0s autopkgtest [22:17:57]: starting date and time: 2024-03-17 22:17:57+0000 0s autopkgtest [22:17:57]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [22:17:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.patyjnft/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@bos02-s390x-5.secgroup --name adt-noble-s390x-proteinortho-20240317-221757-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/ 81s autopkgtest [22:19:18]: testbed dpkg architecture: s390x 81s autopkgtest [22:19:18]: testbed apt version: 2.7.12 81s autopkgtest [22:19:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 82s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 82s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 82s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 82s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3691 kB] 82s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 82s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [639 kB] 82s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 82s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 82s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 82s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3878 kB] 83s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 83s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [33.2 kB] 83s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 85s Fetched 8913 kB in 2s (4013 kB/s) 85s Reading package lists... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 88s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 88s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 88s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 90s Reading package lists... 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Calculating upgrade... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s autopkgtest [22:19:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 93s autopkgtest [22:19:30]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 95s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 95s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 95s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 95s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 95s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 95s gpgv: issuer "tille@debian.org" 95s gpgv: Can't check signature: No public key 95s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 95s autopkgtest [22:19:32]: testing package proteinortho version 6.3.1+dfsg-1 95s autopkgtest [22:19:32]: build not needed 96s autopkgtest [22:19:33]: test run-unit-test: preparing testbed 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Starting pkgProblemResolver with broken count: 0 97s Starting 2 pkgProblemResolver with broken count: 0 97s Done 97s The following additional packages will be installed: 97s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7t64 97s libmbedtls14t64 libmbedx509-1t64 ncbi-blast+ ncbi-data proteinortho 97s Recommended packages: 97s med-config 97s The following NEW packages will be installed: 97s autopkgtest-satdep diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 97s libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 ncbi-blast+ ncbi-data 97s proteinortho 97s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 24.1 MB/24.1 MB of archives. 97s After this operation, 92.6 MB of additional disk space will be used. 97s Get:1 /tmp/autopkgtest.lp8s9r/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 98s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x diamond-aligner s390x 2.1.9-1 [2266 kB] 98s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 98s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 98s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 98s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 98s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedcrypto7t64 s390x 2.28.7-1.1ubuntu1 [216 kB] 98s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedx509-1t64 s390x 2.28.7-1.1ubuntu1 [46.2 kB] 98s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedtls14t64 s390x 2.28.7-1.1ubuntu1 [84.7 kB] 98s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 98s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x ncbi-blast+ s390x 2.12.0+ds-4build1 [12.8 MB] 99s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x proteinortho s390x 6.3.1+dfsg-1 [333 kB] 99s Fetched 24.1 MB in 1s (19.4 MB/s) 99s Selecting previously unselected package diamond-aligner. 99s (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.) 99s Preparing to unpack .../00-diamond-aligner_2.1.9-1_s390x.deb ... 99s Unpacking diamond-aligner (2.1.9-1) ... 99s Selecting previously unselected package libblas3:s390x. 99s Preparing to unpack .../01-libblas3_3.12.0-3_s390x.deb ... 99s Unpacking libblas3:s390x (3.12.0-3) ... 99s Selecting previously unselected package libgfortran5:s390x. 99s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 99s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 99s Selecting previously unselected package libgomp1:s390x. 99s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 99s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 99s Selecting previously unselected package liblapack3:s390x. 99s Preparing to unpack .../04-liblapack3_3.12.0-3_s390x.deb ... 99s Unpacking liblapack3:s390x (3.12.0-3) ... 99s Selecting previously unselected package libmbedcrypto7t64:s390x. 99s Preparing to unpack .../05-libmbedcrypto7t64_2.28.7-1.1ubuntu1_s390x.deb ... 99s Unpacking libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ... 99s Selecting previously unselected package libmbedx509-1t64:s390x. 99s Preparing to unpack .../06-libmbedx509-1t64_2.28.7-1.1ubuntu1_s390x.deb ... 99s Unpacking libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ... 99s Selecting previously unselected package libmbedtls14t64:s390x. 99s Preparing to unpack .../07-libmbedtls14t64_2.28.7-1.1ubuntu1_s390x.deb ... 99s Unpacking libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ... 99s Selecting previously unselected package ncbi-data. 99s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 99s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 99s Selecting previously unselected package ncbi-blast+. 99s Preparing to unpack .../09-ncbi-blast+_2.12.0+ds-4build1_s390x.deb ... 99s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ... 100s Selecting previously unselected package proteinortho. 100s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_s390x.deb ... 100s Unpacking proteinortho (6.3.1+dfsg-1) ... 100s Selecting previously unselected package autopkgtest-satdep. 100s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 100s Unpacking autopkgtest-satdep (0) ... 100s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 100s Setting up libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ... 100s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 100s Setting up diamond-aligner (2.1.9-1) ... 100s Setting up libblas3:s390x (3.12.0-3) ... 100s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 100s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 100s Setting up liblapack3:s390x (3.12.0-3) ... 100s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 100s Setting up libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ... 100s Setting up libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ... 100s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 100s Setting up proteinortho (6.3.1+dfsg-1) ... 100s Setting up autopkgtest-satdep (0) ... 100s Processing triggers for man-db (2.12.0-3) ... 100s Processing triggers for libc-bin (2.39-0ubuntu2) ... 102s (Reading database ... 52508 files and directories currently installed.) 102s Removing autopkgtest-satdep (0) ... 103s autopkgtest [22:19:40]: test run-unit-test: [----------------------- 103s ***************************************************************** 103s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 103s ***************************************************************** 103s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 103s Checking input files. 103s Checking input files. 103s Checking test/C_clean.faa... ok 103s Checking test/C2.faa... ok 103s Checking test/E.faa... ok 103s Checking test/L.faa... ok 103s Checking test/M.faa... ok 103s Checking test/C.faa... 103s  [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 !!! 103s The line is: 103s C_10,test 103s ok 103s Checking test/C2.faa... ok 103s Checking test/L.faa... ok 103s Checking test/C_clean.faa... ok 103s Checking test/E.faa... ok 103s 103s **Step 1** 103s Generating indices anyway (forced). 103s Building database for 'test/C2.faa' (4 sequences) 103s Generating indices anyway (forced). 103s Building database for 'test/C_clean.faa' (218 sequences) 103s Generating indices anyway (forced). 103s Building database for 'test/E.faa' (144 sequences) 103s Generating indices anyway (forced). 103s Building database for 'test/L.faa' (80 sequences) 103s Generating indices anyway (forced). 103s Building database for 'test/M.faa' (40 sequences) 103s 103s **Step 2** using blastp+ 108s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 108s [OUTPUT] -> written to test_blastp.blast-graph 108s 108s **Step 3** 108s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 108s Reading test_blastp.blast-graph 108s 5 species 108s 112 paired proteins 108s 147 bidirectional edges 109s 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 109s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 109s You can extract the fasta files of each orthology group with 109s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/C2.faa' 'test/C_clean.faa' 'test/E.faa' 'test/L.faa' 'test/M.faa' 109s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 109s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 109s # test_blastp.proteinortho.tsv statistics: 109s # number of groups that contains at least p% species: 109s # p species groups genes in groups 109s 0% 0 32 (100%) 112 (100%) 109s 20% 1 32 (100%) 112 (100%) 109s 40% 2 32 (100%) 112 (100%) 109s 60% 3 17 (53.12%) 74 (66.07%) 109s 80% 4 11 (34.37%) 51 (45.53%) 109s 100% 5 1 (3.12%) 5 (4.46%) 109s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 109s # number of groups for each input species: 109s L.faa 32 100% 109s M.faa 32 100% 109s E.faa 15 46.87% 109s C_clean.faa 13 40.62% 109s C2.faa 1 3.12% 109s 109s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 109s 109s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 109s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 109s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 109s 109s All finished. 109s ***************************************************************** 109s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 109s ***************************************************************** 109s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 109s Checking input files. 109s Checking test/C_clean.faa... ok 109s Checking test/C2.faa... ok 109s Checking test/E.faa... ok 109s Checking test/L.faa... ok 109s Checking test/M.faa... ok 109s 109s **Step 1** 109s Generating indices anyway (forced). 109s Building database for 'test/M.faa' (40 sequences) 110s Generating indices anyway (forced). 110s Building database for 'test/L.faa' (40 sequences) 110s Generating indices anyway (forced). 110s Building database for 'test/C_clean.faa' (109 sequences) 110s Generating indices anyway (forced). 110s Building database for 'test/E.faa' (72 sequences) 110s Generating indices anyway (forced). 110s Building database for 'test/C2.faa' (2 sequences) 110s 110s **Step 2** using blastp+ with : synteny 115s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 115s [OUTPUT] -> written to test_synteny.blast-graph 115s 115s **Step 3** 115s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 115s Reading test_synteny.blast-graph 115s 5 species 115s 112 paired proteins 115s 147 bidirectional edges 116s 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 (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 (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 116s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 116s You can extract the fasta files of each orthology group with 116s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/M.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 'test/C2.faa' 116s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 116s Adding singles... 116s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 116s # test_synteny.proteinortho.tsv statistics: 116s # number of groups that contains at least p% species: 116s # p species groups genes in groups 116s 0% 0 182 (100%) 262 (100%) 116s 20% 1 182 (100%) 262 (100%) 116s 40% 2 32 (17.58%) 112 (42.74%) 116s 60% 3 17 (9.34%) 74 (28.24%) 116s 80% 4 11 (6.04%) 51 (19.46%) 116s 100% 5 1 (0.54%) 5 (1.9%) 116s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 116s # groups that contains only one species: 116s single 5 150 (82.41%) 150 (57.25%) 116s # number of groups for each input species: 116s L.faa 32 100% 116s M.faa 32 100% 116s E.faa 15 46.87% 116s C_clean.faa 13 40.62% 116s C2.faa 1 3.12% 116s 116s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 116s 116s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 116s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 116s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 116s 116s 116s Clustering by gene-order (POFF mode) 116s Reading test_synteny.ffadj-graph 116s 5 species 116s 105 paired proteins 116s 106 bidirectional edges 117s Clustering: working on (2@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 (29@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 (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 (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 (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 117s 5 species 117s 105 paired proteins 117s 106 bidirectional edges 118s Clustering: working on (2@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 (29@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 (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 (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 (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 118s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 118s You can extract the fasta files of each orthology group with 118s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/M.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 'test/C2.faa' 118s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 118s Adding singles... 118s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 118s # test_synteny.poff.tsv statistics: 118s # number of groups that contains at least p% species: 118s # p species groups genes in groups 118s 0% 0 195 (100%) 262 (100%) 118s 20% 1 195 (100%) 262 (100%) 118s 40% 2 37 (18.97%) 104 (39.69%) 118s 60% 3 17 (8.71%) 64 (24.42%) 118s 80% 4 10 (5.12%) 43 (16.41%) 118s 100% 5 1 (0.51%) 5 (1.9%) 118s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 118s # groups that contains only one species: 118s single 5 158 (81.02%) 158 (60.3%) 118s # number of groups for each input species: 118s L.faa 37 100% 118s M.faa 37 100% 118s E.faa 14 37.83% 118s C_clean.faa 13 35.13% 118s C2.faa 1 2.7% 118s 118s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 118s 118s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 118s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 118s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 118s 118s All finished. 119s ***************************************************************** 119s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 119s ***************************************************************** 119s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 119s Checking input files. 119s Checking test/C_clean.faa... ok 119s Checking test/C2.faa... ok 119s Checking test/E.faa... ok 119s Checking test/L.faa... ok 119s Checking test/M.faa... ok 119s 119s **Step 1** 119s Generating indices anyway (forced). 119s Building database for 'test/C2.faa' (2 sequences) 119s Generating indices anyway (forced). 119s Building database for 'test/E.faa' (72 sequences) 119s Generating indices anyway (forced). 119s Building database for 'test/M.faa' (40 sequences) 119s Generating indices anyway (forced). 119s Building database for 'test/C_clean.faa' (109 sequences) 119s Generating indices anyway (forced). 119s Building database for 'test/L.faa' (40 sequences) 119s 119s **Step 2** using diamond 127s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 127s [OUTPUT] -> written to test_diamond.blast-graph 127s 127s **Step 3** 127s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 127s Reading test_diamond.blast-graph 127s 5 species 127s 112 paired proteins 127s 145 bidirectional edges 128s 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 (18@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 (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 (2@lapack* + 0@power) connected components 128s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 128s You can extract the fasta files of each orthology group with 128s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/C2.faa' 'test/E.faa' 'test/M.faa' 'test/C_clean.faa' 'test/L.faa' 128s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 128s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 128s # test_diamond.proteinortho.tsv statistics: 128s # number of groups that contains at least p% species: 128s # p species groups genes in groups 128s 0% 0 32 (100%) 111 (100%) 128s 20% 1 32 (100%) 111 (100%) 128s 40% 2 32 (100%) 111 (100%) 128s 60% 3 17 (53.12%) 75 (67.56%) 128s 80% 4 11 (34.37%) 52 (46.84%) 128s 100% 5 1 (3.12%) 5 (4.5%) 128s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 128s # number of groups for each input species: 128s L.faa 32 100% 128s M.faa 32 100% 128s E.faa 15 46.87% 128s C_clean.faa 13 40.62% 128s C2.faa 1 3.12% 128s 128s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 128s 128s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 128s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 128s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 128s 128s All finished. 128s ***************************************************************** 128s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 128s ***************************************************************** 128s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 128s Checking input files. 128s Checking test/C_clean.faa... ok 128s Checking test/C2.faa... ok 128s Checking test/E.faa... ok 128s Checking test/L.faa... ok 128s Checking test/M.faa... ok 128s 128s **Step 1** 128s Generating indices anyway (forced). 128s Building database for 'test/E.faa' (72 sequences) 128s Generating indices anyway (forced). 128s Building database for 'test/M.faa' (40 sequences) 128s Generating indices anyway (forced). 128s Building database for 'test/C2.faa' (2 sequences) 128s Generating indices anyway (forced). 128s Building database for 'test/L.faa' (40 sequences) 128s Generating indices anyway (forced). 128s Building database for 'test/C_clean.faa' (109 sequences) 128s 128s **Step 2** using diamond 138s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 138s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 138s 138s **Step 3** 138s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 138s Reading test_diamondmoresensitive.blast-graph 138s 5 species 138s 112 paired proteins 138s 145 bidirectional edges 139s 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 (18@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 (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 (2@lapack* + 0@power) connected components 139s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 139s You can extract the fasta files of each orthology group with 139s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/E.faa' 'test/M.faa' 'test/C2.faa' 'test/L.faa' 'test/C_clean.faa' 139s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 139s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 139s # test_diamondmoresensitive.proteinortho.tsv statistics: 139s # number of groups that contains at least p% species: 139s # p species groups genes in groups 139s 0% 0 32 (100%) 111 (100%) 139s 20% 1 32 (100%) 111 (100%) 139s 40% 2 32 (100%) 111 (100%) 139s 60% 3 17 (53.12%) 75 (67.56%) 139s 80% 4 11 (34.37%) 52 (46.84%) 139s 100% 5 1 (3.12%) 5 (4.5%) 139s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 139s # number of groups for each input species: 139s L.faa 32 100% 139s M.faa 32 100% 139s E.faa 15 46.87% 139s C_clean.faa 13 40.62% 139s C2.faa 1 3.12% 139s 139s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 139s 139s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 139s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 139s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 139s 139s All finished. 139s ***************************************************************** 139s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 139s ***************************************************************** 139s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 139s Checking input files. 139s Checking test/C_clean.faa... ok 139s Checking test/C2.faa... ok 139s Checking test/E.faa... ok 139s Checking test/L.faa... ok 139s Checking test/M.faa... ok 139s 139s **Step 1** 139s Generating indices anyway (forced). 139s Building database for 'test/C2.faa' (2 sequences) 139s Generating indices anyway (forced). 139s Building database for 'test/M.faa' (40 sequences) 139s Generating indices anyway (forced). 139s Building database for 'test/C_clean.faa' (109 sequences) 139s Generating indices anyway (forced). 139s Building database for 'test/L.faa' (40 sequences) 139s Generating indices anyway (forced). 139s Building database for 'test/E.faa' (72 sequences) 139s 139s **Step 2** using blastp+ 144s 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: 90% (9/10) Running blast analysis: 100% (10/10) Running blast analysis: 100% (10/10) 144s [OUTPUT] -> written to test_blastall.blast-graph 144s 144s **Step 3** 144s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 144s Reading test_blastall.blast-graph 144s 5 species 144s 112 paired proteins 144s 147 bidirectional edges 145s 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 145s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 145s You can extract the fasta files of each orthology group with 145s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C2.faa' 'test/M.faa' 'test/C_clean.faa' 'test/L.faa' 'test/E.faa' 145s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 145s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 145s # test_blastall.proteinortho.tsv statistics: 146s # number of groups that contains at least p% species: 146s # p species groups genes in groups 146s 0% 0 32 (100%) 112 (100%) 146s 20% 1 32 (100%) 112 (100%) 146s 40% 2 32 (100%) 112 (100%) 146s 60% 3 17 (53.12%) 74 (66.07%) 146s 80% 4 11 (34.37%) 51 (45.53%) 146s 100% 5 1 (3.12%) 5 (4.46%) 146s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 146s # number of groups for each input species: 146s L.faa 32 100% 146s M.faa 32 100% 146s E.faa 15 46.87% 146s C_clean.faa 13 40.62% 146s C2.faa 1 3.12% 146s 146s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 146s 146s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 146s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 146s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 146s 146s All finished. 146s - test max_of_diag() : OK 146s - test generate_random_vector() : OK 146s - test get_new_x() : OK 146s - test makeOrthogonal() : OK 146s - test normalize() : OK 146s - test getY() : OK 146s - test lapack() : OK 146s - test power() : OK 146s - test smirnov-grubb() : OK 146s All test passed. 146s Reading test_blastp.blast-graph 146s 5 species 146s 112 paired proteins 146s 147 bidirectional edges 146s 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 # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 147s 5 5 1 C_10 C_10;test E_10 L_10 M_10 147s 4 4 1 * C_11 E_11 L_11 M_11 147s 4 6 0.149 * C_12,C_21 E_313,E_315 L_313 M_313 147s 4 4 1 * C_14 E_14 L_14 M_14 147s 4 4 1 * C_15 E_15 L_15 M_15 147s 4 4 1 * C_16 E_16 L_16 M_16 147s 4 4 1 * C_17 E_17 L_17 M_17 147s 4 4 1 * C_64 E_18 L_18 M_18 147s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 147s 3 3 1 * C_20 * L_20 M_20 147s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 147s 3 3 0.33 * * E_367 L_319 M_319 147s 3 3 0.33 * * E_432 L_328 M_328 147s 2 2 1 * * * L_619 M_619 147s 2 2 1 * * * L_617 M_617 147s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 147s 2 4 0.5 * * * L_645,L_647 M_644,M_646 147s 2 2 1 * * * L_333 M_333 147s 2 2 1 * * * L_3 M_3 147s 2 2 1 * * * L_4 M_4 147s 2 2 1 * * * L_5 M_5 147s 2 2 1 * * * L_6 M_6 147s 2 2 1 * * * L_8 M_8 147s 2 2 1 * * * L_9 M_9 147s 2 2 1 * * * L_623 M_623 147s 4 4 1 * C_13 E_13 L_621 M_621 147s 2 4 0.146 * * * L_637,L_639 M_636,M_638 147s 3 3 0.33 * * E_437 L_317 M_317 147s 2 3 0.33 * * * L_631,L_633 M_632 147s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 147s 2 2 1 * * * L_331 M_331 147s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 147s Reading test_blastp.blast-graph 147s 5 species 147s 112 paired proteins 147s 147 bidirectional edges 147s 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# Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 148s @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 148s 3 3 0.33 * * E_367 L_319 M_319 148s 3 3 0.33 * * E_432 L_328 M_328 148s 2 2 1 * * * L_619 M_619 148s 2 2 1 * * * L_617 M_617 148s 2 2 1 * * * L_333 M_333 148s 2 2 1 * * * L_3 M_3 148s 2 2 1 * * * L_4 M_4 148s 2 2 1 * * * L_5 M_5 148s 2 2 1 * * * L_6 M_6 148s 2 2 1 * * * L_8 M_8 148s 2 2 1 * * * L_9 M_9 148s 5 5 0.687 C_10 C_10;test E_10 L_10 M_10 148s 4 4 0.727 * C_11 E_11 L_11 M_11 148s 4 6 0.137 * C_12,C_21 E_313,E_315 L_313 M_313 148s 2 2 1 * * * L_623 M_623 148s 4 4 0.74 * C_14 E_14 L_14 M_14 148s 4 4 0.814 * C_15 E_15 L_15 M_15 148s 4 4 0.815 * C_16 E_16 L_16 M_16 148s 4 4 0.824 * C_17 E_17 L_17 M_17 148s 4 4 0.779 * C_64 E_18 L_18 M_18 148s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 148s 3 3 0.33 * * E_437 L_317 M_317 148s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 148s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 148s 2 4 0.478 * * * L_645,L_647 M_644,M_646 148s 4 4 0.717 * C_13 E_13 L_621 M_621 148s 2 4 0.145 * * * L_637,L_639 M_636,M_638 148s 2 2 1 * * * L_331 M_331 148s 2 3 0.33 * * * L_631,L_633 M_632 148s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 148s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 148s Test okay 148s autopkgtest [22:20:25]: test run-unit-test: -----------------------] 148s autopkgtest [22:20:25]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 148s run-unit-test PASS 149s autopkgtest [22:20:26]: @@@@@@@@@@@@@@@@@@@@ summary 149s run-unit-test PASS 160s Creating nova instance adt-noble-s390x-proteinortho-20240317-221757-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240316.img (UUID 7afe023c-7cb8-41b6-91a7-c69e7d1e7c0d)...