0s autopkgtest [10:54:49]: starting date and time: 2024-03-26 10:54:49+0000 0s autopkgtest [10:54:49]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [10:54:49]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.50daib2v/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-ppc64el-19.secgroup --name adt-noble-ppc64el-proteinortho-20240326-105448-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 130s autopkgtest [10:56:59]: testbed dpkg architecture: ppc64el 130s autopkgtest [10:56:59]: testbed apt version: 2.7.12 130s autopkgtest [10:56:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 131s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3982 kB] 132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B] 132s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 132s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 132s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [697 kB] 132s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 132s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 132s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 132s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4220 kB] 132s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 132s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 132s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 135s Fetched 9651 kB in 3s (3621 kB/s) 136s Reading package lists... 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Calculating upgrade... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s 0 upgraded, 0 newly installed, 0 to remove and 246 not upgraded. 139s sh: Attempting to set up Debian/Ubuntu apt sources automatically 139s sh: Distribution appears to be Ubuntu 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s eatmydata is already the newest version (131-1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s dbus is already the newest version (1.14.10-4ubuntu1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s rng-tools-debian is already the newest version (2.4). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s The following packages will be REMOVED: 141s cloud-init* python3-configobj* python3-debconf* 141s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 141s After this operation, 3256 kB disk space will be freed. 141s (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 ... 70156 files and directories currently installed.) 141s Removing cloud-init (24.1.2-0ubuntu1) ... 142s Removing python3-configobj (5.0.8-3) ... 142s Removing python3-debconf (1.5.86) ... 142s Processing triggers for man-db (2.12.0-3) ... 143s (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 ... 69767 files and directories currently installed.) 143s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 143s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 143s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 143s invoke-rc.d: policy-rc.d denied execution of try-restart. 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s linux-generic is already the newest version (6.8.0-11.11+1). 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 144s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 144s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 147s Reading package lists... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [10:57:17]: rebooting testbed after setup commands that affected boot 190s autopkgtest [10:57:59]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 192s autopkgtest [10:58:01]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 194s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 194s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 194s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 195s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 195s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 195s gpgv: issuer "tille@debian.org" 195s gpgv: Can't check signature: No public key 195s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 195s autopkgtest [10:58:04]: testing package proteinortho version 6.3.1+dfsg-1 195s autopkgtest [10:58:04]: build not needed 195s autopkgtest [10:58:04]: test run-unit-test: preparing testbed 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Starting pkgProblemResolver with broken count: 0 197s Starting 2 pkgProblemResolver with broken count: 0 197s Done 197s The following additional packages will be installed: 197s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 197s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 197s Recommended packages: 197s med-config 197s The following NEW packages will be installed: 197s autopkgtest-satdep diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 197s libmbedcrypto7 libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 197s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 197s Need to get 24.3 MB/24.3 MB of archives. 197s After this operation, 103 MB of additional disk space will be used. 197s Get:1 /tmp/autopkgtest.HwaQOF/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 197s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el diamond-aligner ppc64el 2.1.9-1 [1959 kB] 199s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 199s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 199s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 199s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 200s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedcrypto7 ppc64el 2.28.7-1ubuntu1 [262 kB] 200s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedx509-1 ppc64el 2.28.7-1ubuntu1 [51.4 kB] 200s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedtls14 ppc64el 2.28.7-1ubuntu1 [89.7 kB] 200s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 200s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-blast+ ppc64el 2.12.0+ds-4 [13.4 MB] 202s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el proteinortho ppc64el 6.3.1+dfsg-1 [374 kB] 202s Fetched 24.3 MB in 5s (5304 kB/s) 202s Selecting previously unselected package diamond-aligner. 202s (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 ... 69712 files and directories currently installed.) 202s Preparing to unpack .../00-diamond-aligner_2.1.9-1_ppc64el.deb ... 202s Unpacking diamond-aligner (2.1.9-1) ... 202s Selecting previously unselected package libblas3:ppc64el. 202s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 202s Unpacking libblas3:ppc64el (3.12.0-3) ... 202s Selecting previously unselected package libgfortran5:ppc64el. 202s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 202s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 202s Selecting previously unselected package libgomp1:ppc64el. 202s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 202s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 202s Selecting previously unselected package liblapack3:ppc64el. 202s Preparing to unpack .../04-liblapack3_3.12.0-3_ppc64el.deb ... 202s Unpacking liblapack3:ppc64el (3.12.0-3) ... 202s Selecting previously unselected package libmbedcrypto7:ppc64el. 202s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_ppc64el.deb ... 202s Unpacking libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 202s Selecting previously unselected package libmbedx509-1:ppc64el. 202s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_ppc64el.deb ... 202s Unpacking libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 202s Selecting previously unselected package libmbedtls14:ppc64el. 202s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_ppc64el.deb ... 202s Unpacking libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 202s Selecting previously unselected package ncbi-data. 202s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 202s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 202s Selecting previously unselected package ncbi-blast+. 202s Preparing to unpack .../09-ncbi-blast+_2.12.0+ds-4_ppc64el.deb ... 202s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 203s Selecting previously unselected package proteinortho. 203s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_ppc64el.deb ... 203s Unpacking proteinortho (6.3.1+dfsg-1) ... 203s Selecting previously unselected package autopkgtest-satdep. 203s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 203s Unpacking autopkgtest-satdep (0) ... 203s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 203s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 203s Setting up diamond-aligner (2.1.9-1) ... 203s Setting up libblas3:ppc64el (3.12.0-3) ... 203s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 203s Setting up libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 203s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 203s Setting up liblapack3:ppc64el (3.12.0-3) ... 203s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 203s Setting up libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 203s Setting up libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 203s Setting up ncbi-blast+ (2.12.0+ds-4) ... 203s Setting up proteinortho (6.3.1+dfsg-1) ... 203s Setting up autopkgtest-satdep (0) ... 203s Processing triggers for man-db (2.12.0-3) ... 203s Processing triggers for libc-bin (2.39-0ubuntu6) ... 205s (Reading database ... 70046 files and directories currently installed.) 205s Removing autopkgtest-satdep (0) ... 206s autopkgtest [10:58:15]: test run-unit-test: [----------------------- 206s ***************************************************************** 206s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 206s ***************************************************************** 206s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 206s Checking input files. 206s Checking input files. 206s Checking test/C_clean.faa... ok 206s Checking test/C2.faa... ok 206s Checking test/E.faa... ok 206s Checking test/L.faa... ok 206s Checking test/M.faa... ok 206s Checking test/C.faa... 206s  [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 !!! 206s The line is: 206s C_10,test 206s ok 206s Checking test/C2.faa... ok 206s Checking test/C_clean.faa... ok 206s Checking test/L.faa... ok 206s Checking test/M.faa... ok 206s 206s **Step 1** 207s Generating indices anyway (forced). 207s Building database for 'test/M.faa' (80 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/C_clean.faa' (218 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/C2.faa' (4 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/L.faa' (80 sequences) 207s Generating indices anyway (forced). 207s Building database for 'test/E.faa' (72 sequences) 207s 207s **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_blastp.blast-graph 213s 213s **Step 3** 213s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 213s Reading test_blastp.blast-graph 213s 5 species 213s 112 paired proteins 213s 147 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 (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 214s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 214s You can extract the fasta files of each orthology group with 214s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/M.faa' 'test/C_clean.faa' 'test/C2.faa' 'test/L.faa' 'test/E.faa' 214s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 214s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 214s # test_blastp.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_blastp.proteinortho-graph.summary 214s 214s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 214s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 214s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 214s 214s All finished. 214s ***************************************************************** 214s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 214s ***************************************************************** 214s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 214s Checking input files. 214s Checking test/C_clean.faa... ok 214s Checking test/C2.faa... ok 214s Checking test/E.faa... ok 214s Checking test/L.faa... ok 214s Checking test/M.faa... ok 214s 214s **Step 1** 214s Generating indices anyway (forced). 214s Building database for 'test/C2.faa' (2 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/L.faa' (40 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/C_clean.faa' (109 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/E.faa' (72 sequences) 214s Generating indices anyway (forced). 214s Building database for 'test/M.faa' (40 sequences) 214s 214s **Step 2** using blastp+ with : synteny 220s 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) 220s [OUTPUT] -> written to test_synteny.blast-graph 220s 220s **Step 3** 220s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 220s Reading test_synteny.blast-graph 220s 5 species 220s 112 paired proteins 220s 147 bidirectional edges 221s 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 221s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 221s You can extract the fasta files of each orthology group with 221s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/C2.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 'test/M.faa' 221s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 221s Adding singles... 221s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 221s # test_synteny.proteinortho.tsv statistics: 221s # number of groups that contains at least p% species: 221s # p species groups genes in groups 221s 0% 0 182 (100%) 262 (100%) 221s 20% 1 182 (100%) 262 (100%) 221s 40% 2 32 (17.58%) 112 (42.74%) 221s 60% 3 17 (9.34%) 74 (28.24%) 221s 80% 4 11 (6.04%) 51 (19.46%) 221s 100% 5 1 (0.54%) 5 (1.9%) 221s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 221s # groups that contains only one species: 221s single 5 150 (82.41%) 150 (57.25%) 221s # number of groups for each input species: 221s L.faa 32 100% 221s M.faa 32 100% 221s E.faa 15 46.87% 221s C_clean.faa 13 40.62% 221s C2.faa 1 3.12% 221s 221s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 221s 221s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 221s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 221s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 221s 221s 221s Clustering by gene-order (POFF mode) 221s Reading test_synteny.ffadj-graph 221s 5 species 221s 105 paired proteins 221s 106 bidirectional edges 222s 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 (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (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 222s 5 species 222s 105 paired proteins 222s 106 bidirectional edges 223s 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 (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (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 223s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 223s You can extract the fasta files of each orthology group with 223s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/C2.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 'test/M.faa' 223s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 223s Adding singles... 223s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 223s # test_synteny.poff.tsv statistics: 223s # number of groups that contains at least p% species: 223s # p species groups genes in groups 223s 0% 0 196 (100%) 262 (100%) 223s 20% 1 196 (100%) 262 (100%) 223s 40% 2 37 (18.87%) 103 (39.31%) 223s 60% 3 15 (7.65%) 59 (22.51%) 223s 80% 4 10 (5.1%) 43 (16.41%) 223s 100% 5 1 (0.51%) 5 (1.9%) 223s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 223s # groups that contains only one species: 223s single 5 159 (81.12%) 159 (60.68%) 223s # number of groups for each input species: 223s L.faa 37 100% 223s M.faa 36 97.29% 223s C_clean.faa 13 35.13% 223s E.faa 13 35.13% 223s C2.faa 1 2.7% 223s 223s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 223s 223s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 223s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 223s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 223s 223s All finished. 224s ***************************************************************** 224s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 224s ***************************************************************** 224s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 224s Checking input files. 224s Checking test/C_clean.faa... ok 224s Checking test/C2.faa... ok 224s Checking test/E.faa... ok 224s Checking test/L.faa... ok 224s Checking test/M.faa... ok 224s 224s **Step 1** 224s Generating indices anyway (forced). 224s Building database for 'test/C_clean.faa' (109 sequences) 224s Generating indices anyway (forced). 224s Building database for 'test/C2.faa' (2 sequences) 224s Generating indices anyway (forced). 224s Building database for 'test/M.faa' (40 sequences) 224s Generating indices anyway (forced). 224s Building database for 'test/E.faa' (72 sequences) 224s Generating indices anyway (forced). 224s Building database for 'test/L.faa' (40 sequences) 224s 224s **Step 2** using diamond 231s 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) 231s [OUTPUT] -> written to test_diamond.blast-graph 231s 231s **Step 3** 231s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 231s Reading test_diamond.blast-graph 231s 5 species 231s 113 paired proteins 231s 147 bidirectional edges 232s 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 232s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 232s You can extract the fasta files of each orthology group with 232s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/C_clean.faa' 'test/C2.faa' 'test/M.faa' 'test/E.faa' 'test/L.faa' 232s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 232s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 233s # test_diamond.proteinortho.tsv statistics: 233s # number of groups that contains at least p% species: 233s # p species groups genes in groups 233s 0% 0 32 (100%) 112 (100%) 233s 20% 1 32 (100%) 112 (100%) 233s 40% 2 32 (100%) 112 (100%) 233s 60% 3 17 (53.12%) 76 (67.85%) 233s 80% 4 11 (34.37%) 53 (47.32%) 233s 100% 5 1 (3.12%) 5 (4.46%) 233s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 233s # number of groups for each input species: 233s L.faa 32 100% 233s M.faa 32 100% 233s E.faa 15 46.87% 233s C_clean.faa 13 40.62% 233s C2.faa 1 3.12% 233s 233s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 233s 233s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 233s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 233s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 233s 233s All finished. 233s ***************************************************************** 233s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 233s ***************************************************************** 233s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 233s Checking input files. 233s Checking test/C_clean.faa... ok 233s Checking test/C2.faa... ok 233s Checking test/E.faa... ok 233s Checking test/L.faa... ok 233s Checking test/M.faa... ok 233s 233s **Step 1** 233s Generating indices anyway (forced). 233s Building database for 'test/E.faa' (72 sequences) 233s Generating indices anyway (forced). 233s Building database for 'test/L.faa' (40 sequences) 233s Generating indices anyway (forced). 233s Building database for 'test/M.faa' (40 sequences) 233s Generating indices anyway (forced). 233s Building database for 'test/C_clean.faa' (109 sequences) 233s Generating indices anyway (forced). 233s Building database for 'test/C2.faa' (2 sequences) 233s 233s **Step 2** using diamond 242s 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) 242s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 242s 242s **Step 3** 242s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 242s Reading test_diamondmoresensitive.blast-graph 242s 5 species 242s 112 paired proteins 242s 145 bidirectional edges 243s 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 243s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 243s You can extract the fasta files of each orthology group with 243s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C_clean.faa' 'test/C2.faa' 243s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 243s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 243s # test_diamondmoresensitive.proteinortho.tsv statistics: 243s # number of groups that contains at least p% species: 243s # p species groups genes in groups 243s 0% 0 32 (100%) 111 (100%) 243s 20% 1 32 (100%) 111 (100%) 243s 40% 2 32 (100%) 111 (100%) 243s 60% 3 17 (53.12%) 75 (67.56%) 243s 80% 4 11 (34.37%) 52 (46.84%) 243s 100% 5 1 (3.12%) 5 (4.5%) 243s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 243s # number of groups for each input species: 243s L.faa 32 100% 243s M.faa 32 100% 243s E.faa 15 46.87% 243s C_clean.faa 13 40.62% 243s C2.faa 1 3.12% 243s 243s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 243s 243s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 243s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 243s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 243s 243s All finished. 244s ***************************************************************** 244s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 244s ***************************************************************** 244s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 244s Checking input files. 244s Checking test/C_clean.faa... ok 244s Checking test/C2.faa... ok 244s Checking test/E.faa... ok 244s Checking test/L.faa... ok 244s Checking test/M.faa... ok 244s 244s **Step 1** 244s Generating indices anyway (forced). 244s Building database for 'test/C_clean.faa' (109 sequences) 244s Generating indices anyway (forced). 244s Building database for 'test/E.faa' (72 sequences) 244s Generating indices anyway (forced). 244s Building database for 'test/L.faa' (40 sequences) 244s Generating indices anyway (forced). 244s Building database for 'test/M.faa' (40 sequences) 244s Generating indices anyway (forced). 244s Building database for 'test/C2.faa' (2 sequences) 244s 244s **Step 2** using blastp+ 251s 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) 251s [OUTPUT] -> written to test_blastall.blast-graph 251s 251s **Step 3** 251s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 251s Reading test_blastall.blast-graph 251s 5 species 251s 112 paired proteins 251s 147 bidirectional edges 252s 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 252s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 252s You can extract the fasta files of each orthology group with 252s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C_clean.faa' 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa' 252s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 252s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 252s # test_blastall.proteinortho.tsv statistics: 252s # number of groups that contains at least p% species: 252s # p species groups genes in groups 252s 0% 0 32 (100%) 112 (100%) 252s 20% 1 32 (100%) 112 (100%) 252s 40% 2 32 (100%) 112 (100%) 252s 60% 3 17 (53.12%) 74 (66.07%) 252s 80% 4 11 (34.37%) 51 (45.53%) 252s 100% 5 1 (3.12%) 5 (4.46%) 252s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 252s # number of groups for each input species: 252s L.faa 32 100% 252s M.faa 32 100% 252s E.faa 15 46.87% 252s C_clean.faa 13 40.62% 252s C2.faa 1 3.12% 252s 252s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 252s 252s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 252s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 252s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 252s 252s All finished. 252s - test max_of_diag() : OK 252s - test generate_random_vector() : OK 252s - test get_new_x() : OK 252s - test makeOrthogonal() : # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 252s OK 252s - test normalize() : OK 252s - test getY() : OK 252s - test lapack() : OK 252s - test power() : OK 252s - test smirnov-grubb() : OK 252s All test passed. 252s Reading test_blastp.blast-graph 252s 5 species 252s 112 paired proteins 252s 147 bidirectional edges 253s 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 253s 4 4 1 * C_11 E_11 L_11 M_11 253s 4 6 0.149 * C_12,C_21 E_313,E_315 L_313 M_313 253s 4 4 1 * C_14 E_14 L_14 M_14 253s 4 4 1 * C_15 E_15 L_15 M_15 253s 4 4 1 * C_16 E_16 L_16 M_16 253s 4 4 1 * C_17 E_17 L_17 M_17 253s 4 4 1 * C_64 E_18 L_18 M_18 253s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 253s 3 3 1 * C_20 * L_20 M_20 253s 3 6 0.333 * C_167,C_2,C_164,C_166 * L_2 M_2 253s 2 2 1 * * * L_619 M_619 253s 3 3 0.33 * * E_367 L_319 M_319 253s 2 2 1 * * * L_617 M_617 253s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 253s 2 4 0.5 * * * L_645,L_647 M_644,M_646 253s 3 3 0.33 * * E_432 L_328 M_328 253s 2 2 1 * * * L_333 M_333 253s 2 2 1 * * * L_3 M_3 253s 2 2 1 * * * L_4 M_4 253s 2 2 1 * * * L_5 M_5 253s 2 2 1 * * * L_6 M_6 253s 2 2 1 * * * L_8 M_8 253s 2 2 1 * * * L_9 M_9 253s 2 2 1 * * * L_623 M_623 253s 4 4 1 * C_13 E_13 L_621 M_621 253s 2 4 0.146 * * * L_637,L_639 M_636,M_638 253s 3 3 0.33 * * E_437 L_317 M_317 253s 2 3 0.33 * * * L_631,L_633 M_632 253s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 253s 2 2 1 * * * L_331 M_331 253s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 253s Reading test_blastp.blast-graph 253s 5 species 253s 112 paired proteins 253s 147 bidirectional edges 253s # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 254s 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 254s 2 2 1 * * * L_619 M_619 254s 3 3 0.33 * * E_367 L_319 M_319 254s 2 2 1 * * * L_617 M_617 254s 3 3 0.33 * * E_432 L_328 M_328 254s 2 2 1 * * * L_333 M_333 254s 2 2 1 * * * L_3 M_3 254s 2 2 1 * * * L_4 M_4 254s 2 2 1 * * * L_5 M_5 254s 2 2 1 * * * L_6 M_6 254s 2 2 1 * * * L_8 M_8 254s 2 2 1 * * * L_9 M_9 254s 5 5 0.687 C_10 C_10;test E_10 L_10 M_10 254s 4 4 0.727 * C_11 E_11 L_11 M_11 254s 4 6 0.137 * C_12,C_21 E_313,E_315 L_313 M_313 254s 2 2 1 * * * L_623 M_623 254s 4 4 0.74 * C_14 E_14 L_14 M_14 254s 4 4 0.814 * C_15 E_15 L_15 M_15 254s 4 4 0.815 * C_16 E_16 L_16 M_16 254s 4 4 0.824 * C_17 E_17 L_17 M_17 254s 4 4 0.779 * C_64 E_18 L_18 M_18 254s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 254s 3 3 0.33 * * E_437 L_317 M_317 254s 3 6 0.314 * C_167,C_2,C_164,C_166 * L_2 M_2 254s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 254s 2 4 0.478 * * * L_645,L_647 M_644,M_646 254s 4 4 0.717 * C_13 E_13 L_621 M_621 254s 2 4 0.145 * * * L_637,L_639 M_636,M_638 254s 2 2 1 * * * L_331 M_331 254s 2 3 0.33 * * * L_631,L_633 M_632 254s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 254s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 254s Test okay 254s autopkgtest [10:59:03]: test run-unit-test: -----------------------] 255s autopkgtest [10:59:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 255s run-unit-test PASS 255s autopkgtest [10:59:04]: @@@@@@@@@@@@@@@@@@@@ summary 255s run-unit-test PASS 267s Creating nova instance adt-noble-ppc64el-proteinortho-20240326-105448-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...