 70s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 71s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 71s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 71s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 71s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 71s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 71s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 71s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 73s Fetched 9189 kB in 3s (3117 kB/s) 73s Reading package lists... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Calculating upgrade... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 78s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 79s Reading package lists... 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [02:08:07]: testbed dpkg architecture: arm64 83s autopkgtest [02:08:08]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 83s autopkgtest [02:08:08]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 85s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 85s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 85s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 85s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 85s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 85s gpgv: issuer "tille@debian.org" 85s gpgv: Can't check signature: No public key 85s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 85s autopkgtest [02:08:10]: testing package proteinortho version 6.3.1+dfsg-1 85s autopkgtest [02:08:10]: build not needed 86s autopkgtest [02:08:11]: test run-unit-test: preparing testbed 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 88s Starting 2 pkgProblemResolver with broken count: 0 88s Done 89s Done 89s Starting pkgProblemResolver with broken count: 0 89s Starting 2 pkgProblemResolver with broken count: 0 89s Done 90s The following additional packages will be installed: 90s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7t64 90s libmbedtls14t64 libmbedx509-1t64 ncbi-blast+ ncbi-data proteinortho 90s Recommended packages: 90s med-config 90s The following NEW packages will be installed: 90s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7t64 90s libmbedtls14t64 libmbedx509-1t64 ncbi-blast+ ncbi-data proteinortho 90s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 90s 1 not fully installed or removed. 90s Need to get 22.0 MB of archives. 90s After this operation, 92.5 MB of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 90s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 90s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 91s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 91s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 91s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB] 91s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB] 91s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB] 91s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB] 92s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 diamond-aligner arm64 2.1.9-1 [1905 kB] 92s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 proteinortho arm64 6.3.1+dfsg-1 [340 kB] 93s Fetched 22.0 MB in 2s (8860 kB/s) 93s Selecting previously unselected package libgomp1:arm64. 93s (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.) 93s Preparing to unpack .../00-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 93s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 93s Selecting previously unselected package libblas3:arm64. 93s Preparing to unpack .../01-libblas3_3.12.0-3_arm64.deb ... 93s Unpacking libblas3:arm64 (3.12.0-3) ... 93s Selecting previously unselected package libgfortran5:arm64. 93s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 93s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 93s Selecting previously unselected package liblapack3:arm64. 93s Preparing to unpack .../03-liblapack3_3.12.0-3_arm64.deb ... 93s Unpacking liblapack3:arm64 (3.12.0-3) ... 93s Selecting previously unselected package ncbi-data. 93s Preparing to unpack .../04-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 93s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 93s Selecting previously unselected package libmbedcrypto7t64:arm64. 93s Preparing to unpack .../05-libmbedcrypto7t64_2.28.7-1.1ubuntu1_arm64.deb ... 93s Unpacking libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 93s Selecting previously unselected package libmbedx509-1t64:arm64. 93s Preparing to unpack .../06-libmbedx509-1t64_2.28.7-1.1ubuntu1_arm64.deb ... 93s Unpacking libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 93s Selecting previously unselected package libmbedtls14t64:arm64. 93s Preparing to unpack .../07-libmbedtls14t64_2.28.7-1.1ubuntu1_arm64.deb ... 93s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 93s Selecting previously unselected package ncbi-blast+. 93s Preparing to unpack .../08-ncbi-blast+_2.12.0+ds-4build1_arm64.deb ... 93s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ... 94s Selecting previously unselected package diamond-aligner. 94s Preparing to unpack .../09-diamond-aligner_2.1.9-1_arm64.deb ... 94s Unpacking diamond-aligner (2.1.9-1) ... 94s Selecting previously unselected package proteinortho. 94s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_arm64.deb ... 94s Unpacking proteinortho (6.3.1+dfsg-1) ... 94s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 94s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 94s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 94s Setting up diamond-aligner (2.1.9-1) ... 94s Setting up libblas3:arm64 (3.12.0-3) ... 94s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 94s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 94s Setting up liblapack3:arm64 (3.12.0-3) ... 94s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 94s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 94s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 94s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 94s Setting up proteinortho (6.3.1+dfsg-1) ... 94s Setting up autopkgtest-satdep (0) ... 94s Processing triggers for man-db (2.12.0-3) ... 94s Processing triggers for libc-bin (2.39-0ubuntu2) ... 98s (Reading database ... 75095 files and directories currently installed.) 98s Removing autopkgtest-satdep (0) ... 99s autopkgtest [02:08:24]: test run-unit-test: [----------------------- 99s ***************************************************************** 99s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 99s ***************************************************************** 99s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 99s Checking input files. 99s Checking input files. 99s Checking test/C_clean.faa... ok 99s Checking test/C2.faa... ok 99s Checking test/E.faa... ok 99s Checking test/L.faa... ok 99s Checking test/M.faa... ok 99s Checking test/C.faa... 99s  [WARNING] input 'test/C.faa' contains a gene-name with a comma, this causes problems with the proteinortho.tsv output, I will clean the file ('test/C_clean.faa') and restart the analysis !!! 99s The line is: 99s C_10,test 99s ok 99s Checking test/M.faa... ok 99s Checking test/C_clean.faa... ok 100s Checking test/E.faa... ok 100s Checking test/L.faa... ok 100s 100s **Step 1** 100s Generating indices anyway (forced). 100s Building database for 'test/C_clean.faa' (218 sequences) 100s Generating indices anyway (forced). 100s Building database for 'test/M.faa' (80 sequences) 100s Generating indices anyway (forced). 100s Building database for 'test/E.faa' (144 sequences) 100s Generating indices anyway (forced). 100s Building database for 'test/L.faa' (80 sequences) 100s Generating indices anyway (forced). 100s Building database for 'test/C2.faa' (2 sequences) 100s 100s **Step 2** using blastp+ 104s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 104s [OUTPUT] -> written to test_blastp.blast-graph 104s 104s **Step 3** 104s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 104s Reading test_blastp.blast-graph 104s 5 species 104s 112 paired proteins 104s 147 bidirectional edges 105s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 105s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 105s You can extract the fasta files of each orthology group with 105s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/C_clean.faa' 'test/M.faa' 'test/E.faa' 'test/L.faa' 'test/C2.faa' 105s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 105s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 105s # test_blastp.proteinortho.tsv statistics: 105s # number of groups that contains at least p% species: 105s # p species groups genes in groups 105s 0% 0 32 (100%) 112 (100%) 105s 20% 1 32 (100%) 112 (100%) 105s 40% 2 32 (100%) 112 (100%) 105s 60% 3 17 (53.12%) 74 (66.07%) 105s 80% 4 11 (34.37%) 51 (45.53%) 105s 100% 5 1 (3.12%) 5 (4.46%) 105s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 105s # number of groups for each input species: 105s L.faa 32 100% 105s M.faa 32 100% 105s E.faa 15 46.87% 105s C_clean.faa 13 40.62% 105s C2.faa 1 3.12% 105s 105s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 105s 105s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 105s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 105s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 105s 105s All finished. 106s ***************************************************************** 106s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 106s ***************************************************************** 106s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 106s Checking input files. 106s Checking test/C_clean.faa... ok 106s Checking test/C2.faa... ok 106s Checking test/E.faa... ok 106s Checking test/L.faa... ok 106s Checking test/M.faa... ok 106s 106s **Step 1** 106s Generating indices anyway (forced). 106s Building database for 'test/E.faa' (72 sequences) 106s Generating indices anyway (forced). 106s Building database for 'test/L.faa' (40 sequences) 106s Generating indices anyway (forced). 106s Building database for 'test/M.faa' (40 sequences) 106s Generating indices anyway (forced). 106s Building database for 'test/C2.faa' (2 sequences) 106s Generating indices anyway (forced). 106s Building database for 'test/C_clean.faa' (109 sequences) 106s 106s **Step 2** using blastp+ with : synteny 110s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 110s [OUTPUT] -> written to test_synteny.blast-graph 110s 110s **Step 3** 110s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 110s Reading test_synteny.blast-graph 110s 5 species 110s 112 paired proteins 110s 149 bidirectional edges 111s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 111s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 111s You can extract the fasta files of each orthology group with 111s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa' 'test/C_clean.faa' 111s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 111s Adding singles... 111s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 111s # test_synteny.proteinortho.tsv statistics: 111s # number of groups that contains at least p% species: 111s # p species groups genes in groups 111s 0% 0 182 (100%) 262 (100%) 111s 20% 1 182 (100%) 262 (100%) 111s 40% 2 32 (17.58%) 112 (42.74%) 111s 60% 3 17 (9.34%) 74 (28.24%) 111s 80% 4 11 (6.04%) 51 (19.46%) 111s 100% 5 1 (0.54%) 5 (1.9%) 111s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 111s # groups that contains only one species: 111s single 5 150 (82.41%) 150 (57.25%) 111s # number of groups for each input species: 111s L.faa 32 100% 111s M.faa 32 100% 111s E.faa 15 46.87% 111s C_clean.faa 13 40.62% 111s C2.faa 1 3.12% 111s 111s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 111s 111s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 111s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 111s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 111s 111s 111s Clustering by gene-order (POFF mode) 111s Reading test_synteny.ffadj-graph 111s 5 species 111s 106 paired proteins 111s 106 bidirectional edges 112s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (35@lapack* + 0@power) connected components Clustering: working on (34@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 112s 5 species 112s 106 paired proteins 112s 106 bidirectional edges 113s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (35@lapack* + 0@power) connected components Clustering: working on (34@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 113s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 113s You can extract the fasta files of each orthology group with 113s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa' 'test/C_clean.faa' 113s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 113s Adding singles... 113s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 114s # test_synteny.poff.tsv statistics: 114s # number of groups that contains at least p% species: 114s # p species groups genes in groups 114s 0% 0 195 (100%) 262 (100%) 114s 20% 1 195 (100%) 262 (100%) 114s 40% 2 38 (19.48%) 105 (40.07%) 114s 60% 3 17 (8.71%) 63 (24.04%) 114s 80% 4 10 (5.12%) 42 (16.03%) 114s 100% 5 1 (0.51%) 5 (1.9%) 114s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 114s # groups that contains only one species: 114s single 5 157 (80.51%) 157 (59.92%) 114s # number of groups for each input species: 114s L.faa 37 97.36% 114s M.faa 37 97.36% 114s E.faa 15 39.47% 114s C_clean.faa 14 36.84% 114s C2.faa 1 2.63% 114s 114s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 114s 114s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 114s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 114s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 114s 114s All finished. 114s ***************************************************************** 114s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 114s ***************************************************************** 114s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 114s Checking input files. 114s Checking test/C_clean.faa... ok 114s Checking test/C2.faa... ok 114s Checking test/E.faa... ok 114s Checking test/L.faa... ok 114s Checking test/M.faa... ok 114s 114s **Step 1** 114s Generating indices anyway (forced). 114s Building database for 'test/E.faa' (72 sequences) 114s Generating indices anyway (forced). 114s Building database for 'test/L.faa' (40 sequences) 114s Generating indices anyway (forced). 114s Building database for 'test/C_clean.faa' (109 sequences) 114s Generating indices anyway (forced). 114s Building database for 'test/M.faa' (40 sequences) 114s Generating indices anyway (forced). 114s Building database for 'test/C2.faa' (2 sequences) 114s 114s **Step 2** using diamond 118s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 118s [OUTPUT] -> written to test_diamond.blast-graph 118s 118s **Step 3** 118s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 118s Reading test_diamond.blast-graph 118s 5 species 118s 112 paired proteins 118s 145 bidirectional edges 119s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 119s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 119s You can extract the fasta files of each orthology group with 119s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/E.faa' 'test/L.faa' 'test/C_clean.faa' 'test/M.faa' 'test/C2.faa' 119s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 119s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 119s # test_diamond.proteinortho.tsv statistics: 119s # number of groups that contains at least p% species: 119s # p species groups genes in groups 119s 0% 0 32 (100%) 111 (100%) 119s 20% 1 32 (100%) 111 (100%) 119s 40% 2 32 (100%) 111 (100%) 119s 60% 3 17 (53.12%) 75 (67.56%) 119s 80% 4 11 (34.37%) 52 (46.84%) 119s 100% 5 1 (3.12%) 5 (4.5%) 119s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 119s # number of groups for each input species: 119s L.faa 32 100% 119s M.faa 32 100% 119s E.faa 15 46.87% 119s C_clean.faa 13 40.62% 119s C2.faa 1 3.12% 119s 119s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 119s 119s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 119s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 119s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 119s 120s All finished. 120s ***************************************************************** 120s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 120s ***************************************************************** 120s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 120s Checking input files. 120s Checking test/C_clean.faa... ok 120s Checking test/C2.faa... ok 120s Checking test/E.faa... ok 120s Checking test/L.faa... ok 120s Checking test/M.faa... ok 120s 120s **Step 1** 120s Generating indices anyway (forced). 120s Building database for 'test/M.faa' (40 sequences) 120s Generating indices anyway (forced). 120s Building database for 'test/C_clean.faa' (109 sequences) 120s Generating indices anyway (forced). 120s Building database for 'test/C2.faa' (2 sequences) 120s Generating indices anyway (forced). 120s Building database for 'test/E.faa' (72 sequences) 120s Generating indices anyway (forced). 120s Building database for 'test/L.faa' (40 sequences) 120s 120s **Step 2** using diamond 124s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 124s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 124s 124s **Step 3** 124s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 124s Reading test_diamondmoresensitive.blast-graph 124s 5 species 124s 113 paired proteins 124s 147 bidirectional edges 125s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 125s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 125s You can extract the fasta files of each orthology group with 125s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/M.faa' 'test/C_clean.faa' 'test/C2.faa' 'test/E.faa' 'test/L.faa' 125s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 125s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 125s # test_diamondmoresensitive.proteinortho.tsv statistics: 125s # number of groups that contains at least p% species: 125s # p species groups genes in groups 125s 0% 0 32 (100%) 112 (100%) 125s 20% 1 32 (100%) 112 (100%) 125s 40% 2 32 (100%) 112 (100%) 125s 60% 3 17 (53.12%) 76 (67.85%) 125s 80% 4 11 (34.37%) 53 (47.32%) 125s 100% 5 1 (3.12%) 5 (4.46%) 125s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 125s # number of groups for each input species: 125s L.faa 32 100% 125s M.faa 32 100% 125s E.faa 15 46.87% 125s C_clean.faa 13 40.62% 125s C2.faa 1 3.12% 125s 125s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 125s 125s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 125s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 125s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 125s 125s All finished. 125s ***************************************************************** 125s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 125s ***************************************************************** 125s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 125s Checking input files. 125s Checking test/C_clean.faa... ok 125s Checking test/C2.faa... ok 125s Checking test/E.faa... ok 125s Checking test/L.faa... ok 125s Checking test/M.faa... ok 125s 125s **Step 1** 125s Generating indices anyway (forced). 125s Building database for 'test/C2.faa' (2 sequences) 125s Generating indices anyway (forced). 125s Building database for 'test/E.faa' (72 sequences) 125s Generating indices anyway (forced). 125s Building database for 'test/M.faa' (40 sequences) 125s Generating indices anyway (forced). 125s Building database for 'test/C_clean.faa' (109 sequences) 126s Generating indices anyway (forced). 126s Building database for 'test/L.faa' (40 sequences) 126s 126s **Step 2** using blastp+ 130s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 130s [OUTPUT] -> written to test_blastall.blast-graph 130s 130s **Step 3** 130s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 130s Reading test_blastall.blast-graph 130s 5 species 130s 112 paired proteins 130s 149 bidirectional edges 131s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 131s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 131s You can extract the fasta files of each orthology group with 131s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C2.faa' 'test/E.faa' 'test/M.faa' 'test/C_clean.faa' 'test/L.faa' 131s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 131s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 131s # test_blastall.proteinortho.tsv statistics: 131s # number of groups that contains at least p% species: 131s # p species groups genes in groups 131s 0% 0 32 (100%) 112 (100%) 131s 20% 1 32 (100%) 112 (100%) 131s 40% 2 32 (100%) 112 (100%) 131s 60% 3 17 (53.12%) 74 (66.07%) 131s 80% 4 11 (34.37%) 51 (45.53%) 131s 100% 5 1 (3.12%) 5 (4.46%) 131s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 131s # number of groups for each input species: 131s L.faa 32 100% 131s M.faa 32 100% 131s E.faa 15 46.87% 131s C_clean.faa 13 40.62% 131s C2.faa 1 3.12% 131s 131s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 131s 131s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 131s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 131s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 131s 131s All finished. 131s - test max_of_diag() : OK 131s - test generate_random_vector() : OK 131s - test get_new_x() : OK 131s - test makeOrthogonal() : OK 131s - test normalize() : OK 131s - test getY() : OK 131s - test lapack() : OK 131s - test power() : OK 131s - test smirnov-grubb() : OK 131s All test passed. 131s Reading test_blastp.blast-graph 131s 5 species 131s 112 paired proteins 131s 147 bidirectional edges 131s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 132s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 5 5 1 C_10 C_10;test E_10 L_10 M_10 132s 4 4 1 * C_11 E_11 L_11 M_11 132s 4 6 0.149 * C_12,C_21 E_313,E_315 L_313 M_313 132s 4 4 1 * C_14 E_14 L_14 M_14 132s 4 4 1 * C_15 E_15 L_15 M_15 132s 4 4 1 * C_16 E_16 L_16 M_16 132s 4 4 1 * C_17 E_17 L_17 M_17 132s 4 4 1 * C_64 E_18 L_18 M_18 132s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 132s 3 3 1 * C_20 * L_20 M_20 132s 3 6 0.333 * C_167,C_2,C_164,C_166 * L_2 M_2 132s 2 2 1 * * * L_619 M_619 132s 3 3 0.33 * * E_367 L_319 M_319 132s 2 2 1 * * * L_617 M_617 132s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 132s 2 4 0.5 * * * L_645,L_647 M_644,M_646 132s 3 3 0.33 * * E_432 L_328 M_328 132s 2 2 1 * * * L_333 M_333 132s 2 2 1 * * * L_3 M_3 132s 2 2 1 * * * L_4 M_4 132s 2 2 1 * * * L_5 M_5 132s 2 2 1 * * * L_6 M_6 132s 2 2 1 * * * L_8 M_8 132s 2 2 1 * * * L_9 M_9 132s 2 2 1 * * * L_623 M_623 132s 4 4 1 * C_13 E_13 L_621 M_621 132s 2 4 0.146 * * * L_637,L_639 M_636,M_638 132s 3 3 0.33 * * E_437 L_317 M_317 132s 2 3 0.33 * * * L_631,L_633 M_632 132s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 132s 2 2 1 * * * L_331 M_331 132s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 132s Reading test_blastp.blast-graph 132s 5 species 132s 112 paired proteins 132s 147 bidirectional edges 132s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 133s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 1@power) connected components Clustering: working on (13@lapack* + 2@power) connected components Clustering: working on (12@lapack* + 3@power) connected components Clustering: working on (11@lapack* + 4@power) connected components Clustering: working on (10@lapack* + 5@power) connected components Clustering: working on (9@lapack* + 6@power) connected components Clustering: working on (8@lapack* + 7@power) connected components Clustering: working on (7@lapack* + 8@power) connected components Clustering: working on (6@lapack* + 9@power) connected components Clustering: working on (5@lapack* + 10@power) connected components Clustering: working on (4@lapack* + 11@power) connected components Clustering: working on (3@lapack* + 12@power) connected components Clustering: working on (2@lapack* + 13@power) connected components Clustering: working on (0@lapack + 15@power*) connected components Clustering: working on (0@lapack + 14@power*) connected components Clustering: working on (0@lapack + 13@power*) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (3@lapack* + 10@power) connected components Clustering: working on (2@lapack* + 10@power) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (0@lapack + 11@power*) connected components Clustering: working on (0@lapack + 10@power*) connected components Clustering: working on (0@lapack + 9@power*) connected components Clustering: working on (0@lapack + 8@power*) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (4@lapack* + 4@power) connected components Clustering: working on (3@lapack* + 4@power) connected components Clustering: working on (2@lapack* + 5@power) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (0@lapack + 5@power*) connected components Clustering: working on (0@lapack + 4@power*) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components 3 3 1 * C_20 * L_20 M_20 133s 2 2 1 * * * L_619 M_619 133s 3 3 0.33 * * E_367 L_319 M_319 133s 2 2 1 * * * L_617 M_617 133s 3 3 0.33 * * E_432 L_328 M_328 133s 2 2 1 * * * L_333 M_333 133s 2 2 1 * * * L_3 M_3 133s 2 2 1 * * * L_4 M_4 133s 2 2 1 * * * L_5 M_5 133s 2 2 1 * * * L_6 M_6 133s 2 2 1 * * * L_8 M_8 133s 2 2 1 * * * L_9 M_9 133s 5 5 0.687 C_10 C_10;test E_10 L_10 M_10 133s 4 4 0.727 * C_11 E_11 L_11 M_11 133s 4 6 0.137 * C_12,C_21 E_313,E_315 L_313 M_313 133s 2 2 1 * * * L_623 M_623 133s 4 4 0.74 * C_14 E_14 L_14 M_14 133s 4 4 0.814 * C_15 E_15 L_15 M_15 133s 4 4 0.815 * C_16 E_16 L_16 M_16 133s 4 4 0.824 * C_17 E_17 L_17 M_17 133s 4 4 0.779 * C_64 E_18 L_18 M_18 133s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 133s 3 3 0.33 * * E_437 L_317 M_317 133s 3 6 0.314 * C_167,C_2,C_164,C_166 * L_2 M_2 133s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 133s 2 4 0.478 * * * L_645,L_647 M_644,M_646 133s 4 4 0.717 * C_13 E_13 L_621 M_621 133s 2 4 0.145 * * * L_637,L_639 M_636,M_638 133s 2 2 1 * * * L_331 M_331 133s 2 3 0.33 * * * L_631,L_633 M_632 133s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 133s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 133s Test okay 133s autopkgtest [02:08:58]: test run-unit-test: -----------------------] 134s autopkgtest [02:08:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 134s run-unit-test PASS 134s autopkgtest [02:08:59]: @@@@@@@@@@@@@@@@@@@@ summary 134s run-unit-test PASS 146s Creating nova instance adt-noble-arm64-proteinortho-20240318-020645-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...