0s autopkgtest [19:51:50]: starting date and time: 2024-03-24 19:51:50+0000 0s autopkgtest [19:51:50]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:51:50]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l9u7ty9z/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=src:procps --apt-upgrade proteinortho --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=procps/2:4.0.4-4ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-12.secgroup --name adt-noble-ppc64el-proteinortho-20240324-195150-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 293s autopkgtest [19:56:43]: testbed dpkg architecture: ppc64el 293s autopkgtest [19:56:43]: testbed apt version: 2.7.12 293s autopkgtest [19:56:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 294s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 294s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 294s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 294s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 294s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 294s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 295s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 295s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 295s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 295s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4263 kB] 295s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 295s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.1 kB] 295s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 298s Fetched 9694 kB in 3s (3835 kB/s) 299s Reading package lists... 301s Reading package lists... 302s Building dependency tree... 302s Reading state information... 302s Calculating upgrade... 302s The following packages will be upgraded: 302s libproc2-0 procps 302s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 302s Need to get 804 kB of archives. 302s After this operation, 4096 B of additional disk space will be used. 302s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu2 [68.8 kB] 302s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el procps ppc64el 2:4.0.4-4ubuntu2 [736 kB] 303s Fetched 804 kB in 1s (798 kB/s) 303s (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.) 303s Preparing to unpack .../libproc2-0_2%3a4.0.4-4ubuntu2_ppc64el.deb ... 303s Unpacking libproc2-0:ppc64el (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 303s Preparing to unpack .../procps_2%3a4.0.4-4ubuntu2_ppc64el.deb ... 303s Unpacking procps (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 304s Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu2) ... 304s Setting up procps (2:4.0.4-4ubuntu2) ... 304s Processing triggers for man-db (2.12.0-3) ... 305s Processing triggers for libc-bin (2.39-0ubuntu6) ... 305s Reading package lists... 306s Building dependency tree... 306s Reading state information... 306s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 306s sh: Attempting to set up Debian/Ubuntu apt sources automatically 306s sh: Distribution appears to be Ubuntu 307s Reading package lists... 307s Building dependency tree... 307s Reading state information... 308s eatmydata is already the newest version (131-1). 308s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s Reading package lists... 308s Building dependency tree... 308s Reading state information... 308s dbus is already the newest version (1.14.10-4ubuntu1). 308s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s Reading package lists... 308s Building dependency tree... 308s Reading state information... 308s rng-tools-debian is already the newest version (2.4). 308s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s Reading package lists... 309s Building dependency tree... 309s Reading state information... 309s The following packages will be REMOVED: 309s cloud-init* python3-configobj* python3-debconf* 309s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 309s After this operation, 3256 kB disk space will be freed. 309s (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 ... 70157 files and directories currently installed.) 309s Removing cloud-init (24.1.2-0ubuntu1) ... 310s Removing python3-configobj (5.0.8-3) ... 310s Removing python3-debconf (1.5.86) ... 310s Processing triggers for man-db (2.12.0-3) ... 310s (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 ... 69768 files and directories currently installed.) 310s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 311s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 311s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 311s invoke-rc.d: policy-rc.d denied execution of try-restart. 311s Reading package lists... 311s Building dependency tree... 311s Reading state information... 311s linux-generic is already the newest version (6.8.0-11.11+1). 311s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 312s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 312s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 312s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 314s Reading package lists... 315s Reading package lists... 315s Building dependency tree... 315s Reading state information... 315s Calculating upgrade... 315s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 315s Reading package lists... 315s Building dependency tree... 315s Reading state information... 315s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 316s autopkgtest [19:57:06]: rebooting testbed after setup commands that affected boot 482s autopkgtest [19:59:52]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 484s autopkgtest [19:59:54]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 486s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 486s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 486s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 486s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 486s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 486s gpgv: issuer "tille@debian.org" 486s gpgv: Can't check signature: No public key 486s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 486s autopkgtest [19:59:56]: testing package proteinortho version 6.3.1+dfsg-1 487s autopkgtest [19:59:57]: build not needed 488s autopkgtest [19:59:58]: test run-unit-test: preparing testbed 491s Reading package lists... 491s Building dependency tree... 491s Reading state information... 491s Starting pkgProblemResolver with broken count: 0 491s Starting 2 pkgProblemResolver with broken count: 0 491s Done 491s The following additional packages will be installed: 491s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 491s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 491s Recommended packages: 491s med-config 491s The following NEW packages will be installed: 491s autopkgtest-satdep diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 491s libmbedcrypto7 libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 491s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 491s Need to get 24.3 MB/24.3 MB of archives. 491s After this operation, 103 MB of additional disk space will be used. 491s Get:1 /tmp/autopkgtest.DeGs7e/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 492s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el diamond-aligner ppc64el 2.1.9-1 [1959 kB] 493s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 493s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 493s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 493s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 494s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedcrypto7 ppc64el 2.28.7-1ubuntu1 [262 kB] 494s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedx509-1 ppc64el 2.28.7-1ubuntu1 [51.4 kB] 494s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedtls14 ppc64el 2.28.7-1ubuntu1 [89.7 kB] 494s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 494s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-blast+ ppc64el 2.12.0+ds-4 [13.4 MB] 495s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el proteinortho ppc64el 6.3.1+dfsg-1 [374 kB] 496s Fetched 24.3 MB in 4s (6207 kB/s) 496s Selecting previously unselected package diamond-aligner. 496s (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 ... 69713 files and directories currently installed.) 496s Preparing to unpack .../00-diamond-aligner_2.1.9-1_ppc64el.deb ... 496s Unpacking diamond-aligner (2.1.9-1) ... 496s Selecting previously unselected package libblas3:ppc64el. 496s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 496s Unpacking libblas3:ppc64el (3.12.0-3) ... 496s Selecting previously unselected package libgfortran5:ppc64el. 496s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 496s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 496s Selecting previously unselected package libgomp1:ppc64el. 496s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 496s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 496s Selecting previously unselected package liblapack3:ppc64el. 496s Preparing to unpack .../04-liblapack3_3.12.0-3_ppc64el.deb ... 496s Unpacking liblapack3:ppc64el (3.12.0-3) ... 496s Selecting previously unselected package libmbedcrypto7:ppc64el. 496s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_ppc64el.deb ... 496s Unpacking libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 496s Selecting previously unselected package libmbedx509-1:ppc64el. 496s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_ppc64el.deb ... 496s Unpacking libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 496s Selecting previously unselected package libmbedtls14:ppc64el. 496s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_ppc64el.deb ... 496s Unpacking libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 496s Selecting previously unselected package ncbi-data. 496s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 496s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 496s Selecting previously unselected package ncbi-blast+. 496s Preparing to unpack .../09-ncbi-blast+_2.12.0+ds-4_ppc64el.deb ... 496s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 497s Selecting previously unselected package proteinortho. 497s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_ppc64el.deb ... 497s Unpacking proteinortho (6.3.1+dfsg-1) ... 497s Selecting previously unselected package autopkgtest-satdep. 497s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 497s Unpacking autopkgtest-satdep (0) ... 497s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 497s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 497s Setting up diamond-aligner (2.1.9-1) ... 497s Setting up libblas3:ppc64el (3.12.0-3) ... 497s 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 497s Setting up libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ... 497s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 497s Setting up liblapack3:ppc64el (3.12.0-3) ... 497s 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 497s Setting up libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ... 497s Setting up libmbedtls14:ppc64el (2.28.7-1ubuntu1) ... 497s Setting up ncbi-blast+ (2.12.0+ds-4) ... 497s Setting up proteinortho (6.3.1+dfsg-1) ... 497s Setting up autopkgtest-satdep (0) ... 497s Processing triggers for man-db (2.12.0-3) ... 497s Processing triggers for libc-bin (2.39-0ubuntu6) ... 499s (Reading database ... 70047 files and directories currently installed.) 499s Removing autopkgtest-satdep (0) ... 500s autopkgtest [20:00:10]: test run-unit-test: [----------------------- 500s ***************************************************************** 500s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 500s ***************************************************************** 500s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 500s Checking input files. 500s Checking input files. 500s Checking test/C_clean.faa... ok 500s Checking test/C2.faa... ok 500s Checking test/E.faa... ok 500s Checking test/L.faa... ok 500s Checking test/M.faa... ok 500s Checking test/C.faa... 500s  [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 !!! 500s The line is: 500s C_10,test 500s ok 500s Checking test/M.faa... ok 500s Checking test/L.faa... ok 500s Checking test/E.faa... ok 500s Checking test/C2.faa... ok 500s 500s **Step 1** 500s Generating indices anyway (forced). 500s Building database for 'test/M.faa' (80 sequences) 500s Generating indices anyway (forced). 500s Building database for 'test/E.faa' (144 sequences) 500s Generating indices anyway (forced). 500s Building database for 'test/L.faa' (80 sequences) 500s Generating indices anyway (forced). 500s Building database for 'test/C2.faa' (4 sequences) 500s Generating indices anyway (forced). 500s Building database for 'test/C_clean.faa' (109 sequences) 501s 501s **Step 2** using blastp+ 507s 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) 507s [OUTPUT] -> written to test_blastp.blast-graph 507s 507s **Step 3** 507s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 507s Reading test_blastp.blast-graph 507s 5 species 507s 112 paired proteins 507s 149 bidirectional edges 508s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (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 508s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 508s You can extract the fasta files of each orthology group with 508s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/M.faa' 'test/E.faa' 'test/L.faa' 'test/C2.faa' 'test/C_clean.faa' 508s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 508s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 508s # test_blastp.proteinortho.tsv statistics: 508s # number of groups that contains at least p% species: 508s # p species groups genes in groups 508s 0% 0 32 (100%) 112 (100%) 508s 20% 1 32 (100%) 112 (100%) 508s 40% 2 32 (100%) 112 (100%) 508s 60% 3 17 (53.12%) 74 (66.07%) 508s 80% 4 11 (34.37%) 51 (45.53%) 508s 100% 5 1 (3.12%) 5 (4.46%) 508s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 508s # number of groups for each input species: 508s L.faa 32 100% 508s M.faa 32 100% 508s E.faa 15 46.87% 508s C_clean.faa 13 40.62% 508s C2.faa 1 3.12% 508s 508s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 508s 508s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 508s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 508s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 508s 508s All finished. 508s ***************************************************************** 508s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 508s ***************************************************************** 508s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 508s Checking input files. 508s Checking test/C_clean.faa... ok 508s Checking test/C2.faa... ok 508s Checking test/E.faa... ok 508s Checking test/L.faa... ok 508s Checking test/M.faa... ok 508s 508s **Step 1** 508s Generating indices anyway (forced). 508s Building database for 'test/M.faa' (40 sequences) 508s Generating indices anyway (forced). 508s Building database for 'test/L.faa' (40 sequences) 508s Generating indices anyway (forced). 508s Building database for 'test/C2.faa' (2 sequences) 508s Generating indices anyway (forced). 508s Building database for 'test/C_clean.faa' (109 sequences) 508s Generating indices anyway (forced). 508s Building database for 'test/E.faa' (72 sequences) 508s 508s **Step 2** using blastp+ with : synteny 515s 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) 515s [OUTPUT] -> written to test_synteny.blast-graph 515s 515s **Step 3** 515s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 515s Reading test_synteny.blast-graph 515s 5 species 515s 112 paired proteins 515s 147 bidirectional edges 516s 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 516s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 516s You can extract the fasta files of each orthology group with 516s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/M.faa' 'test/L.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/E.faa' 516s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 516s Adding singles... 516s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 516s # test_synteny.proteinortho.tsv statistics: 516s # number of groups that contains at least p% species: 516s # p species groups genes in groups 516s 0% 0 182 (100%) 262 (100%) 516s 20% 1 182 (100%) 262 (100%) 516s 40% 2 32 (17.58%) 112 (42.74%) 516s 60% 3 17 (9.34%) 74 (28.24%) 516s 80% 4 11 (6.04%) 51 (19.46%) 516s 100% 5 1 (0.54%) 5 (1.9%) 516s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 516s # groups that contains only one species: 516s single 5 150 (82.41%) 150 (57.25%) 516s # number of groups for each input species: 516s L.faa 32 100% 516s M.faa 32 100% 516s E.faa 15 46.87% 516s C_clean.faa 13 40.62% 516s C2.faa 1 3.12% 516s 516s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 516s 516s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 516s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 516s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 516s 516s 516s Clustering by gene-order (POFF mode) 516s Reading test_synteny.ffadj-graph 516s 5 species 516s 105 paired proteins 516s 106 bidirectional edges 517s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 518s 5 species 518s 105 paired proteins 518s 106 bidirectional edges 518s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 518s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 518s You can extract the fasta files of each orthology group with 518s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/M.faa' 'test/L.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/E.faa' 518s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 518s Adding singles... 518s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 519s # test_synteny.poff.tsv statistics: 519s # number of groups that contains at least p% species: 519s # p species groups genes in groups 519s 0% 0 195 (100%) 262 (100%) 519s 20% 1 195 (100%) 262 (100%) 519s 40% 2 37 (18.97%) 104 (39.69%) 519s 60% 3 17 (8.71%) 64 (24.42%) 519s 80% 4 10 (5.12%) 43 (16.41%) 519s 100% 5 1 (0.51%) 5 (1.9%) 519s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 519s # groups that contains only one species: 519s single 5 158 (81.02%) 158 (60.3%) 519s # number of groups for each input species: 519s L.faa 37 100% 519s M.faa 37 100% 519s E.faa 14 37.83% 519s C_clean.faa 13 35.13% 519s C2.faa 1 2.7% 519s 519s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 519s 519s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 519s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 519s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 519s 519s All finished. 519s ***************************************************************** 519s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 519s ***************************************************************** 519s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 519s Checking input files. 519s Checking test/C_clean.faa... ok 519s Checking test/C2.faa... ok 519s Checking test/E.faa... ok 519s Checking test/L.faa... ok 519s Checking test/M.faa... ok 519s 519s **Step 1** 519s Generating indices anyway (forced). 519s Building database for 'test/C2.faa' (2 sequences) 519s Generating indices anyway (forced). 519s Building database for 'test/E.faa' (72 sequences) 519s Generating indices anyway (forced). 519s Building database for 'test/C_clean.faa' (109 sequences) 519s Generating indices anyway (forced). 519s Building database for 'test/M.faa' (40 sequences) 519s Generating indices anyway (forced). 519s Building database for 'test/L.faa' (40 sequences) 519s 519s **Step 2** using diamond 527s 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) 527s [OUTPUT] -> written to test_diamond.blast-graph 527s 527s **Step 3** 527s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 527s Reading test_diamond.blast-graph 527s 5 species 527s 112 paired proteins 527s 145 bidirectional edges 529s 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 529s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 529s You can extract the fasta files of each orthology group with 529s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/C2.faa' 'test/E.faa' 'test/C_clean.faa' 'test/M.faa' 'test/L.faa' 529s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 529s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 529s # test_diamond.proteinortho.tsv statistics: 529s # number of groups that contains at least p% species: 529s # p species groups genes in groups 529s 0% 0 32 (100%) 111 (100%) 529s 20% 1 32 (100%) 111 (100%) 529s 40% 2 32 (100%) 111 (100%) 529s 60% 3 17 (53.12%) 75 (67.56%) 529s 80% 4 11 (34.37%) 52 (46.84%) 529s 100% 5 1 (3.12%) 5 (4.5%) 529s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 529s # number of groups for each input species: 529s L.faa 32 100% 529s M.faa 32 100% 529s E.faa 15 46.87% 529s C_clean.faa 13 40.62% 529s C2.faa 1 3.12% 529s 529s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 529s 529s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 529s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 529s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 529s 529s All finished. 529s ***************************************************************** 529s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 529s ***************************************************************** 529s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 529s Checking input files. 529s Checking test/C_clean.faa... ok 529s Checking test/C2.faa... ok 529s Checking test/E.faa... ok 529s Checking test/L.faa... ok 529s Checking test/M.faa... ok 529s 529s **Step 1** 529s Generating indices anyway (forced). 529s Building database for 'test/C2.faa' (2 sequences) 529s Generating indices anyway (forced). 529s Building database for 'test/L.faa' (40 sequences) 529s Generating indices anyway (forced). 529s Building database for 'test/C_clean.faa' (109 sequences) 529s Generating indices anyway (forced). 529s Building database for 'test/E.faa' (72 sequences) 529s Generating indices anyway (forced). 529s Building database for 'test/M.faa' (40 sequences) 529s 529s **Step 2** using diamond 539s 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) 539s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 539s 539s **Step 3** 539s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 539s Reading test_diamondmoresensitive.blast-graph 539s 5 species 539s 113 paired proteins 539s 147 bidirectional edges 540s 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 540s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 540s You can extract the fasta files of each orthology group with 540s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/C2.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 'test/M.faa' 540s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 540s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 540s # test_diamondmoresensitive.proteinortho.tsv statistics: 540s # number of groups that contains at least p% species: 540s # p species groups genes in groups 540s 0% 0 32 (100%) 112 (100%) 540s 20% 1 32 (100%) 112 (100%) 540s 40% 2 32 (100%) 112 (100%) 540s 60% 3 17 (53.12%) 76 (67.85%) 540s 80% 4 11 (34.37%) 53 (47.32%) 540s 100% 5 1 (3.12%) 5 (4.46%) 540s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 540s # number of groups for each input species: 540s L.faa 32 100% 540s M.faa 32 100% 540s E.faa 15 46.87% 540s C_clean.faa 13 40.62% 540s C2.faa 1 3.12% 540s 540s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 540s 540s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 540s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 540s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 540s 540s All finished. 540s ***************************************************************** 540s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 540s ***************************************************************** 540s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 540s Checking input files. 540s Checking test/C_clean.faa... ok 540s Checking test/C2.faa... ok 540s Checking test/E.faa... ok 540s Checking test/L.faa... ok 540s Checking test/M.faa... ok 540s 540s **Step 1** 540s Generating indices anyway (forced). 540s Building database for 'test/C2.faa' (2 sequences) 540s Generating indices anyway (forced). 540s Building database for 'test/M.faa' (40 sequences) 540s Generating indices anyway (forced). 540s Building database for 'test/C_clean.faa' (109 sequences) 540s Generating indices anyway (forced). 540s Building database for 'test/E.faa' (72 sequences) 540s Generating indices anyway (forced). 540s Building database for 'test/L.faa' (40 sequences) 540s 540s **Step 2** using blastp+ 547s 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) 547s [OUTPUT] -> written to test_blastall.blast-graph 547s 547s **Step 3** 547s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 547s Reading test_blastall.blast-graph 547s 5 species 547s 112 paired proteins 547s 147 bidirectional edges 548s 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 548s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 548s You can extract the fasta files of each orthology group with 548s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C2.faa' 'test/M.faa' 'test/C_clean.faa' 'test/E.faa' 'test/L.faa' 548s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 548s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 548s # test_blastall.proteinortho.tsv statistics: 548s # number of groups that contains at least p% species: 548s # p species groups genes in groups 548s 0% 0 32 (100%) 112 (100%) 548s 20% 1 32 (100%) 112 (100%) 548s 40% 2 32 (100%) 112 (100%) 548s 60% 3 17 (53.12%) 74 (66.07%) 548s 80% 4 11 (34.37%) 51 (45.53%) 548s 100% 5 1 (3.12%) 5 (4.46%) 548s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 548s # number of groups for each input species: 548s L.faa 32 100% 548s M.faa 32 100% 548s E.faa 15 46.87% 548s C_clean.faa 13 40.62% 548s C2.faa 1 3.12% 548s 548s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 548s 548s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 548s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 548s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 548s 548s All finished. 548s - test max_of_diag() : OK 548s - test generate_random_vector() : OK 548s - test get_new_x() : OK 548s - test makeOrthogonal() : OK 548s - test normalize() : OK 548s - test getY() : OK 548s - test lapack() : OK 548s - test power() : OK 548s - test smirnov-grubb() : OK 548s All test passed. 548s Reading test_blastp.blast-graph 548s 5 species 548s 112 paired proteins 548s 149 bidirectional edges 548s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 549s 5 5 1 C_10 C_10;test E_10 L_10 M_10 549s 4 4 1 * C_11 E_11 L_11 M_11 549s 4 6 0.333 * C_12,C_21 E_313,E_315 L_313 M_313 549s 4 4 1 * C_14 E_14 L_14 M_14 549s 4 4 1 * C_15 E_15 L_15 M_15 549s 4 4 1 * C_16 E_16 L_16 M_16 549s 4 4 1 * C_17 E_17 L_17 M_17 549s 4 4 1 * C_64 E_18 L_18 M_18 549s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 549s 3 3 0.33 * * E_367 L_319 M_319 549s 3 3 0.33 * * E_432 L_328 M_328 549s 2 2 1 * * * L_619 M_619 549s 2 2 1 * * * L_617 M_617 549s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 549s 2 4 0.5 * * * L_645,L_647 M_644,M_646 549s 2 2 1 * * * L_333 M_333 549s 3 3 1 * C_20 * L_20 M_20 549s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 549s 2 2 1 * * * L_3 M_3 549s 2 2 1 * * * L_4 M_4 549s 2 2 1 * * * L_5 M_5 549s 2 2 1 * * * L_6 M_6 549s 2 2 1 * * * L_8 M_8 549s 2 2 1 * * * L_9 M_9 549s 2 2 1 * * * L_623 M_623 549s 4 4 1 * C_13 E_13 L_621 M_621 549s 2 4 0.146 * * * L_637,L_639 M_636,M_638 549s 3 3 0.33 * * E_437 L_317 M_317 549s 2 3 0.33 * * * L_631,L_633 M_632 549s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 549s 2 2 1 * * * L_331 M_331 549s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 549s Reading test_blastp.blast-graph 549s 5 species 549s 112 paired proteins 549s 149 bidirectional edges 549s 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# Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 550s *) 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 0.33 * * E_367 L_319 M_319 550s 3 3 0.33 * * E_432 L_328 M_328 550s 2 2 1 * * * L_619 M_619 550s 2 2 1 * * * L_617 M_617 550s 2 2 1 * * * L_333 M_333 550s 3 3 1 * C_20 * L_20 M_20 550s 2 2 1 * * * L_3 M_3 550s 2 2 1 * * * L_4 M_4 550s 2 2 1 * * * L_5 M_5 550s 2 2 1 * * * L_6 M_6 550s 2 2 1 * * * L_8 M_8 550s 2 2 1 * * * L_9 M_9 550s 5 5 0.694 C_10 C_10;test E_10 L_10 M_10 550s 4 4 0.727 * C_11 E_11 L_11 M_11 550s 4 6 0.297 * C_12,C_21 E_313,E_315 L_313 M_313 550s 2 2 1 * * * L_623 M_623 550s 4 4 0.743 * C_14 E_14 L_14 M_14 550s 4 4 0.818 * C_15 E_15 L_15 M_15 550s 4 4 0.815 * C_16 E_16 L_16 M_16 550s 4 4 0.824 * C_17 E_17 L_17 M_17 550s 4 4 0.777 * C_64 E_18 L_18 M_18 550s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 550s 3 3 0.33 * * E_437 L_317 M_317 550s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 550s 2 4 0.478 * * * L_645,L_647 M_644,M_646 550s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 550s 4 4 0.702 * C_13 E_13 L_621 M_621 550s 2 4 0.145 * * * L_637,L_639 M_636,M_638 550s 2 2 1 * * * L_331 M_331 550s 2 3 0.33 * * * L_631,L_633 M_632 550s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 550s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 550s Test okay 550s autopkgtest [20:01:00]: test run-unit-test: -----------------------] 551s run-unit-test PASS 551s autopkgtest [20:01:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 551s autopkgtest [20:01:01]: @@@@@@@@@@@@@@@@@@@@ summary 551s run-unit-test PASS 569s Creating nova instance adt-noble-ppc64el-proteinortho-20240324-195150-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240324.img (UUID 456c38b1-f024-4aa9-9fc9-7cea731b220e)...