0s autopkgtest [19:56:32]: starting date and time: 2024-03-24 19:56:32+0000 0s autopkgtest [19:56:32]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:56:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sfycn_s9/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-2@bos01-s390x-20.secgroup --name adt-noble-s390x-proteinortho-20240324-195631-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 91s autopkgtest [19:58:03]: testbed dpkg architecture: s390x 91s autopkgtest [19:58:03]: testbed apt version: 2.7.12 91s autopkgtest [19:58:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 92s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 92s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 92s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 92s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 92s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 92s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 92s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 92s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 92s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4195 kB] 93s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 93s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.2 kB] 93s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 95s Fetched 9603 kB in 3s (3518 kB/s) 95s Reading package lists... 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 99s The following packages will be upgraded: 99s libproc2-0 procps 100s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 784 kB of archives. 100s After this operation, 4096 B of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu2 [60.1 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x procps s390x 2:4.0.4-4ubuntu2 [724 kB] 101s Fetched 784 kB in 1s (867 kB/s) 101s (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 ... 51777 files and directories currently installed.) 101s Preparing to unpack .../libproc2-0_2%3a4.0.4-4ubuntu2_s390x.deb ... 101s Unpacking libproc2-0:s390x (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 101s Preparing to unpack .../procps_2%3a4.0.4-4ubuntu2_s390x.deb ... 101s Unpacking procps (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 101s Setting up libproc2-0:s390x (2:4.0.4-4ubuntu2) ... 101s Setting up procps (2:4.0.4-4ubuntu2) ... 101s Processing triggers for man-db (2.12.0-3) ... 102s Processing triggers for libc-bin (2.39-0ubuntu6) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Unknown architecture, assuming PC-style ttyS0 104s sh: Attempting to set up Debian/Ubuntu apt sources automatically 104s sh: Distribution appears to be Ubuntu 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s eatmydata is already the newest version (131-1). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s dbus is already the newest version (1.14.10-4ubuntu1). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s rng-tools-debian is already the newest version (2.4). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s The following packages will be REMOVED: 107s cloud-init* python3-configobj* python3-debconf* 107s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 107s After this operation, 3256 kB disk space will be freed. 107s (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 ... 51778 files and directories currently installed.) 107s Removing cloud-init (24.1.2-0ubuntu1) ... 108s Removing python3-configobj (5.0.8-3) ... 108s Removing python3-debconf (1.5.86) ... 108s Processing triggers for man-db (2.12.0-3) ... 108s (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 ... 51389 files and directories currently installed.) 108s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 109s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 109s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 109s invoke-rc.d: policy-rc.d denied execution of try-restart. 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s linux-generic is already the newest version (6.8.0-11.11+1). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 110s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 110s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 113s Reading package lists... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [19:58:27]: rebooting testbed after setup commands that affected boot 252s autopkgtest [20:00:44]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 255s autopkgtest [20:00:47]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 257s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 257s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 257s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 257s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 257s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 257s gpgv: issuer "tille@debian.org" 257s gpgv: Can't check signature: No public key 257s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 257s autopkgtest [20:00:49]: testing package proteinortho version 6.3.1+dfsg-1 258s autopkgtest [20:00:50]: build not needed 258s autopkgtest [20:00:50]: test run-unit-test: preparing testbed 260s Reading package lists... 261s Building dependency tree... 261s Reading state information... 261s Starting pkgProblemResolver with broken count: 0 261s Starting 2 pkgProblemResolver with broken count: 0 261s Done 261s The following additional packages will be installed: 261s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 261s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 261s Recommended packages: 261s med-config 261s The following NEW packages will be installed: 261s autopkgtest-satdep diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 261s libmbedcrypto7 libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 261s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 261s Need to get 23.9 MB/23.9 MB of archives. 261s After this operation, 91.0 MB of additional disk space will be used. 261s Get:1 /tmp/autopkgtest.fs1Lc1/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 261s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x diamond-aligner s390x 2.1.9-1 [2266 kB] 263s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 263s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 263s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 263s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 264s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedcrypto7 s390x 2.28.7-1ubuntu1 [216 kB] 264s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedx509-1 s390x 2.28.7-1ubuntu1 [46.0 kB] 264s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedtls14 s390x 2.28.7-1ubuntu1 [84.5 kB] 264s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 264s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-blast+ s390x 2.12.0+ds-4 [12.6 MB] 265s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x proteinortho s390x 6.3.1+dfsg-1 [333 kB] 266s Fetched 23.9 MB in 4s (5658 kB/s) 266s Selecting previously unselected package diamond-aligner. 266s (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 ... 51332 files and directories currently installed.) 266s Preparing to unpack .../00-diamond-aligner_2.1.9-1_s390x.deb ... 266s Unpacking diamond-aligner (2.1.9-1) ... 266s Selecting previously unselected package libblas3:s390x. 266s Preparing to unpack .../01-libblas3_3.12.0-3_s390x.deb ... 266s Unpacking libblas3:s390x (3.12.0-3) ... 266s Selecting previously unselected package libgfortran5:s390x. 266s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 266s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 266s Selecting previously unselected package libgomp1:s390x. 266s Preparing to unpack .../03-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 266s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 266s Selecting previously unselected package liblapack3:s390x. 266s Preparing to unpack .../04-liblapack3_3.12.0-3_s390x.deb ... 266s Unpacking liblapack3:s390x (3.12.0-3) ... 266s Selecting previously unselected package libmbedcrypto7:s390x. 266s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_s390x.deb ... 266s Unpacking libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 266s Selecting previously unselected package libmbedx509-1:s390x. 266s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_s390x.deb ... 266s Unpacking libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 266s Selecting previously unselected package libmbedtls14:s390x. 266s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_s390x.deb ... 266s Unpacking libmbedtls14:s390x (2.28.7-1ubuntu1) ... 266s Selecting previously unselected package ncbi-data. 266s Preparing to unpack .../08-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 266s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 266s Selecting previously unselected package ncbi-blast+. 266s Preparing to unpack .../09-ncbi-blast+_2.12.0+ds-4_s390x.deb ... 266s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 267s Selecting previously unselected package proteinortho. 267s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_s390x.deb ... 267s Unpacking proteinortho (6.3.1+dfsg-1) ... 267s Selecting previously unselected package autopkgtest-satdep. 267s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 267s Unpacking autopkgtest-satdep (0) ... 267s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 267s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 267s Setting up diamond-aligner (2.1.9-1) ... 267s Setting up libblas3:s390x (3.12.0-3) ... 267s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 267s Setting up libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 267s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 267s Setting up liblapack3:s390x (3.12.0-3) ... 267s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 267s Setting up libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 267s Setting up libmbedtls14:s390x (2.28.7-1ubuntu1) ... 267s Setting up ncbi-blast+ (2.12.0+ds-4) ... 267s Setting up proteinortho (6.3.1+dfsg-1) ... 267s Setting up autopkgtest-satdep (0) ... 267s Processing triggers for man-db (2.12.0-3) ... 267s Processing triggers for libc-bin (2.39-0ubuntu6) ... 270s (Reading database ... 51666 files and directories currently installed.) 270s Removing autopkgtest-satdep (0) ... 271s autopkgtest [20:01:03]: test run-unit-test: [----------------------- 271s ***************************************************************** 271s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 271s ***************************************************************** 271s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 271s Checking input files. 271s Checking input files. 271s Checking test/C_clean.faa... ok 271s Checking test/C2.faa... ok 271s Checking test/E.faa... ok 271s Checking test/L.faa... ok 271s Checking test/M.faa... ok 271s Checking test/C.faa... 271s  [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 !!! 271s The line is: 271s C_10,test 271s ok 271s Checking test/L.faa... ok 271s Checking test/E.faa... ok 271s Checking test/M.faa... ok 271s Checking test/C2.faa... ok 271s 271s **Step 1** 271s Generating indices anyway (forced). 271s Building database for 'test/E.faa' (144 sequences) 271s Generating indices anyway (forced). 271s Building database for 'test/M.faa' (80 sequences) 271s Generating indices anyway (forced). 271s Building database for 'test/C2.faa' (4 sequences) 271s Generating indices anyway (forced). 271s Building database for 'test/C_clean.faa' (109 sequences) 271s Generating indices anyway (forced). 271s Building database for 'test/L.faa' (80 sequences) 271s 271s **Step 2** using blastp+ 278s 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) 278s [OUTPUT] -> written to test_blastp.blast-graph 278s 278s **Step 3** 278s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 278s Reading test_blastp.blast-graph 278s 5 species 278s 112 paired proteins 278s 149 bidirectional edges 279s 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 279s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 279s You can extract the fasta files of each orthology group with 279s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/E.faa' 'test/M.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/L.faa' 279s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 279s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 279s # test_blastp.proteinortho.tsv statistics: 279s # number of groups that contains at least p% species: 279s # p species groups genes in groups 279s 0% 0 32 (100%) 112 (100%) 279s 20% 1 32 (100%) 112 (100%) 279s 40% 2 32 (100%) 112 (100%) 279s 60% 3 17 (53.12%) 74 (66.07%) 279s 80% 4 11 (34.37%) 51 (45.53%) 279s 100% 5 1 (3.12%) 5 (4.46%) 279s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 279s # number of groups for each input species: 279s L.faa 32 100% 279s M.faa 32 100% 279s E.faa 15 46.87% 279s C_clean.faa 13 40.62% 279s C2.faa 1 3.12% 279s 279s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 279s 279s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 279s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 279s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 279s 279s All finished. 279s ***************************************************************** 279s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 279s ***************************************************************** 279s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 279s Checking input files. 279s Checking test/C_clean.faa... ok 279s Checking test/C2.faa... ok 279s Checking test/E.faa... ok 279s Checking test/L.faa... ok 279s Checking test/M.faa... ok 279s 279s **Step 1** 279s Generating indices anyway (forced). 279s Building database for 'test/L.faa' (40 sequences) 279s Generating indices anyway (forced). 279s Building database for 'test/E.faa' (72 sequences) 279s Generating indices anyway (forced). 279s Building database for 'test/C2.faa' (2 sequences) 279s Generating indices anyway (forced). 279s Building database for 'test/C_clean.faa' (109 sequences) 279s Generating indices anyway (forced). 279s Building database for 'test/M.faa' (40 sequences) 279s 279s **Step 2** using blastp+ with : synteny 286s 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) 286s [OUTPUT] -> written to test_synteny.blast-graph 286s 286s **Step 3** 286s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 286s Reading test_synteny.blast-graph 286s 5 species 286s 112 paired proteins 286s 149 bidirectional edges 287s 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 287s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 287s You can extract the fasta files of each orthology group with 287s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/L.faa' 'test/E.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 287s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 287s Adding singles... 287s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 287s # test_synteny.proteinortho.tsv statistics: 287s # number of groups that contains at least p% species: 287s # p species groups genes in groups 287s 0% 0 182 (100%) 262 (100%) 287s 20% 1 182 (100%) 262 (100%) 287s 40% 2 32 (17.58%) 112 (42.74%) 287s 60% 3 17 (9.34%) 74 (28.24%) 287s 80% 4 11 (6.04%) 51 (19.46%) 287s 100% 5 1 (0.54%) 5 (1.9%) 287s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 287s # groups that contains only one species: 287s single 5 150 (82.41%) 150 (57.25%) 287s # number of groups for each input species: 287s L.faa 32 100% 287s M.faa 32 100% 287s E.faa 15 46.87% 287s C_clean.faa 13 40.62% 287s C2.faa 1 3.12% 287s 287s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 287s 287s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 287s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 287s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 287s 287s 287s Clustering by gene-order (POFF mode) 287s Reading test_synteny.ffadj-graph 287s 5 species 287s 106 paired proteins 287s 106 bidirectional edges 288s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (35@lapack* + 0@power) connected components Clustering: working on (34@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (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 (28@lapack* + 0@power) connected components Clustering: working on (27@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 (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 (2@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 288s 5 species 288s 106 paired proteins 288s 106 bidirectional edges 289s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (35@lapack* + 0@power) connected components Clustering: working on (34@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (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 (28@lapack* + 0@power) connected components Clustering: working on (27@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 (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 (2@lapack* + 0@power) connected components 289s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 289s You can extract the fasta files of each orthology group with 289s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/L.faa' 'test/E.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 289s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 289s Adding singles... 289s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 289s # test_synteny.poff.tsv statistics: 289s # number of groups that contains at least p% species: 289s # p species groups genes in groups 289s 0% 0 195 (100%) 262 (100%) 289s 20% 1 195 (100%) 262 (100%) 289s 40% 2 38 (19.48%) 105 (40.07%) 289s 60% 3 17 (8.71%) 63 (24.04%) 289s 80% 4 10 (5.12%) 42 (16.03%) 289s 100% 5 1 (0.51%) 5 (1.9%) 289s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 289s # groups that contains only one species: 289s single 5 157 (80.51%) 157 (59.92%) 289s # number of groups for each input species: 289s L.faa 37 97.36% 289s M.faa 37 97.36% 289s E.faa 15 39.47% 289s C_clean.faa 14 36.84% 289s C2.faa 1 2.63% 289s 289s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 289s 289s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 289s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 289s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 289s 289s All finished. 289s ***************************************************************** 289s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 289s ***************************************************************** 289s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 289s Checking input files. 289s Checking test/C_clean.faa... ok 289s Checking test/C2.faa... ok 289s Checking test/E.faa... ok 289s Checking test/L.faa... ok 289s Checking test/M.faa... ok 289s 289s **Step 1** 289s Generating indices anyway (forced). 289s Building database for 'test/L.faa' (40 sequences) 289s Generating indices anyway (forced). 289s Building database for 'test/C2.faa' (2 sequences) 289s Generating indices anyway (forced). 289s Building database for 'test/E.faa' (72 sequences) 289s Generating indices anyway (forced). 289s Building database for 'test/C_clean.faa' (109 sequences) 289s Generating indices anyway (forced). 289s Building database for 'test/M.faa' (40 sequences) 289s 289s **Step 2** using diamond 299s 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) 299s [OUTPUT] -> written to test_diamond.blast-graph 299s 299s **Step 3** 299s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 299s Reading test_diamond.blast-graph 299s 5 species 299s 112 paired proteins 299s 145 bidirectional edges 300s 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 300s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 300s You can extract the fasta files of each orthology group with 300s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/L.faa' 'test/C2.faa' 'test/E.faa' 'test/C_clean.faa' 'test/M.faa' 300s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 300s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 300s # test_diamond.proteinortho.tsv statistics: 300s # number of groups that contains at least p% species: 300s # p species groups genes in groups 300s 0% 0 32 (100%) 111 (100%) 300s 20% 1 32 (100%) 111 (100%) 300s 40% 2 32 (100%) 111 (100%) 300s 60% 3 17 (53.12%) 75 (67.56%) 300s 80% 4 11 (34.37%) 52 (46.84%) 300s 100% 5 1 (3.12%) 5 (4.5%) 300s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 300s # number of groups for each input species: 300s L.faa 32 100% 300s M.faa 32 100% 300s E.faa 15 46.87% 300s C_clean.faa 13 40.62% 300s C2.faa 1 3.12% 300s 300s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 300s 300s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 300s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 300s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 300s 300s All finished. 300s ***************************************************************** 300s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 300s ***************************************************************** 300s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 300s Checking input files. 300s Checking test/C_clean.faa... ok 300s Checking test/C2.faa... ok 300s Checking test/E.faa... ok 301s Checking test/L.faa... ok 301s Checking test/M.faa... ok 301s 301s **Step 1** 301s Generating indices anyway (forced). 301s Building database for 'test/L.faa' (40 sequences) 301s Generating indices anyway (forced). 301s Building database for 'test/C2.faa' (2 sequences) 301s Generating indices anyway (forced). 301s Building database for 'test/C_clean.faa' (109 sequences) 301s Generating indices anyway (forced). 301s Building database for 'test/M.faa' (40 sequences) 301s Generating indices anyway (forced). 301s Building database for 'test/E.faa' (72 sequences) 301s 301s **Step 2** using diamond 313s 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) 313s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 313s 313s **Step 3** 313s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 313s Reading test_diamondmoresensitive.blast-graph 313s 5 species 313s 113 paired proteins 313s 147 bidirectional edges 314s 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 314s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 314s You can extract the fasta files of each orthology group with 314s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/L.faa' 'test/C2.faa' 'test/C_clean.faa' 'test/M.faa' 'test/E.faa' 314s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 314s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 314s # test_diamondmoresensitive.proteinortho.tsv statistics: 314s # number of groups that contains at least p% species: 314s # p species groups genes in groups 314s 0% 0 32 (100%) 112 (100%) 314s 20% 1 32 (100%) 112 (100%) 314s 40% 2 32 (100%) 112 (100%) 314s 60% 3 17 (53.12%) 76 (67.85%) 314s 80% 4 11 (34.37%) 53 (47.32%) 314s 100% 5 1 (3.12%) 5 (4.46%) 314s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 314s # number of groups for each input species: 314s L.faa 32 100% 314s M.faa 32 100% 314s E.faa 15 46.87% 314s C_clean.faa 13 40.62% 314s C2.faa 1 3.12% 314s 314s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 314s 314s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 314s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 314s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 314s 314s All finished. 314s ***************************************************************** 314s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 314s ***************************************************************** 314s Detected 1 CPU threads (1 threads per processes each with 1 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 314s Checking input files. 314s Checking test/C_clean.faa... ok 314s Checking test/C2.faa... ok 314s Checking test/E.faa... ok 314s Checking test/L.faa... ok 314s Checking test/M.faa... ok 314s 314s **Step 1** 314s Generating indices anyway (forced). 314s Building database for 'test/C_clean.faa' (109 sequences) 314s Generating indices anyway (forced). 314s Building database for 'test/E.faa' (72 sequences) 314s Generating indices anyway (forced). 314s Building database for 'test/M.faa' (40 sequences) 314s Generating indices anyway (forced). 314s Building database for 'test/L.faa' (40 sequences) 315s Generating indices anyway (forced). 315s Building database for 'test/C2.faa' (2 sequences) 315s 315s **Step 2** using blastp+ 320s 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) 320s [OUTPUT] -> written to test_blastall.blast-graph 320s 320s **Step 3** 320s Clustering by similarity (Proteinortho mode) using 1 cpu core(s). Please wait... 320s Reading test_blastall.blast-graph 320s 5 species 320s 112 paired proteins 320s 147 bidirectional edges 321s 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 321s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 321s You can extract the fasta files of each orthology group with 321s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/C_clean.faa' 'test/E.faa' 'test/M.faa' 'test/L.faa' 'test/C2.faa' 321s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 321s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 321s # test_blastall.proteinortho.tsv statistics: 321s # number of groups that contains at least p% species: 321s # p species groups genes in groups 321s 0% 0 32 (100%) 112 (100%) 321s 20% 1 32 (100%) 112 (100%) 321s 40% 2 32 (100%) 112 (100%) 321s 60% 3 17 (53.12%) 74 (66.07%) 321s 80% 4 11 (34.37%) 51 (45.53%) 321s 100% 5 1 (3.12%) 5 (4.46%) 321s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 321s # number of groups for each input species: 321s L.faa 32 100% 321s M.faa 32 100% 321s E.faa 15 46.87% 321s C_clean.faa 13 40.62% 321s C2.faa 1 3.12% 321s 321s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 321s 321s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 321s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 321s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 321s 321s All finished. 321s - test max_of_diag() : OK 321s - test generate_random_vector() : OK 321s - test get_new_x() : OK 321s - test makeOrthogonal() : OK 321s - test normalize() : OK 321s - test getY() : OK 321s - test lapack() : OK 321s - test power() : OK 321s - test smirnov-grubb() : OK 321s All test passed. 321s Reading test_blastp.blast-graph 321s 5 species 321s 112 paired proteins 321s 149 bidirectional edges 321s 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 321s 5 5 1 C_10 C_10;test E_10 L_10 M_10 321s 4 4 1 * C_11 E_11 L_11 M_11 321s 4 6 0.333 * C_12,C_21 E_313,E_315 L_313 M_313 321s 4 4 1 * C_14 E_14 L_14 M_14 321s 4 4 1 * C_15 E_15 L_15 M_15 321s 4 4 1 * C_16 E_16 L_16 M_16 321s 4 4 1 * C_17 E_17 L_17 M_17 321s 4 4 1 * C_64 E_18 L_18 M_18 321s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 321s 3 3 0.33 * * E_367 L_319 M_319 321s 3 3 0.33 * * E_432 L_328 M_328 321s 3 3 1 * C_20 * L_20 M_20 321s 3 6 0.333 * C_167,C_2,C_164,C_166 * L_2 M_2 321s 2 2 1 * * * L_619 M_619 321s 2 2 1 * * * L_617 M_617 321s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 321s 2 4 0.5 * * * L_645,L_647 M_644,M_646 321s 2 2 1 * * * L_333 M_333 321s 2 2 1 * * * L_3 M_3 321s 2 2 1 * * * L_4 M_4 321s 2 2 1 * * * L_5 M_5 321s 2 2 1 * * * L_6 M_6 321s 2 2 1 * * * L_8 M_8 321s 2 2 1 * * * L_9 M_9 321s 2 2 1 * * * L_623 M_623 321s 4 4 1 * C_13 E_13 L_621 M_621 321s 2 4 0.146 * * * L_637,L_639 M_636,M_638 321s 3 3 0.33 * * E_437 L_317 M_317 321s 2 3 0.33 * * * L_631,L_633 M_632 321s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 321s 2 2 1 * * * L_331 M_331 321s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 321s Reading # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 321s test_blastp.blast-graph 321s 5 species 321s 112 paired proteins 321s 149 bidirectional edges 322s 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 0.33 * * E_367 L_319 M_319 322s 3 3 0.33 * * E_432 L_328 M_328 322s 3 3 1 * C_20 * L_20 M_20 322s 2 2 1 * * * L_619 M_619 322s 2 2 1 * * * L_617 M_617 322s 2 2 1 * * * L_333 M_333 322s 2 2 1 * * * L_3 M_3 322s 2 2 1 * * * L_4 M_4 322s 2 2 1 * * * L_5 M_5 322s 2 2 1 * * * L_6 M_6 322s 2 2 1 * * * L_8 M_8 322s 2 2 1 * * * L_9 M_9 322s 5 5 0.694 C_10 C_10;test E_10 L_10 M_10 322s 4 4 0.727 * C_11 E_11 L_11 M_11 322s 4 6 0.297 * C_12,C_21 E_313,E_315 L_313 M_313 322s 2 2 1 * * * L_623 M_623 322s 4 4 0.743 * C_14 E_14 L_14 M_14 322s 4 4 0.818 * C_15 E_15 L_15 M_15 322s 4 4 0.815 * C_16 E_16 L_16 M_16 322s 4 4 0.824 * C_17 E_17 L_17 M_17 322s 4 4 0.777 * C_64 E_18 L_18 M_18 322s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 322s 3 3 0.33 * * E_437 L_317 M_317 322s 3 6 0.314 * C_167,C_2,C_164,C_166 * L_2 M_2 322s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 322s 2 4 0.478 * * * L_645,L_647 M_644,M_646 322s 4 4 0.702 * C_13 E_13 L_621 M_621 322s 2 4 0.145 * * * L_637,L_639 M_636,M_638 322s 2 2 1 * * * L_331 M_331 322s 2 3 0.33 * * * L_631,L_633 M_632 322s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 322s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 322s Test okay 322s autopkgtest [20:01:54]: test run-unit-test: -----------------------] 323s autopkgtest [20:01:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 323s run-unit-test PASS 323s autopkgtest [20:01:55]: @@@@@@@@@@@@@@@@@@@@ summary 323s run-unit-test PASS 337s Creating nova instance adt-noble-s390x-proteinortho-20240324-195631-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240324.img (UUID e72c9cf8-77d4-4e3d-be82-5e850d5031de)...