0s autopkgtest [10:44:19]: starting date and time: 2024-03-26 10:44:19+0000 0s autopkgtest [10:44:19]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [10:44:19]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.roq34urd/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade proteinortho --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.2-0ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-3.secgroup --name adt-noble-s390x-proteinortho-20240326-104419-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/ 118s autopkgtest [10:46:17]: testbed dpkg architecture: s390x 118s autopkgtest [10:46:17]: testbed apt version: 2.7.12 118s autopkgtest [10:46:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 119s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 120s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B] 120s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 120s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3982 kB] 122s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [690 kB] 122s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 122s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 122s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 122s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4126 kB] 123s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 123s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 123s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 124s Fetched 9535 kB in 5s (2073 kB/s) 125s Reading package lists... 126s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Calculating upgrade... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 242 not upgraded. 128s Unknown architecture, assuming PC-style ttyS0 128s sh: Attempting to set up Debian/Ubuntu apt sources automatically 128s sh: Distribution appears to be Ubuntu 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s eatmydata is already the newest version (131-1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s dbus is already the newest version (1.14.10-4ubuntu1). 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s rng-tools-debian is already the newest version (2.4). 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s The following packages will be REMOVED: 130s cloud-init* python3-configobj* python3-debconf* 130s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 130s After this operation, 3256 kB disk space will be freed. 130s (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 ... 52170 files and directories currently installed.) 130s Removing cloud-init (24.1.2-0ubuntu1) ... 131s Removing python3-configobj (5.0.8-3) ... 131s Removing python3-debconf (1.5.86) ... 131s Processing triggers for man-db (2.12.0-3) ... 131s (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 ... 51781 files and directories currently installed.) 131s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 132s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 132s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 132s invoke-rc.d: policy-rc.d denied execution of try-restart. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s linux-generic is already the newest version (6.8.0-11.11+1). 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 133s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 134s Reading package lists... 134s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s autopkgtest [10:46:34]: rebooting testbed after setup commands that affected boot 150s autopkgtest [10:46:49]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 153s autopkgtest [10:46:52]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 156s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 156s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 156s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 156s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 156s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 156s gpgv: issuer "tille@debian.org" 156s gpgv: Can't check signature: No public key 156s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 156s autopkgtest [10:46:55]: testing package proteinortho version 6.3.1+dfsg-1 156s autopkgtest [10:46:55]: build not needed 157s autopkgtest [10:46:56]: test run-unit-test: preparing testbed 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 160s The following additional packages will be installed: 160s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 160s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 160s Recommended packages: 160s med-config 160s The following NEW packages will be installed: 160s autopkgtest-satdep diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 160s libmbedcrypto7 libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 160s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 160s Need to get 23.9 MB/23.9 MB of archives. 160s After this operation, 91.0 MB of additional disk space will be used. 160s Get:1 /tmp/autopkgtest.AgohIZ/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 160s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x diamond-aligner s390x 2.1.9-1 [2266 kB] 161s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 161s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 161s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 162s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 162s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedcrypto7 s390x 2.28.7-1ubuntu1 [216 kB] 162s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedx509-1 s390x 2.28.7-1ubuntu1 [46.0 kB] 162s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedtls14 s390x 2.28.7-1ubuntu1 [84.5 kB] 162s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 163s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-blast+ s390x 2.12.0+ds-4 [12.6 MB] 165s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x proteinortho s390x 6.3.1+dfsg-1 [333 kB] 165s Fetched 23.9 MB in 5s (5018 kB/s) 165s Selecting previously unselected package diamond-aligner. 165s (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 ... 51726 files and directories currently installed.) 165s Preparing to unpack .../00-diamond-aligner_2.1.9-1_s390x.deb ... 165s Unpacking diamond-aligner (2.1.9-1) ... 165s Selecting previously unselected package libblas3:s390x. 165s Preparing to unpack .../01-libblas3_3.12.0-3_s390x.deb ... 165s Unpacking libblas3:s390x (3.12.0-3) ... 165s Selecting previously unselected package libgfortran5:s390x. 165s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 165s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 165s Selecting previously unselected package libgomp1:s390x. 165s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 165s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 165s Selecting previously unselected package liblapack3:s390x. 165s Preparing to unpack .../04-liblapack3_3.12.0-3_s390x.deb ... 165s Unpacking liblapack3:s390x (3.12.0-3) ... 165s Selecting previously unselected package libmbedcrypto7:s390x. 165s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_s390x.deb ... 165s Unpacking libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 165s Selecting previously unselected package libmbedx509-1:s390x. 165s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_s390x.deb ... 165s Unpacking libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 165s Selecting previously unselected package libmbedtls14:s390x. 165s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_s390x.deb ... 165s Unpacking libmbedtls14:s390x (2.28.7-1ubuntu1) ... 165s Selecting previously unselected package ncbi-data. 165s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 165s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 166s Selecting previously unselected package ncbi-blast+. 166s Preparing to unpack .../09-ncbi-blast+_2.12.0+ds-4_s390x.deb ... 166s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 166s Selecting previously unselected package proteinortho. 166s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_s390x.deb ... 166s Unpacking proteinortho (6.3.1+dfsg-1) ... 166s Selecting previously unselected package autopkgtest-satdep. 166s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 166s Unpacking autopkgtest-satdep (0) ... 166s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 166s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 166s Setting up diamond-aligner (2.1.9-1) ... 166s Setting up libblas3:s390x (3.12.0-3) ... 166s 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 166s Setting up libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 166s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 166s Setting up liblapack3:s390x (3.12.0-3) ... 166s 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 166s Setting up libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 166s Setting up libmbedtls14:s390x (2.28.7-1ubuntu1) ... 166s Setting up ncbi-blast+ (2.12.0+ds-4) ... 166s Setting up proteinortho (6.3.1+dfsg-1) ... 166s Setting up autopkgtest-satdep (0) ... 166s Processing triggers for man-db (2.12.0-3) ... 166s Processing triggers for libc-bin (2.39-0ubuntu6) ... 169s (Reading database ... 52060 files and directories currently installed.) 169s Removing autopkgtest-satdep (0) ... 169s autopkgtest [10:47:08]: test run-unit-test: [----------------------- 170s ***************************************************************** 170s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 170s ***************************************************************** 170s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 170s Checking input files. 170s Checking input files. 170s Checking test/C_clean.faa... ok 170s Checking test/C2.faa... ok 170s Checking test/E.faa... ok 170s Checking test/L.faa... ok 170s Checking test/M.faa... ok 170s Checking test/C.faa... 170s  [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 !!! 170s The line is: 170s C_10,test 170s ok 170s Checking test/C_clean.faa... ok 170s Checking test/L.faa... ok 170s Checking test/E.faa... ok 170s Checking test/M.faa... ok 170s 170s **Step 1** 170s Generating indices anyway (forced). 170s Building database for 'test/C_clean.faa' (218 sequences) 170s Generating indices anyway (forced). 170s Building database for 'test/L.faa' (80 sequences) 170s Generating indices anyway (forced). 170s Building database for 'test/E.faa' (144 sequences) 170s Generating indices anyway (forced). 170s Building database for 'test/M.faa' (80 sequences) 170s Generating indices anyway (forced). 170s Building database for 'test/C2.faa' (2 sequences) 170s 170s **Step 2** using blastp+ 175s 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) 175s [OUTPUT] -> written to test_blastp.blast-graph 175s 175s **Step 3** 175s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 175s Reading test_blastp.blast-graph 175s 5 species 175s 112 paired proteins 175s 147 bidirectional edges 176s 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 176s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 176s You can extract the fasta files of each orthology group with 176s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/C_clean.faa' 'test/L.faa' 'test/E.faa' 'test/M.faa' 'test/C2.faa' 176s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 176s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 176s # test_blastp.proteinortho.tsv statistics: 176s # number of groups that contains at least p% species: 176s # p species groups genes in groups 176s 0% 0 32 (100%) 112 (100%) 176s 20% 1 32 (100%) 112 (100%) 176s 40% 2 32 (100%) 112 (100%) 176s 60% 3 17 (53.12%) 74 (66.07%) 176s 80% 4 11 (34.37%) 51 (45.53%) 176s 100% 5 1 (3.12%) 5 (4.46%) 176s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 176s # number of groups for each input species: 176s L.faa 32 100% 176s M.faa 32 100% 176s E.faa 15 46.87% 176s C_clean.faa 13 40.62% 176s C2.faa 1 3.12% 176s 176s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 176s 176s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 176s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 176s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 176s 176s All finished. 176s ***************************************************************** 176s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 176s ***************************************************************** 176s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 176s Checking input files. 176s Checking test/C_clean.faa... ok 176s Checking test/C2.faa... ok 176s Checking test/E.faa... ok 176s Checking test/L.faa... ok 176s Checking test/M.faa... ok 176s 176s **Step 1** 176s Generating indices anyway (forced). 176s Building database for 'test/C2.faa' (2 sequences) 177s Generating indices anyway (forced). 177s Building database for 'test/C_clean.faa' (109 sequences) 177s Generating indices anyway (forced). 177s Building database for 'test/M.faa' (40 sequences) 177s Generating indices anyway (forced). 177s Building database for 'test/L.faa' (40 sequences) 177s Generating indices anyway (forced). 177s Building database for 'test/E.faa' (72 sequences) 177s 177s **Step 2** using blastp+ with : synteny 183s 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) 183s [OUTPUT] -> written to test_synteny.blast-graph 183s 183s **Step 3** 183s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 183s Reading test_synteny.blast-graph 183s 5 species 183s 112 paired proteins 183s 147 bidirectional edges 184s 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 184s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 184s You can extract the fasta files of each orthology group with 184s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 'test/L.faa' 'test/E.faa' 184s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 184s Adding singles... 184s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 184s # test_synteny.proteinortho.tsv statistics: 184s # number of groups that contains at least p% species: 184s # p species groups genes in groups 184s 0% 0 182 (100%) 262 (100%) 184s 20% 1 182 (100%) 262 (100%) 184s 40% 2 32 (17.58%) 112 (42.74%) 184s 60% 3 17 (9.34%) 74 (28.24%) 184s 80% 4 11 (6.04%) 51 (19.46%) 184s 100% 5 1 (0.54%) 5 (1.9%) 184s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 184s # groups that contains only one species: 184s single 5 150 (82.41%) 150 (57.25%) 184s # number of groups for each input species: 184s L.faa 32 100% 184s M.faa 32 100% 184s E.faa 15 46.87% 184s C_clean.faa 13 40.62% 184s C2.faa 1 3.12% 184s 184s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 184s 184s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 184s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 184s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 184s 184s 184s Clustering by gene-order (POFF mode) 184s Reading test_synteny.ffadj-graph 184s 5 species 184s 105 paired proteins 184s 106 bidirectional edges 185s 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 (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 (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 (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 185s 5 species 185s 105 paired proteins 185s 106 bidirectional edges 186s 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 (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 (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 (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 186s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 186s You can extract the fasta files of each orthology group with 186s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 'test/L.faa' 'test/E.faa' 186s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 186s Adding singles... 186s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 186s # test_synteny.poff.tsv statistics: 186s # number of groups that contains at least p% species: 186s # p species groups genes in groups 186s 0% 0 195 (100%) 262 (100%) 186s 20% 1 195 (100%) 262 (100%) 186s 40% 2 37 (18.97%) 104 (39.69%) 186s 60% 3 17 (8.71%) 64 (24.42%) 186s 80% 4 10 (5.12%) 43 (16.41%) 186s 100% 5 1 (0.51%) 5 (1.9%) 186s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 186s # groups that contains only one species: 186s single 5 158 (81.02%) 158 (60.3%) 186s # number of groups for each input species: 186s L.faa 37 100% 186s M.faa 37 100% 186s E.faa 14 37.83% 186s C_clean.faa 13 35.13% 186s C2.faa 1 2.7% 186s 186s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 186s 186s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 186s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 186s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 186s 186s All finished. 187s ***************************************************************** 187s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 187s ***************************************************************** 187s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 187s Checking input files. 187s Checking test/C_clean.faa... ok 187s Checking test/C2.faa... ok 187s Checking test/E.faa... ok 187s Checking test/L.faa... ok 187s Checking test/M.faa... ok 187s 187s **Step 1** 187s Generating indices anyway (forced). 187s Building database for 'test/C2.faa' (2 sequences) 187s Generating indices anyway (forced). 187s Building database for 'test/C_clean.faa' (109 sequences) 187s Generating indices anyway (forced). 187s Building database for 'test/M.faa' (40 sequences) 187s Generating indices anyway (forced). 187s Building database for 'test/E.faa' (72 sequences) 187s Generating indices anyway (forced). 187s Building database for 'test/L.faa' (40 sequences) 187s 187s **Step 2** using diamond 195s 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) 195s [OUTPUT] -> written to test_diamond.blast-graph 195s 195s **Step 3** 195s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 195s Reading test_diamond.blast-graph 195s 5 species 195s 113 paired proteins 195s 147 bidirectional edges 196s 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 (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 196s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 196s You can extract the fasta files of each orthology group with 196s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 'test/E.faa' 'test/L.faa' 196s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 196s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 196s # test_diamond.proteinortho.tsv statistics: 196s # number of groups that contains at least p% species: 196s # p species groups genes in groups 196s 0% 0 32 (100%) 112 (100%) 196s 20% 1 32 (100%) 112 (100%) 196s 40% 2 32 (100%) 112 (100%) 196s 60% 3 17 (53.12%) 76 (67.85%) 196s 80% 4 11 (34.37%) 53 (47.32%) 196s 100% 5 1 (3.12%) 5 (4.46%) 196s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 196s # number of groups for each input species: 196s L.faa 32 100% 196s M.faa 32 100% 196s E.faa 15 46.87% 196s C_clean.faa 13 40.62% 196s C2.faa 1 3.12% 196s 196s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 196s 196s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 196s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 196s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 196s 196s All finished. 196s ***************************************************************** 196s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 196s ***************************************************************** 196s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 196s Checking input files. 196s Checking test/C_clean.faa... ok 196s Checking test/C2.faa... ok 196s Checking test/E.faa... ok 196s Checking test/L.faa... ok 196s Checking test/M.faa... ok 196s 196s **Step 1** 196s Generating indices anyway (forced). 196s Building database for 'test/M.faa' (40 sequences) 196s Generating indices anyway (forced). 196s Building database for 'test/C2.faa' (2 sequences) 196s Generating indices anyway (forced). 196s Building database for 'test/C_clean.faa' (109 sequences) 196s Generating indices anyway (forced). 196s Building database for 'test/L.faa' (40 sequences) 196s Generating indices anyway (forced). 196s Building database for 'test/E.faa' (72 sequences) 196s 196s **Step 2** using diamond 207s 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) 207s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 207s 207s **Step 3** 207s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 207s Reading test_diamondmoresensitive.blast-graph 207s 5 species 207s 113 paired proteins 207s 147 bidirectional edges 208s 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 (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 208s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 208s You can extract the fasta files of each orthology group with 208s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/M.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/L.faa' 'test/E.faa' 208s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 208s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 208s # test_diamondmoresensitive.proteinortho.tsv statistics: 208s # number of groups that contains at least p% species: 208s # p species groups genes in groups 208s 0% 0 32 (100%) 112 (100%) 208s 20% 1 32 (100%) 112 (100%) 208s 40% 2 32 (100%) 112 (100%) 208s 60% 3 17 (53.12%) 76 (67.85%) 208s 80% 4 11 (34.37%) 53 (47.32%) 208s 100% 5 1 (3.12%) 5 (4.46%) 208s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 208s # number of groups for each input species: 208s L.faa 32 100% 208s M.faa 32 100% 208s E.faa 15 46.87% 208s C_clean.faa 13 40.62% 208s C2.faa 1 3.12% 208s 208s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 208s 208s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 208s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 208s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 208s 208s All finished. 208s ***************************************************************** 208s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 208s ***************************************************************** 208s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 208s Checking input files. 208s Checking test/C_clean.faa... ok 208s Checking test/C2.faa... ok 208s Checking test/E.faa... ok 208s Checking test/L.faa... ok 208s Checking test/M.faa... ok 208s 208s **Step 1** 208s Generating indices anyway (forced). 208s Building database for 'test/L.faa' (40 sequences) 208s Generating indices anyway (forced). 208s Building database for 'test/M.faa' (40 sequences) 208s Generating indices anyway (forced). 208s Building database for 'test/E.faa' (72 sequences) 208s Generating indices anyway (forced). 208s Building database for 'test/C_clean.faa' (109 sequences) 208s Generating indices anyway (forced). 208s Building database for 'test/C2.faa' (2 sequences) 208s 208s **Step 2** using blastp+ 213s 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) 213s [OUTPUT] -> written to test_blastall.blast-graph 213s 213s **Step 3** 213s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 213s Reading test_blastall.blast-graph 213s 5 species 213s 112 paired proteins 213s 149 bidirectional edges 214s 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 214s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 214s You can extract the fasta files of each orthology group with 214s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/L.faa' 'test/M.faa' 'test/E.faa' 'test/C_clean.faa' 'test/C2.faa' 214s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 214s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 214s # test_blastall.proteinortho.tsv statistics: 214s # number of groups that contains at least p% species: 214s # p species groups genes in groups 214s 0% 0 32 (100%) 112 (100%) 214s 20% 1 32 (100%) 112 (100%) 214s 40% 2 32 (100%) 112 (100%) 214s 60% 3 17 (53.12%) 74 (66.07%) 214s 80% 4 11 (34.37%) 51 (45.53%) 214s 100% 5 1 (3.12%) 5 (4.46%) 214s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 214s # number of groups for each input species: 214s L.faa 32 100% 214s M.faa 32 100% 214s E.faa 15 46.87% 214s C_clean.faa 13 40.62% 214s C2.faa 1 3.12% 214s 214s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 214s 214s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 214s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 214s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 214s 214s All finished. 214s - test max_of_diag() : OK 214s - test generate_random_vector() : OK 214s - test get_new_x() : OK 214s - test makeOrthogonal() : OK 214s - test normalize() : OK 214s - test getY() : OK 214s - test lapack() : OK 214s - test power() : OK 214s - test smirnov-grubb() : OK 214s All test passed. 214s Reading test_blastp.blast-graph 214s 5 species 214s 112 paired proteins 214s 147 bidirectional edges 214s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 215s 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 215s 4 4 1 * C_11 E_11 L_11 M_11 215s 4 6 0.149 * C_12,C_21 E_313,E_315 L_313 M_313 215s 4 4 1 * C_14 E_14 L_14 M_14 215s 4 4 1 * C_15 E_15 L_15 M_15 215s 4 4 1 * C_16 E_16 L_16 M_16 215s 4 4 1 * C_17 E_17 L_17 M_17 215s 4 4 1 * C_64 E_18 L_18 M_18 215s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 215s 3 3 1 * C_20 * L_20 M_20 215s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 215s 2 2 1 * * * L_619 M_619 215s 3 3 0.33 * * E_367 L_319 M_319 215s 2 2 1 * * * L_617 M_617 215s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 215s 2 4 0.5 * * * L_645,L_647 M_644,M_646 215s 3 3 0.33 * * E_432 L_328 M_328 215s 2 2 1 * * * L_333 M_333 215s 2 2 1 * * * L_3 M_3 215s 2 2 1 * * * L_4 M_4 215s 2 2 1 * * * L_5 M_5 215s 2 2 1 * * * L_6 M_6 215s 2 2 1 * * * L_8 M_8 215s 2 2 1 * * * L_9 M_9 215s 2 2 1 * * * L_623 M_623 215s 4 4 1 * C_13 E_13 L_621 M_621 215s 2 4 0.146 * * * L_637,L_639 M_636,M_638 215s 3 3 0.33 * * E_437 L_317 M_317 215s 2 3 0.33 * * * L_631,L_633 M_632 215s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 215s 2 2 1 * * * L_331 M_331 215s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 215s Reading test_blastp.blast-graph 215s 5 species 215s 112 paired proteins 215s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 215s 147 bidirectional edges 216s 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 216s 2 2 1 * * * L_619 M_619 216s 3 3 0.33 * * E_367 L_319 M_319 216s 2 2 1 * * * L_617 M_617 216s 3 3 0.33 * * E_432 L_328 M_328 216s 2 2 1 * * * L_333 M_333 216s 2 2 1 * * * L_3 M_3 216s 2 2 1 * * * L_4 M_4 216s 2 2 1 * * * L_5 M_5 216s 2 2 1 * * * L_6 M_6 216s 2 2 1 * * * L_8 M_8 216s 2 2 1 * * * L_9 M_9 216s 5 5 0.687 C_10 C_10;test E_10 L_10 M_10 216s 4 4 0.727 * C_11 E_11 L_11 M_11 216s 4 6 0.137 * C_12,C_21 E_313,E_315 L_313 M_313 216s 2 2 1 * * * L_623 M_623 216s 4 4 0.74 * C_14 E_14 L_14 M_14 216s 4 4 0.814 * C_15 E_15 L_15 M_15 216s 4 4 0.815 * C_16 E_16 L_16 M_16 216s 4 4 0.824 * C_17 E_17 L_17 M_17 216s 4 4 0.779 * C_64 E_18 L_18 M_18 216s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 216s 3 3 0.33 * * E_437 L_317 M_317 216s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 216s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 216s 2 4 0.478 * * * L_645,L_647 M_644,M_646 216s 4 4 0.717 * C_13 E_13 L_621 M_621 216s 2 4 0.145 * * * L_637,L_639 M_636,M_638 216s 2 2 1 * * * L_331 M_331 216s 2 3 0.33 * * * L_631,L_633 M_632 216s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 216s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 216s Test okay 217s autopkgtest [10:47:56]: test run-unit-test: -----------------------] 217s autopkgtest [10:47:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 217s run-unit-test PASS 218s autopkgtest [10:47:57]: @@@@@@@@@@@@@@@@@@@@ summary 218s run-unit-test PASS 229s Creating nova instance adt-noble-s390x-proteinortho-20240326-104419-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240326.img (UUID c527e0e4-2e65-4e86-ad63-05d7f665f2fb)...