0s autopkgtest [03:34:27]: starting date and time: 2024-03-26 03:34:27+0000 0s autopkgtest [03:34:27]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [03:34:27]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yc2xgky0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade physamp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=libbpp-seq/2.4.1-12 libbpp-core/2.4.1-11.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-16.secgroup --name adt-noble-s390x-physamp-20240326-033426-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-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/ 85s autopkgtest [03:35:52]: testbed dpkg architecture: s390x 85s autopkgtest [03:35:52]: testbed apt version: 2.7.12 85s autopkgtest [03:35:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 86s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 86s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 86s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 86s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4027 kB] 86s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 86s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 86s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 86s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 86s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 86s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4131 kB] 87s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 87s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 87s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 89s Fetched 9585 kB in 2s (4072 kB/s) 89s Reading package lists... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Calculating upgrade... 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 91s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s 0 upgraded, 0 newly installed, 0 to remove and 242 not upgraded. 92s Unknown architecture, assuming PC-style ttyS0 92s sh: Attempting to set up Debian/Ubuntu apt sources automatically 92s sh: Distribution appears to be Ubuntu 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s eatmydata is already the newest version (131-1). 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s dbus is already the newest version (1.14.10-4ubuntu1). 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s rng-tools-debian is already the newest version (2.4). 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s The following packages will be REMOVED: 95s cloud-init* python3-configobj* python3-debconf* 95s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 95s After this operation, 3256 kB disk space will be freed. 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 95s Removing cloud-init (24.1.2-0ubuntu1) ... 96s Removing python3-configobj (5.0.8-3) ... 96s Removing python3-debconf (1.5.86) ... 96s Processing triggers for man-db (2.12.0-3) ... 96s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51781 files and directories currently installed.) 96s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 97s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 97s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 97s invoke-rc.d: policy-rc.d denied execution of try-restart. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s linux-generic is already the newest version (6.8.0-11.11+1). 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 98s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 98s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 100s Reading package lists... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s autopkgtest [03:36:08]: rebooting testbed after setup commands that affected boot 114s autopkgtest [03:36:21]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 117s autopkgtest [03:36:24]: @@@@@@@@@@@@@@@@@@@@ apt-source physamp 119s Get:1 http://ftpmaster.internal/ubuntu noble/universe physamp 1.1.0-4 (dsc) [2026 B] 119s Get:2 http://ftpmaster.internal/ubuntu noble/universe physamp 1.1.0-4 (tar) [242 kB] 119s Get:3 http://ftpmaster.internal/ubuntu noble/universe physamp 1.1.0-4 (diff) [3884 B] 119s gpgv: Signature made Thu Nov 24 18:24:42 2022 UTC 119s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 119s gpgv: issuer "tille@debian.org" 119s gpgv: Can't check signature: No public key 119s dpkg-source: warning: cannot verify inline signature for ./physamp_1.1.0-4.dsc: no acceptable signature found 119s autopkgtest [03:36:26]: testing package physamp version 1.1.0-4 119s autopkgtest [03:36:26]: build not needed 120s autopkgtest [03:36:27]: test run-unit-test: preparing testbed 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 121s The following additional packages will be installed: 121s libbpp-core4 libbpp-phyl12 libbpp-seq12 physamp 121s The following NEW packages will be installed: 121s autopkgtest-satdep libbpp-core4 libbpp-phyl12 libbpp-seq12 physamp 121s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 3160 kB/3161 kB of archives. 121s After this operation, 16.3 MB of additional disk space will be used. 121s Get:1 /tmp/autopkgtest.prxFwR/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 122s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x libbpp-core4 s390x 2.4.1-11 [548 kB] 122s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libbpp-seq12 s390x 2.4.1-10 [434 kB] 122s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libbpp-phyl12 s390x 2.4.1-9ubuntu1 [2005 kB] 122s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x physamp s390x 1.1.0-4 [173 kB] 122s Fetched 3160 kB in 1s (4022 kB/s) 122s Selecting previously unselected package libbpp-core4:s390x. 123s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51726 files and directories currently installed.) 123s Preparing to unpack .../libbpp-core4_2.4.1-11_s390x.deb ... 123s Unpacking libbpp-core4:s390x (2.4.1-11) ... 123s Selecting previously unselected package libbpp-seq12:s390x. 123s Preparing to unpack .../libbpp-seq12_2.4.1-10_s390x.deb ... 123s Unpacking libbpp-seq12:s390x (2.4.1-10) ... 123s Selecting previously unselected package libbpp-phyl12:s390x. 123s Preparing to unpack .../libbpp-phyl12_2.4.1-9ubuntu1_s390x.deb ... 123s Unpacking libbpp-phyl12:s390x (2.4.1-9ubuntu1) ... 123s Selecting previously unselected package physamp. 123s Preparing to unpack .../physamp_1.1.0-4_s390x.deb ... 123s Unpacking physamp (1.1.0-4) ... 123s Selecting previously unselected package autopkgtest-satdep. 123s Preparing to unpack .../1-autopkgtest-satdep.deb ... 123s Unpacking autopkgtest-satdep (0) ... 123s Setting up libbpp-core4:s390x (2.4.1-11) ... 123s Setting up libbpp-seq12:s390x (2.4.1-10) ... 123s Setting up libbpp-phyl12:s390x (2.4.1-9ubuntu1) ... 123s Setting up physamp (1.1.0-4) ... 123s Setting up autopkgtest-satdep (0) ... 123s Processing triggers for man-db (2.12.0-3) ... 123s Processing triggers for install-info (7.1-3) ... 123s Processing triggers for libc-bin (2.39-0ubuntu6) ... 125s (Reading database ... 51763 files and directories currently installed.) 125s Removing autopkgtest-satdep (0) ... 126s autopkgtest [03:36:33]: test run-unit-test: [----------------------- 126s ****************************************************************** 126s * Bio++ Alignment Optimizer, version 1.1.0. * 126s * Author: J. Dutheil Last Modif. 14/03/18 * 126s * E. Figuet * 126s ****************************************************************** 126s 126s Parsing options: 126s Parsing file AlnOptimFasttree.bpp for options. 126s Alphabet type .........................: Proteic 126s Sequence file .........................: PF01049_full.txt 126s Sequence format .......................: FASTA file 126s Minimum amount of data per site........: 0.7 126s Filter gap characters..................: yes 126s Filter unresolved characters...........: yes 126s Number of reference sequences..........: 0 126s Total number of sequences..............: 1652 126s Total number of sites..................: 656 126s Input tree file .......................: PF01049_fasttree.dnd 126s Input tree format .....................: Newick 126s Comparison criterion:..................: MaxSites 126s Number of sequences in alignment.......: 1652 126s Number of sites in alignment...........: 129 126s Number of chars in alignment...........: 182603 126s Mean site entropy in alignment.........: 0.394104 126s Choice Node #seq %seq #sites %sites #chars %chars 126s 1) 2030 1647 -5 131 +2 184714 2111 126s Number of sequences in alignment.......: 1647 126s Number of sites in alignment...........: 131 126s Number of chars in alignment...........: 184714 126s Mean site entropy in alignment.........: 0.394129 126s Choice Node #seq %seq #sites %sites #chars %chars 126s 1) 1930 1645 -2 132 +1 185794 1080 126s Number of sequences in alignment.......: 1645 126s Number of sites in alignment...........: 132 126s Number of chars in alignment...........: 185794 126s Mean site entropy in alignment.........: 0.394195 126s Choice Node #seq %seq #sites %sites #chars %chars 126s 1) 1882 1644 -1 133 +1 186920 1126 127s Number of sequences in alignment.......: 1644 127s Number of sites in alignment...........: 133 127s Number of chars in alignment...........: 186920 127s Mean site entropy in alignment.........: 0.394263 127s Choice Node #seq %seq #sites %sites #chars %chars 127s 1) 386 1634 -10 134 +1 187634 714 127s Number of sequences in alignment.......: 1634 127s Number of sites in alignment...........: 134 127s Number of chars in alignment...........: 187634 127s Mean site entropy in alignment.........: 0.394887 127s Choice Node #seq %seq #sites %sites #chars %chars 127s 1) 357 1627 -7 135 +1 188437 803 127s Number of sequences in alignment.......: 1627 127s Number of sites in alignment...........: 135 127s Number of chars in alignment...........: 188437 127s Mean site entropy in alignment.........: 0.394741 127s Choice Node #seq %seq #sites %sites #chars %chars 127s 1) 1736 1614 -13 136 +1 188713 276 127s Number of sequences in alignment.......: 1614 127s Number of sites in alignment...........: 136 127s Number of chars in alignment...........: 188713 127s Mean site entropy in alignment.........: 0.394145 127s Choice Node #seq %seq #sites %sites #chars %chars 127s 1) 1489 1527 -87 137 +1 181488 -7225 127s Number of sequences in alignment.......: 1527 127s Number of sites in alignment...........: 137 127s Number of chars in alignment...........: 181488 127s Mean site entropy in alignment.........: 0.378687 127s Choice Node #seq %seq #sites %sites #chars %chars 127s 1) 2247 1524 -3 138 +1 182435 947 127s Number of sequences in alignment.......: 1524 127s Number of sites in alignment...........: 138 127s Number of chars in alignment...........: 182435 127s Mean site entropy in alignment.........: 0.378731 127s Choice Node #seq %seq #sites %sites #chars %chars 127s 1) 408 1515 -9 139 +1 183008 573 127s Number of sequences in alignment.......: 1515 127s Number of sites in alignment...........: 139 127s Number of chars in alignment...........: 183008 127s Mean site entropy in alignment.........: 0.377294 127s Choice Node #seq %seq #sites %sites #chars %chars 127s 1) 1819 1488 -27 140 +1 182208 -800 128s Number of sequences in alignment.......: 1488 128s Number of sites in alignment...........: 140 128s Number of chars in alignment...........: 182208 128s Mean site entropy in alignment.........: 0.374188 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 1676 1464 -24 141 +1 180695 -1513 128s Number of sequences in alignment.......: 1464 128s Number of sites in alignment...........: 141 128s Number of chars in alignment...........: 180695 128s Mean site entropy in alignment.........: 0.371696 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 416 1457 -7 142 +1 181323 628 128s Number of sequences in alignment.......: 1457 128s Number of sites in alignment...........: 142 128s Number of chars in alignment...........: 181323 128s Mean site entropy in alignment.........: 0.36917 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 1823 1371 -86 143 +1 176415 -4908 128s Number of sequences in alignment.......: 1371 128s Number of sites in alignment...........: 143 128s Number of chars in alignment...........: 176415 128s Mean site entropy in alignment.........: 0.359961 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 783 1355 -16 144 +1 175237 -1178 128s Number of sequences in alignment.......: 1355 128s Number of sites in alignment...........: 144 128s Number of chars in alignment...........: 175237 128s Mean site entropy in alignment.........: 0.360644 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 953 1307 -48 145 +1 169472 -5765 128s Number of sequences in alignment.......: 1307 128s Number of sites in alignment...........: 145 128s Number of chars in alignment...........: 169472 128s Mean site entropy in alignment.........: 0.363152 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2269 476 -831 146 +1 66187 -103285 128s Number of sequences in alignment.......: 476 128s Number of sites in alignment...........: 146 128s Number of chars in alignment...........: 66187 128s Mean site entropy in alignment.........: 0.249565 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2488 413 -63 147 +1 57456 -8731 128s Number of sequences in alignment.......: 413 128s Number of sites in alignment...........: 147 128s Number of chars in alignment...........: 57456 128s Mean site entropy in alignment.........: 0.249617 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2372 411 -2 148 +1 57619 163 128s Number of sequences in alignment.......: 411 128s Number of sites in alignment...........: 148 128s Number of chars in alignment...........: 57619 128s Mean site entropy in alignment.........: 0.248169 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 179 391 -20 149 +1 55008 -2611 128s Number of sequences in alignment.......: 391 128s Number of sites in alignment...........: 149 128s Number of chars in alignment...........: 55008 128s Mean site entropy in alignment.........: 0.249151 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2697 54 -337 151 +2 7794 -47214 128s Number of sequences in alignment.......: 54 128s Number of sites in alignment...........: 151 128s Number of chars in alignment...........: 7794 128s Mean site entropy in alignment.........: 0.0871024 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2628 50 -4 152 +1 7230 -564 128s Number of sequences in alignment.......: 50 128s Number of sites in alignment...........: 152 128s Number of chars in alignment...........: 7230 128s Mean site entropy in alignment.........: 0.0864589 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2692 48 -2 153 +1 7110 -120 128s Number of sequences in alignment.......: 48 128s Number of sites in alignment...........: 153 128s Number of chars in alignment...........: 7110 128s Mean site entropy in alignment.........: 0.0765764 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2695 10 -38 154 +1 1526 -5584 128s Number of sequences in alignment.......: 10 128s Number of sites in alignment...........: 154 128s Number of chars in alignment...........: 1526 128s Mean site entropy in alignment.........: 0.0596881 128s Choice Node #seq %seq #sites %sites #chars %chars 128s 1) 2611 2 -8 156 +2 312 -1214 128s Number of sequences in alignment.......: 2 128s Number of sites in alignment...........: 156 128s Number of chars in alignment...........: 312 128s Mean site entropy in alignment.........: 0.0190193 128s Choice Node #seq %seq #sites %sites #chars %chars 128s BppAlnOpt's done. Bye. 128s Total execution time: 0.000000d, 0.000000h, 0.000000m, 3.000000s. 128s ****************************************************************** 128s * Bio++ Alignment Optimizer, version 1.1.0. * 128s * Author: J. Dutheil Last Modif. 14/03/18 * 128s * E. Figuet * 128s ****************************************************************** 128s 128s Parsing options: 128s Parsing file AlnOptimAuto.bpp for options. 128s Alphabet type .........................: Proteic 128s Sequence file .........................: PF01049_full.txt 128s Sequence format .......................: FASTA file 128s Minimum amount of data per site........: 0.7 128s Filter gap characters..................: yes 128s Filter unresolved characters...........: yes 128s Number of reference sequences..........: 0 128s Total number of sequences..............: 1652 128s Total number of sites..................: 656 128s Compressing sequences..................: 128s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 128s Memory required to store distances (Mb): 20 128s Computing pairwise overlap matrix......: 133s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 133s Clustering linkage mode................: complete 133s Computing cluster tree.................: 143s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 144s Comparison criterion:..................: MaxSites 144s Number of sequences in alignment.......: 1652 144s Number of sites in alignment...........: 129 144s Number of chars in alignment...........: 182603 144s Mean site entropy in alignment.........: 0.394104 144s Choice Node #seq %seq #sites %sites #chars %chars 144s 1) 3294 1647 -5 131 +2 184716 2113 144s Number of sequences in alignment.......: 1647 144s Number of sites in alignment...........: 131 144s Number of chars in alignment...........: 184716 144s Mean site entropy in alignment.........: 0.394659 144s Choice Node #seq %seq #sites %sites #chars %chars 144s 1) 3286 1645 -2 132 +1 185817 1101 144s Number of sequences in alignment.......: 1645 144s Number of sites in alignment...........: 132 144s Number of chars in alignment...........: 185817 144s Mean site entropy in alignment.........: 0.394872 144s Choice Node #seq %seq #sites %sites #chars %chars 144s 1) 536 1644 -1 133 +1 186943 1126 144s Number of sequences in alignment.......: 1644 144s Number of sites in alignment...........: 133 144s Number of chars in alignment...........: 186943 144s Mean site entropy in alignment.........: 0.39494 144s Choice Node #seq %seq #sites %sites #chars %chars 144s 1) 3270 1634 -10 134 +1 187657 714 144s Number of sequences in alignment.......: 1634 144s Number of sites in alignment...........: 134 144s Number of chars in alignment...........: 187657 144s Mean site entropy in alignment.........: 0.395564 144s Choice Node #seq %seq #sites %sites #chars %chars 144s 1) 2951 1627 -7 135 +1 188449 792 144s Number of sequences in alignment.......: 1627 144s Number of sites in alignment...........: 135 144s Number of chars in alignment...........: 188449 144s Mean site entropy in alignment.........: 0.392385 144s Choice Node #seq %seq #sites %sites #chars %chars 144s 1) 3021 1614 -13 136 +1 188658 209 144s Number of sequences in alignment.......: 1614 144s Number of sites in alignment...........: 136 144s Number of chars in alignment...........: 188658 144s Mean site entropy in alignment.........: 0.391197 144s Choice Node #seq %seq #sites %sites #chars %chars 144s 1) 3235 1545 -69 137 +1 185332 -3326 145s Number of sequences in alignment.......: 1545 145s Number of sites in alignment...........: 137 145s Number of chars in alignment...........: 185332 145s Mean site entropy in alignment.........: 0.389695 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 3249 1542 -3 138 +1 186300 968 145s Number of sequences in alignment.......: 1542 145s Number of sites in alignment...........: 138 145s Number of chars in alignment...........: 186300 145s Mean site entropy in alignment.........: 0.389735 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 3247 1537 -5 139 +1 187136 836 145s Number of sequences in alignment.......: 1537 145s Number of sites in alignment...........: 139 145s Number of chars in alignment...........: 187136 145s Mean site entropy in alignment.........: 0.389763 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 2816 1521 -16 140 +1 186509 -627 145s Number of sequences in alignment.......: 1521 145s Number of sites in alignment...........: 140 145s Number of chars in alignment...........: 186509 145s Mean site entropy in alignment.........: 0.38832 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 3130 1471 -50 141 +1 183898 -2611 145s Number of sequences in alignment.......: 1471 145s Number of sites in alignment...........: 141 145s Number of chars in alignment...........: 183898 145s Mean site entropy in alignment.........: 0.370103 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 1147 1470 -1 142 +1 184902 1004 145s Number of sequences in alignment.......: 1470 145s Number of sites in alignment...........: 142 145s Number of chars in alignment...........: 184902 145s Mean site entropy in alignment.........: 0.370154 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 3251 1465 -5 143 +1 185674 772 145s Number of sequences in alignment.......: 1465 145s Number of sites in alignment...........: 143 145s Number of chars in alignment...........: 185674 145s Mean site entropy in alignment.........: 0.370155 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 3280 1391 -74 144 +1 181655 -4019 145s Number of sequences in alignment.......: 1391 145s Number of sites in alignment...........: 144 145s Number of chars in alignment...........: 181655 145s Mean site entropy in alignment.........: 0.359169 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 2928 1340 -51 145 +1 177148 -4507 145s Number of sequences in alignment.......: 1340 145s Number of sites in alignment...........: 145 145s Number of chars in alignment...........: 177148 145s Mean site entropy in alignment.........: 0.351822 145s Choice Node #seq %seq #sites %sites #chars %chars 145s 1) 3168 1159 -181 146 +1 163916 -13232 146s Number of sequences in alignment.......: 1159 146s Number of sites in alignment...........: 146 146s Number of chars in alignment...........: 163916 146s Mean site entropy in alignment.........: 0.32945 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 2651 1117 -42 147 +1 158726 -5190 146s Number of sequences in alignment.......: 1117 146s Number of sites in alignment...........: 147 146s Number of chars in alignment...........: 158726 146s Mean site entropy in alignment.........: 0.331341 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 2242 1097 -20 148 +1 156673 -2053 146s Number of sequences in alignment.......: 1097 146s Number of sites in alignment...........: 148 146s Number of chars in alignment...........: 156673 146s Mean site entropy in alignment.........: 0.324708 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 2221 1078 -19 149 +1 154673 -2000 146s Number of sequences in alignment.......: 1078 146s Number of sites in alignment...........: 149 146s Number of chars in alignment...........: 154673 146s Mean site entropy in alignment.........: 0.326137 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 2944 993 -85 150 +1 144901 -9772 146s Number of sequences in alignment.......: 993 146s Number of sites in alignment...........: 150 146s Number of chars in alignment...........: 144901 146s Mean site entropy in alignment.........: 0.302006 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 2554 941 -52 151 +1 137854 -7047 146s Number of sequences in alignment.......: 941 146s Number of sites in alignment...........: 151 146s Number of chars in alignment...........: 137854 146s Mean site entropy in alignment.........: 0.304205 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 2675 234 -707 157 +6 36220 -101634 146s Number of sequences in alignment.......: 234 146s Number of sites in alignment...........: 157 146s Number of chars in alignment...........: 36220 146s Mean site entropy in alignment.........: 0.18992 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 2046 230 -4 158 +1 35777 -443 146s Number of sequences in alignment.......: 230 146s Number of sites in alignment...........: 158 146s Number of chars in alignment...........: 35777 146s Mean site entropy in alignment.........: 0.188188 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 1950 24 -206 160 +2 3795 -31982 146s Number of sequences in alignment.......: 24 146s Number of sites in alignment...........: 160 146s Number of chars in alignment...........: 3795 146s Mean site entropy in alignment.........: 0.185344 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 1896 20 -4 161 +1 3193 -602 146s Number of sequences in alignment.......: 20 146s Number of sites in alignment...........: 161 146s Number of chars in alignment...........: 3193 146s Mean site entropy in alignment.........: 0.133241 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 1795 18 -2 163 +2 2911 -282 146s Number of sequences in alignment.......: 18 146s Number of sites in alignment...........: 163 146s Number of chars in alignment...........: 2911 146s Mean site entropy in alignment.........: 0.122561 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 1718 14 -4 165 +2 2294 -617 146s Number of sequences in alignment.......: 14 146s Number of sites in alignment...........: 165 146s Number of chars in alignment...........: 2294 146s Mean site entropy in alignment.........: 0.0452968 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 1707 12 -2 166 +1 1983 -311 146s Number of sequences in alignment.......: 12 146s Number of sites in alignment...........: 166 146s Number of chars in alignment...........: 1983 146s Mean site entropy in alignment.........: 0.0379699 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 397 11 -1 168 +2 1838 -145 146s Number of sequences in alignment.......: 11 146s Number of sites in alignment...........: 168 146s Number of chars in alignment...........: 1838 146s Mean site entropy in alignment.........: 0.03305 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 1682 8 -3 169 +1 1349 -489 146s Number of sequences in alignment.......: 8 146s Number of sites in alignment...........: 169 146s Number of chars in alignment...........: 1349 146s Mean site entropy in alignment.........: 0.0183685 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 46 7 -1 172 +3 1196 -153 146s Number of sequences in alignment.......: 7 146s Number of sites in alignment...........: 172 146s Number of chars in alignment...........: 1196 146s Mean site entropy in alignment.........: 0.0178367 146s Choice Node #seq %seq #sites %sites #chars %chars 146s 1) 1664 2 -5 176 +4 352 -844 146s Number of sequences in alignment.......: 2 146s Number of sites in alignment...........: 176 146s Number of chars in alignment...........: 352 146s Mean site entropy in alignment.........: 0.010038 146s Choice Node #seq %seq #sites %sites #chars %chars 146s BppAlnOpt's done. Bye. 146s Total execution time: 0.000000d, 0.000000h, 0.000000m, 19.000000s. 146s ****************************************************************** 146s * Bio++ Alignment Optimizer, version 1.1.0. * 146s * Author: J. Dutheil Last Modif. 14/03/18 * 146s * E. Figuet * 146s ****************************************************************** 146s 146s Parsing options: 146s Parsing file AlnOptimAuto.bpp for options. 146s Alphabet type .........................: Proteic 146s Sequence file .........................: PF01049_full.txt 146s Sequence format .......................: FASTA file 146s Minimum amount of data per site........: 0.7 146s Filter gap characters..................: yes 146s Filter unresolved characters...........: yes 146s Number of reference sequences..........: 0 146s Total number of sequences..............: 1652 146s Total number of sites..................: 656 146s Compressing sequences..................: 146s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 146s Memory required to store distances (Mb): 20 146s Computing pairwise overlap matrix......: 150s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 150s Clustering linkage mode................: single 150s Computing cluster tree.................: 161s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 161s Comparison criterion:..................: MaxSites 161s Number of sequences in alignment.......: 1652 161s Number of sites in alignment...........: 129 161s Number of chars in alignment...........: 182603 161s Mean site entropy in alignment.........: 0.394104 161s Choice Node #seq %seq #sites %sites #chars %chars 161s 1) 3297 1647 -5 131 +2 184776 2173 161s Number of sequences in alignment.......: 1647 161s Number of sites in alignment...........: 131 161s Number of chars in alignment...........: 184776 161s Mean site entropy in alignment.........: 0.394536 161s Choice Node #seq %seq #sites %sites #chars %chars 161s 1) 3295 1645 -2 132 +1 185874 1098 162s Number of sequences in alignment.......: 1645 162s Number of sites in alignment...........: 132 162s Number of chars in alignment...........: 185874 162s Mean site entropy in alignment.........: 0.394721 162s Choice Node #seq %seq #sites %sites #chars %chars 162s 1) 181 1644 -1 133 +1 186998 1124 162s Number of sequences in alignment.......: 1644 162s Number of sites in alignment...........: 133 162s Number of chars in alignment...........: 186998 162s Mean site entropy in alignment.........: 0.394677 162s Choice Node #seq %seq #sites %sites #chars %chars 162s 1) 3285 1634 -10 134 +1 187772 774 162s Number of sequences in alignment.......: 1634 162s Number of sites in alignment...........: 134 162s Number of chars in alignment...........: 187772 162s Mean site entropy in alignment.........: 0.395614 162s Choice Node #seq %seq #sites %sites #chars %chars 162s 1) 3278 1627 -7 135 +1 188620 848 162s Number of sequences in alignment.......: 1627 162s Number of sites in alignment...........: 135 162s Number of chars in alignment...........: 188620 162s Mean site entropy in alignment.........: 0.396053 162s Choice Node #seq %seq #sites %sites #chars %chars 162s 1) 3265 1614 -13 136 +1 189192 572 162s Number of sequences in alignment.......: 1614 162s Number of sites in alignment...........: 136 162s Number of chars in alignment...........: 189192 162s Mean site entropy in alignment.........: 0.396866 162s Choice Node #seq %seq #sites %sites #chars %chars 162s 1) 3157 1505 -109 137 +1 184306 -4886 163s Number of sequences in alignment.......: 1505 163s Number of sites in alignment...........: 137 163s Number of chars in alignment...........: 184306 163s Mean site entropy in alignment.........: 0.397698 163s Choice Node #seq %seq #sites %sites #chars %chars 163s 1) 3139 1488 -17 138 +1 184277 -29 163s Number of sequences in alignment.......: 1488 163s Number of sites in alignment...........: 138 163s Number of chars in alignment...........: 184277 163s Mean site entropy in alignment.........: 0.396924 163s Choice Node #seq %seq #sites %sites #chars %chars 163s 1) 3136 1485 -3 139 +1 185134 857 163s Number of sequences in alignment.......: 1485 163s Number of sites in alignment...........: 139 163s Number of chars in alignment...........: 185134 163s Mean site entropy in alignment.........: 0.396707 163s Choice Node #seq %seq #sites %sites #chars %chars 163s 1) 3122 1471 -14 140 +1 185214 80 163s Number of sequences in alignment.......: 1471 163s Number of sites in alignment...........: 140 163s Number of chars in alignment...........: 185214 163s Mean site entropy in alignment.........: 0.396624 163s Choice Node #seq %seq #sites %sites #chars %chars 163s 1) 2848 1437 -34 141 +1 183753 -1461 163s Number of sequences in alignment.......: 1437 163s Number of sites in alignment...........: 141 163s Number of chars in alignment...........: 183753 163s Mean site entropy in alignment.........: 0.379676 163s Choice Node #seq %seq #sites %sites #chars %chars 163s 1) 3110 1425 -12 142 +1 183898 145 163s Number of sequences in alignment.......: 1425 163s Number of sites in alignment...........: 142 163s Number of chars in alignment...........: 183898 163s Mean site entropy in alignment.........: 0.379975 163s Choice Node #seq %seq #sites %sites #chars %chars 163s 1) 3073 1387 -38 143 +1 182369 -1529 164s Number of sequences in alignment.......: 1387 164s Number of sites in alignment...........: 143 164s Number of chars in alignment...........: 182369 164s Mean site entropy in alignment.........: 0.376594 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 2904 1380 -7 144 +1 182593 224 164s Number of sequences in alignment.......: 1380 164s Number of sites in alignment...........: 144 164s Number of chars in alignment...........: 182593 164s Mean site entropy in alignment.........: 0.375989 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 2941 1206 -174 145 +1 167869 -14724 164s Number of sequences in alignment.......: 1206 164s Number of sites in alignment...........: 145 164s Number of chars in alignment...........: 167869 164s Mean site entropy in alignment.........: 0.346494 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 2829 1145 -61 146 +1 162413 -5456 164s Number of sequences in alignment.......: 1145 164s Number of sites in alignment...........: 146 164s Number of chars in alignment...........: 162413 164s Mean site entropy in alignment.........: 0.332586 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 2751 1071 -74 147 +1 153723 -8690 164s Number of sequences in alignment.......: 1071 164s Number of sites in alignment...........: 147 164s Number of chars in alignment...........: 153723 164s Mean site entropy in alignment.........: 0.320762 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 1751 998 -73 148 +1 144121 -9602 164s Number of sequences in alignment.......: 998 164s Number of sites in alignment...........: 148 164s Number of chars in alignment...........: 144121 164s Mean site entropy in alignment.........: 0.298818 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 2100 985 -13 149 +1 142964 -1157 164s Number of sequences in alignment.......: 985 164s Number of sites in alignment...........: 149 164s Number of chars in alignment...........: 142964 164s Mean site entropy in alignment.........: 0.298279 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 2427 665 -320 150 +1 97526 -45438 164s Number of sequences in alignment.......: 665 164s Number of sites in alignment...........: 150 164s Number of chars in alignment...........: 97526 164s Mean site entropy in alignment.........: 0.293825 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 1379 664 -1 151 +1 97882 356 164s Number of sequences in alignment.......: 664 164s Number of sites in alignment...........: 151 164s Number of chars in alignment...........: 97882 164s Mean site entropy in alignment.........: 0.292162 164s Choice Node #seq %seq #sites %sites #chars %chars 164s 1) 2203 441 -223 152 +1 65487 -32395 165s Number of sequences in alignment.......: 441 165s Number of sites in alignment...........: 152 165s Number of chars in alignment...........: 65487 165s Mean site entropy in alignment.........: 0.29729 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 2189 427 -14 153 +1 63726 -1761 165s Number of sequences in alignment.......: 427 165s Number of sites in alignment...........: 153 165s Number of chars in alignment...........: 63726 165s Mean site entropy in alignment.........: 0.295662 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 2082 334 -93 154 +1 50320 -13406 165s Number of sequences in alignment.......: 334 165s Number of sites in alignment...........: 154 165s Number of chars in alignment...........: 50320 165s Mean site entropy in alignment.........: 0.268583 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 2006 258 -76 155 +1 39190 -11130 165s Number of sequences in alignment.......: 258 165s Number of sites in alignment...........: 155 165s Number of chars in alignment...........: 39190 165s Mean site entropy in alignment.........: 0.230649 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 1987 254 -4 156 +1 38780 -410 165s Number of sequences in alignment.......: 254 165s Number of sites in alignment...........: 156 165s Number of chars in alignment...........: 38780 165s Mean site entropy in alignment.........: 0.228398 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 1915 247 -7 157 +1 37896 -884 165s Number of sequences in alignment.......: 247 165s Number of sites in alignment...........: 157 165s Number of chars in alignment...........: 37896 165s Mean site entropy in alignment.........: 0.226904 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 1876 130 -117 158 +1 20276 -17620 165s Number of sequences in alignment.......: 130 165s Number of sites in alignment...........: 158 165s Number of chars in alignment...........: 20276 165s Mean site entropy in alignment.........: 0.134572 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 1704 3 -127 163 +5 489 -19787 165s Number of sequences in alignment.......: 3 165s Number of sites in alignment...........: 163 165s Number of chars in alignment...........: 489 165s Mean site entropy in alignment.........: 0.065727 165s Choice Node #seq %seq #sites %sites #chars %chars 165s 1) 1474 2 -1 167 +4 334 -155 165s Number of sequences in alignment.......: 2 165s Number of sites in alignment...........: 167 165s Number of chars in alignment...........: 334 165s Mean site entropy in alignment.........: 0.0338121 165s Choice Node #seq %seq #sites %sites #chars %chars 165s BppAlnOpt's done. Bye. 165s Total execution time: 0.000000d, 0.000000h, 0.000000m, 19.000000s. 165s ****************************************************************** 165s * Bio++ Alignment Optimizer, version 1.1.0. * 165s * Author: J. Dutheil Last Modif. 14/03/18 * 165s * E. Figuet * 165s ****************************************************************** 165s 165s Parsing options: 165s Parsing file AlnOptimAuto.bpp for options. 165s Alphabet type .........................: Proteic 165s Sequence file .........................: PF01049_full.txt 165s Sequence format .......................: FASTA file 165s Minimum amount of data per site........: 0.7 165s Filter gap characters..................: yes 165s Filter unresolved characters...........: yes 165s Number of reference sequences..........: 0 165s Total number of sequences..............: 1652 165s Total number of sites..................: 656 165s Compressing sequences..................: 165s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 165s Memory required to store distances (Mb): 20 165s Computing pairwise overlap matrix......: 169s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 169s Clustering linkage mode................: average 169s Computing cluster tree.................: 180s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 180s Comparison criterion:..................: MaxSites 180s Number of sequences in alignment.......: 1652 180s Number of sites in alignment...........: 129 180s Number of chars in alignment...........: 182603 180s Mean site entropy in alignment.........: 0.394104 180s Choice Node #seq %seq #sites %sites #chars %chars 180s 1) 3299 1647 -5 131 +2 184774 2171 181s Number of sequences in alignment.......: 1647 181s Number of sites in alignment...........: 131 181s Number of chars in alignment...........: 184774 181s Mean site entropy in alignment.........: 0.394431 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 3293 1645 -2 132 +1 185875 1101 181s Number of sequences in alignment.......: 1645 181s Number of sites in alignment...........: 132 181s Number of chars in alignment...........: 185875 181s Mean site entropy in alignment.........: 0.394643 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 181 1644 -1 133 +1 186999 1124 181s Number of sequences in alignment.......: 1644 181s Number of sites in alignment...........: 133 181s Number of chars in alignment...........: 186999 181s Mean site entropy in alignment.........: 0.394599 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 3287 1634 -10 134 +1 187779 780 181s Number of sequences in alignment.......: 1634 181s Number of sites in alignment...........: 134 181s Number of chars in alignment...........: 187779 181s Mean site entropy in alignment.........: 0.395631 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 3276 1627 -7 135 +1 188617 838 181s Number of sequences in alignment.......: 1627 181s Number of sites in alignment...........: 135 181s Number of chars in alignment...........: 188617 181s Mean site entropy in alignment.........: 0.396076 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 3238 1614 -13 136 +1 189013 396 181s Number of sequences in alignment.......: 1614 181s Number of sites in alignment...........: 136 181s Number of chars in alignment...........: 189013 181s Mean site entropy in alignment.........: 0.395128 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 3023 1533 -81 138 +2 185240 -3773 181s Number of sequences in alignment.......: 1533 181s Number of sites in alignment...........: 138 181s Number of chars in alignment...........: 185240 181s Mean site entropy in alignment.........: 0.372196 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 1629 1532 -1 139 +1 186276 1036 181s Number of sequences in alignment.......: 1532 181s Number of sites in alignment...........: 139 181s Number of chars in alignment...........: 186276 181s Mean site entropy in alignment.........: 0.372208 181s Choice Node #seq %seq #sites %sites #chars %chars 181s 1) 3282 1521 -11 140 +1 186867 591 182s Number of sequences in alignment.......: 1521 182s Number of sites in alignment...........: 140 182s Number of chars in alignment...........: 186867 182s Mean site entropy in alignment.........: 0.372497 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 3105 1482 -39 141 +1 185210 -1657 182s Number of sequences in alignment.......: 1482 182s Number of sites in alignment...........: 141 182s Number of chars in alignment...........: 185210 182s Mean site entropy in alignment.........: 0.368185 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 3135 1471 -11 142 +1 185562 352 182s Number of sequences in alignment.......: 1471 182s Number of sites in alignment...........: 142 182s Number of chars in alignment...........: 185562 182s Mean site entropy in alignment.........: 0.367384 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 2863 1455 -16 143 +1 184869 -693 182s Number of sequences in alignment.......: 1455 182s Number of sites in alignment...........: 143 182s Number of chars in alignment...........: 184869 182s Mean site entropy in alignment.........: 0.366056 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 3166 1413 -42 144 +1 183102 -1767 182s Number of sequences in alignment.......: 1413 182s Number of sites in alignment...........: 144 182s Number of chars in alignment...........: 183102 182s Mean site entropy in alignment.........: 0.362023 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 2996 1204 -209 145 +1 168239 -14863 182s Number of sequences in alignment.......: 1204 182s Number of sites in alignment...........: 145 182s Number of chars in alignment...........: 168239 182s Mean site entropy in alignment.........: 0.339856 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 2960 1154 -50 146 +1 163602 -4637 182s Number of sequences in alignment.......: 1154 182s Number of sites in alignment...........: 146 182s Number of chars in alignment...........: 163602 182s Mean site entropy in alignment.........: 0.330406 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 2809 1097 -57 147 +1 157455 -6147 182s Number of sequences in alignment.......: 1097 182s Number of sites in alignment...........: 147 182s Number of chars in alignment...........: 157455 182s Mean site entropy in alignment.........: 0.314798 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 2635 1063 -34 148 +1 153359 -4096 182s Number of sequences in alignment.......: 1063 182s Number of sites in alignment...........: 148 182s Number of chars in alignment...........: 153359 182s Mean site entropy in alignment.........: 0.316144 182s Choice Node #seq %seq #sites %sites #chars %chars 182s 1) 1948 1048 -15 149 +1 151998 -1361 183s Number of sequences in alignment.......: 1048 183s Number of sites in alignment...........: 149 183s Number of chars in alignment...........: 151998 183s Mean site entropy in alignment.........: 0.31084 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 2069 1031 -17 150 +1 150327 -1671 183s Number of sequences in alignment.......: 1031 183s Number of sites in alignment...........: 150 183s Number of chars in alignment...........: 150327 183s Mean site entropy in alignment.........: 0.303727 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 2640 451 -580 151 +1 67067 -83260 183s Number of sequences in alignment.......: 451 183s Number of sites in alignment...........: 151 183s Number of chars in alignment...........: 67067 183s Mean site entropy in alignment.........: 0.278258 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 2555 425 -26 152 +1 63569 -3498 183s Number of sequences in alignment.......: 425 183s Number of sites in alignment...........: 152 183s Number of chars in alignment...........: 63569 183s Mean site entropy in alignment.........: 0.276822 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 2332 391 -34 153 +1 58841 -4728 183s Number of sequences in alignment.......: 391 183s Number of sites in alignment...........: 153 183s Number of chars in alignment...........: 58841 183s Mean site entropy in alignment.........: 0.269678 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 2039 342 -49 154 +1 51693 -7148 183s Number of sequences in alignment.......: 342 183s Number of sites in alignment...........: 154 183s Number of chars in alignment...........: 51693 183s Mean site entropy in alignment.........: 0.250803 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 2337 280 -62 155 +1 42698 -8995 183s Number of sequences in alignment.......: 280 183s Number of sites in alignment...........: 155 183s Number of chars in alignment...........: 42698 183s Mean site entropy in alignment.........: 0.230831 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 1969 277 -3 156 +1 42454 -244 183s Number of sequences in alignment.......: 277 183s Number of sites in alignment...........: 156 183s Number of chars in alignment...........: 42454 183s Mean site entropy in alignment.........: 0.228862 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 2097 246 -31 157 +1 37949 -4505 183s Number of sequences in alignment.......: 246 183s Number of sites in alignment...........: 157 183s Number of chars in alignment...........: 37949 183s Mean site entropy in alignment.........: 0.216654 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 884 245 -1 158 +1 37976 27 183s Number of sequences in alignment.......: 245 183s Number of sites in alignment...........: 158 183s Number of chars in alignment...........: 37976 183s Mean site entropy in alignment.........: 0.215946 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 1937 19 -226 163 +5 3067 -34909 183s Number of sequences in alignment.......: 19 183s Number of sites in alignment...........: 163 183s Number of chars in alignment...........: 3067 183s Mean site entropy in alignment.........: 0.115126 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 1719 14 -5 165 +2 2297 -770 183s Number of sequences in alignment.......: 14 183s Number of sites in alignment...........: 165 183s Number of chars in alignment...........: 2297 183s Mean site entropy in alignment.........: 0.0991142 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 1699 12 -2 166 +1 1983 -314 183s Number of sequences in alignment.......: 12 183s Number of sites in alignment...........: 166 183s Number of chars in alignment...........: 1983 183s Mean site entropy in alignment.........: 0.0379699 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 397 11 -1 168 +2 1838 -145 183s Number of sequences in alignment.......: 11 183s Number of sites in alignment...........: 168 183s Number of chars in alignment...........: 1838 183s Mean site entropy in alignment.........: 0.03305 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 1684 8 -3 169 +1 1349 -489 183s Number of sequences in alignment.......: 8 183s Number of sites in alignment...........: 169 183s Number of chars in alignment...........: 1349 183s Mean site entropy in alignment.........: 0.0183685 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 46 7 -1 172 +3 1196 -153 183s Number of sequences in alignment.......: 7 183s Number of sites in alignment...........: 172 183s Number of chars in alignment...........: 1196 183s Mean site entropy in alignment.........: 0.0178367 183s Choice Node #seq %seq #sites %sites #chars %chars 183s 1) 1664 2 -5 176 +4 352 -844 183s Number of sequences in alignment.......: 2 183s Number of sites in alignment...........: 176 183s Number of chars in alignment...........: 352 183s Mean site entropy in alignment.........: 0.010038 183s Choice Node #seq %seq #sites %sites #chars %chars 183s BppAlnOpt's done. Bye. 183s Total execution time: 0.000000d, 0.000000h, 0.000000m, 18.000000s. 183s ****************************************************************** 183s * Bio++ Alignment Optimizer, version 1.1.0. * 183s * Author: J. Dutheil Last Modif. 14/03/18 * 183s * E. Figuet * 183s ****************************************************************** 183s 183s Parsing options: 183s Parsing file AlnOptimAuto.bpp for options. 183s Alphabet type .........................: Proteic 183s Sequence file .........................: PF01049_full.txt 183s Sequence format .......................: FASTA file 183s Minimum amount of data per site........: 0.7 183s Filter gap characters..................: yes 183s Filter unresolved characters...........: yes 183s Number of reference sequences..........: 0 183s Total number of sequences..............: 1652 183s Total number of sites..................: 656 183s Compressing sequences..................: 183s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 183s Memory required to store distances (Mb): 20 183s Computing pairwise overlap matrix......: 187s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 187s Clustering linkage mode................: median 187s Computing cluster tree.................: 197s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 198s Comparison criterion:..................: MaxSites 198s Number of sequences in alignment.......: 1652 198s Number of sites in alignment...........: 129 198s Number of chars in alignment...........: 182603 198s Mean site entropy in alignment.........: 0.394104 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 3297 1647 -5 131 +2 184774 2171 198s Number of sequences in alignment.......: 1647 198s Number of sites in alignment...........: 131 198s Number of chars in alignment...........: 184774 198s Mean site entropy in alignment.........: 0.394431 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 3295 1645 -2 132 +1 185873 1099 198s Number of sequences in alignment.......: 1645 198s Number of sites in alignment...........: 132 198s Number of chars in alignment...........: 185873 198s Mean site entropy in alignment.........: 0.394618 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 275 1644 -1 133 +1 186998 1125 198s Number of sequences in alignment.......: 1644 198s Number of sites in alignment...........: 133 198s Number of chars in alignment...........: 186998 198s Mean site entropy in alignment.........: 0.394724 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 3280 1630 -14 134 +1 187559 561 198s Number of sequences in alignment.......: 1630 198s Number of sites in alignment...........: 134 198s Number of chars in alignment...........: 187559 198s Mean site entropy in alignment.........: 0.39546 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 3272 1622 -8 135 +1 188376 817 199s Number of sequences in alignment.......: 1622 199s Number of sites in alignment...........: 135 199s Number of chars in alignment...........: 188376 199s Mean site entropy in alignment.........: 0.396213 199s Choice Node #seq %seq #sites %sites #chars %chars 199s 1) 3261 1611 -11 136 +1 189031 655 200s Number of sequences in alignment.......: 1611 200s Number of sites in alignment...........: 136 200s Number of chars in alignment...........: 189031 200s Mean site entropy in alignment.........: 0.396902 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 3184 1534 -77 137 +1 185562 -3469 200s Number of sequences in alignment.......: 1534 200s Number of sites in alignment...........: 137 200s Number of chars in alignment...........: 185562 200s Mean site entropy in alignment.........: 0.396433 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 3182 1532 -2 138 +1 186503 941 200s Number of sequences in alignment.......: 1532 200s Number of sites in alignment...........: 138 200s Number of chars in alignment...........: 186503 200s Mean site entropy in alignment.........: 0.396422 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 513 1531 -1 139 +1 187535 1032 200s Number of sequences in alignment.......: 1531 200s Number of sites in alignment...........: 139 200s Number of chars in alignment...........: 187535 200s Mean site entropy in alignment.........: 0.396222 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 3169 1518 -13 140 +1 187760 225 200s Number of sequences in alignment.......: 1518 200s Number of sites in alignment...........: 140 200s Number of chars in alignment...........: 187760 200s Mean site entropy in alignment.........: 0.395785 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 3125 1475 -43 141 +1 185962 -1798 200s Number of sequences in alignment.......: 1475 200s Number of sites in alignment...........: 141 200s Number of chars in alignment...........: 185962 200s Mean site entropy in alignment.........: 0.388512 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 3117 1467 -8 142 +1 186502 540 200s Number of sequences in alignment.......: 1467 200s Number of sites in alignment...........: 142 200s Number of chars in alignment...........: 186502 200s Mean site entropy in alignment.........: 0.388016 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 3102 1452 -15 143 +1 186490 -12 200s Number of sequences in alignment.......: 1452 200s Number of sites in alignment...........: 143 200s Number of chars in alignment...........: 186490 200s Mean site entropy in alignment.........: 0.386609 200s Choice Node #seq %seq #sites %sites #chars %chars 200s 1) 3052 1402 -50 144 +1 183727 -2763 201s Number of sequences in alignment.......: 1402 201s Number of sites in alignment...........: 144 201s Number of chars in alignment...........: 183727 201s Mean site entropy in alignment.........: 0.379315 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2877 1227 -175 145 +1 170235 -13492 201s Number of sequences in alignment.......: 1227 201s Number of sites in alignment...........: 145 201s Number of chars in alignment...........: 170235 201s Mean site entropy in alignment.........: 0.34859 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2788 1138 -89 146 +1 161621 -8614 201s Number of sequences in alignment.......: 1138 201s Number of sites in alignment...........: 146 201s Number of chars in alignment...........: 161621 201s Mean site entropy in alignment.........: 0.330459 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2731 1081 -57 147 +1 155136 -6485 201s Number of sequences in alignment.......: 1081 201s Number of sites in alignment...........: 147 201s Number of chars in alignment...........: 155136 201s Mean site entropy in alignment.........: 0.319787 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 1701 1030 -51 148 +1 148555 -6581 201s Number of sequences in alignment.......: 1030 201s Number of sites in alignment...........: 148 201s Number of chars in alignment...........: 148555 201s Mean site entropy in alignment.........: 0.305707 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2499 798 -232 149 +1 116805 -31750 201s Number of sequences in alignment.......: 798 201s Number of sites in alignment...........: 149 201s Number of chars in alignment...........: 116805 201s Mean site entropy in alignment.........: 0.273968 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2468 767 -31 150 +1 112894 -3911 201s Number of sequences in alignment.......: 767 201s Number of sites in alignment...........: 150 201s Number of chars in alignment...........: 112894 201s Mean site entropy in alignment.........: 0.272075 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2239 538 -229 151 +1 79674 -33220 201s Number of sequences in alignment.......: 538 201s Number of sites in alignment...........: 151 201s Number of chars in alignment...........: 79674 201s Mean site entropy in alignment.........: 0.280963 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2196 495 -43 152 +1 73702 -5972 201s Number of sequences in alignment.......: 495 201s Number of sites in alignment...........: 152 201s Number of chars in alignment...........: 73702 201s Mean site entropy in alignment.........: 0.28148 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2076 375 -120 153 +1 56316 -17386 201s Number of sequences in alignment.......: 375 201s Number of sites in alignment...........: 153 201s Number of chars in alignment...........: 56316 201s Mean site entropy in alignment.........: 0.267502 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 2018 317 -58 154 +1 47977 -8339 201s Number of sequences in alignment.......: 317 201s Number of sites in alignment...........: 154 201s Number of chars in alignment...........: 47977 201s Mean site entropy in alignment.........: 0.249671 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 1949 248 -69 155 +1 37817 -10160 201s Number of sequences in alignment.......: 248 201s Number of sites in alignment...........: 155 201s Number of chars in alignment...........: 37817 201s Mean site entropy in alignment.........: 0.215239 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 1938 237 -11 156 +1 36376 -1441 201s Number of sequences in alignment.......: 237 201s Number of sites in alignment...........: 156 201s Number of chars in alignment...........: 36376 201s Mean site entropy in alignment.........: 0.201826 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 1926 225 -12 157 +1 34752 -1624 201s Number of sequences in alignment.......: 225 201s Number of sites in alignment...........: 157 201s Number of chars in alignment...........: 34752 201s Mean site entropy in alignment.........: 0.184033 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 1779 78 -147 158 +1 12282 -22470 201s Number of sequences in alignment.......: 78 201s Number of sites in alignment...........: 158 201s Number of chars in alignment...........: 12282 201s Mean site entropy in alignment.........: 0.0830049 201s Choice Node #seq %seq #sites %sites #chars %chars 201s 1) 1703 2 -76 160 +2 320 -11962 201s Number of sequences in alignment.......: 2 201s Number of sites in alignment...........: 160 201s Number of chars in alignment...........: 320 201s Mean site entropy in alignment.........: 0 201s Choice Node #seq %seq #sites %sites #chars %chars 201s BppAlnOpt's done. Bye. 201s Total execution time: 0.000000d, 0.000000h, 0.000000m, 18.000000s. 201s ****************************************************************** 201s * Bio++ Alignment Optimizer, version 1.1.0. * 201s * Author: J. Dutheil Last Modif. 14/03/18 * 201s * E. Figuet * 201s ****************************************************************** 201s 201s Parsing options: 201s Parsing file AlnOptimAuto.bpp for options. 201s Alphabet type .........................: Proteic 201s Sequence file .........................: PF01049_full.txt 201s Sequence format .......................: FASTA file 201s Minimum amount of data per site........: 0.7 201s Filter gap characters..................: yes 201s Filter unresolved characters...........: yes 201s Number of reference sequences..........: 0 201s Total number of sequences..............: 1652 201s Total number of sites..................: 656 201s Compressing sequences..................: 201s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 201s Memory required to store distances (Mb): 20 201s Computing pairwise overlap matrix......: 205s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 205s Clustering linkage mode................: centroid 205s Computing cluster tree.................: 216s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 216s Comparison criterion:..................: MaxSites 216s Number of sequences in alignment.......: 1652 216s Number of sites in alignment...........: 129 216s Number of chars in alignment...........: 182603 216s Mean site entropy in alignment.........: 0.394104 216s Choice Node #seq %seq #sites %sites #chars %chars 216s 1) 3297 1647 -5 131 +2 184783 2180 217s Number of sequences in alignment.......: 1647 217s Number of sites in alignment...........: 131 217s Number of chars in alignment...........: 184783 217s Mean site entropy in alignment.........: 0.394537 217s Choice Node #seq %seq #sites %sites #chars %chars 217s 1) 3295 1645 -2 132 +1 185880 1097 217s Number of sequences in alignment.......: 1645 217s Number of sites in alignment...........: 132 217s Number of chars in alignment...........: 185880 217s Mean site entropy in alignment.........: 0.394662 217s Choice Node #seq %seq #sites %sites #chars %chars 217s 1) 181 1644 -1 133 +1 187004 1124 217s Number of sequences in alignment.......: 1644 217s Number of sites in alignment...........: 133 217s Number of chars in alignment...........: 187004 217s Mean site entropy in alignment.........: 0.394618 217s Choice Node #seq %seq #sites %sites #chars %chars 217s 1) 3284 1634 -10 134 +1 187785 781 217s Number of sequences in alignment.......: 1634 217s Number of sites in alignment...........: 134 217s Number of chars in alignment...........: 187785 217s Mean site entropy in alignment.........: 0.395449 217s Choice Node #seq %seq #sites %sites #chars %chars 217s 1) 3277 1627 -7 135 +1 188649 864 218s Number of sequences in alignment.......: 1627 218s Number of sites in alignment...........: 135 218s Number of chars in alignment...........: 188649 218s Mean site entropy in alignment.........: 0.395884 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3264 1614 -13 136 +1 189270 621 218s Number of sequences in alignment.......: 1614 218s Number of sites in alignment...........: 136 218s Number of chars in alignment...........: 189270 218s Mean site entropy in alignment.........: 0.396209 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3158 1508 -106 137 +1 184807 -4463 218s Number of sequences in alignment.......: 1508 218s Number of sites in alignment...........: 137 218s Number of chars in alignment...........: 184807 218s Mean site entropy in alignment.........: 0.391659 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3141 1491 -17 138 +1 184810 3 218s Number of sequences in alignment.......: 1491 218s Number of sites in alignment...........: 138 218s Number of chars in alignment...........: 184810 218s Mean site entropy in alignment.........: 0.389899 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3135 1485 -6 139 +1 185468 658 218s Number of sequences in alignment.......: 1485 218s Number of sites in alignment...........: 139 218s Number of chars in alignment...........: 185468 218s Mean site entropy in alignment.........: 0.389868 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3124 1474 -11 140 +1 185788 320 219s Number of sequences in alignment.......: 1474 219s Number of sites in alignment...........: 140 219s Number of chars in alignment...........: 185788 219s Mean site entropy in alignment.........: 0.389071 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3091 1441 -33 141 +1 184655 -1133 219s Number of sequences in alignment.......: 1441 219s Number of sites in alignment...........: 141 219s Number of chars in alignment...........: 184655 219s Mean site entropy in alignment.........: 0.38709 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3077 1427 -14 142 +1 184714 59 219s Number of sequences in alignment.......: 1427 219s Number of sites in alignment...........: 142 219s Number of chars in alignment...........: 184714 219s Mean site entropy in alignment.........: 0.386526 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3055 1405 -22 144 +2 185186 472 219s Number of sequences in alignment.......: 1405 219s Number of sites in alignment...........: 144 219s Number of chars in alignment...........: 185186 219s Mean site entropy in alignment.........: 0.383626 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 2907 1257 -148 145 +1 173927 -11259 219s Number of sequences in alignment.......: 1257 219s Number of sites in alignment...........: 145 219s Number of chars in alignment...........: 173927 219s Mean site entropy in alignment.........: 0.350796 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 2807 1157 -100 146 +1 163983 -9944 219s Number of sequences in alignment.......: 1157 219s Number of sites in alignment...........: 146 219s Number of chars in alignment...........: 163983 219s Mean site entropy in alignment.........: 0.329626 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 2748 1098 -59 147 +1 157592 -6391 220s Number of sequences in alignment.......: 1098 220s Number of sites in alignment...........: 147 220s Number of chars in alignment...........: 157592 220s Mean site entropy in alignment.........: 0.314432 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 1678 1070 -28 148 +1 154399 -3193 220s Number of sequences in alignment.......: 1070 220s Number of sites in alignment...........: 148 220s Number of chars in alignment...........: 154399 220s Mean site entropy in alignment.........: 0.303382 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2620 942 -128 149 +1 137516 -16883 220s Number of sequences in alignment.......: 942 220s Number of sites in alignment...........: 149 220s Number of chars in alignment...........: 137516 220s Mean site entropy in alignment.........: 0.284952 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2615 937 -5 150 +1 137462 -54 220s Number of sequences in alignment.......: 937 220s Number of sites in alignment...........: 150 220s Number of chars in alignment...........: 137462 220s Mean site entropy in alignment.........: 0.285064 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2320 642 -295 151 +1 95140 -42322 220s Number of sequences in alignment.......: 642 220s Number of sites in alignment...........: 151 220s Number of chars in alignment...........: 95140 220s Mean site entropy in alignment.........: 0.276628 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2179 501 -141 152 +1 74734 -20406 220s Number of sequences in alignment.......: 501 220s Number of sites in alignment...........: 152 220s Number of chars in alignment...........: 74734 220s Mean site entropy in alignment.........: 0.281366 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2108 430 -71 153 +1 64604 -10130 220s Number of sequences in alignment.......: 430 220s Number of sites in alignment...........: 153 220s Number of chars in alignment...........: 64604 220s Mean site entropy in alignment.........: 0.282214 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2038 360 -70 154 +1 54522 -10082 220s Number of sequences in alignment.......: 360 220s Number of sites in alignment...........: 154 220s Number of chars in alignment...........: 54522 220s Mean site entropy in alignment.........: 0.265356 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 1969 291 -69 155 +1 44461 -10061 220s Number of sequences in alignment.......: 291 220s Number of sites in alignment...........: 155 220s Number of chars in alignment...........: 44461 220s Mean site entropy in alignment.........: 0.240018 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 1956 278 -13 156 +1 42693 -1768 220s Number of sequences in alignment.......: 278 220s Number of sites in alignment...........: 156 220s Number of chars in alignment...........: 42693 220s Mean site entropy in alignment.........: 0.236678 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 1925 247 -31 157 +1 38195 -4498 220s Number of sequences in alignment.......: 247 220s Number of sites in alignment...........: 157 220s Number of chars in alignment...........: 38195 220s Mean site entropy in alignment.........: 0.216008 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 1923 245 -2 158 +1 38065 -130 220s Number of sequences in alignment.......: 245 220s Number of sites in alignment...........: 158 220s Number of chars in alignment...........: 38065 220s Mean site entropy in alignment.........: 0.215165 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 610 1 -244 177 +19 177 -37888 220s Number of sequences in alignment.......: 1 220s Number of sites in alignment...........: 177 220s Number of chars in alignment...........: 177 220s Mean site entropy in alignment.........: 0 220s Choice Node #seq %seq #sites %sites #chars %chars 220s BppAlnOpt's done. Bye. 220s Total execution time: 0.000000d, 0.000000h, 0.000000m, 19.000000s. 220s ****************************************************************** 220s * Bio++ Alignment Optimizer, version 1.1.0. * 220s * Author: J. Dutheil Last Modif. 14/03/18 * 220s * E. Figuet * 220s ****************************************************************** 220s 220s Parsing options: 220s Parsing file AlnOptimAuto.bpp for options. 220s Alphabet type .........................: Proteic 220s Sequence file .........................: PF01049_full.txt 220s Sequence format .......................: FASTA file 220s Minimum amount of data per site........: 0.7 220s Filter gap characters..................: yes 220s Filter unresolved characters...........: yes 220s Number of reference sequences..........: 0 220s Total number of sequences..............: 1652 220s Total number of sites..................: 656 220s Compressing sequences..................: 220s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 220s Memory required to store distances (Mb): 20 220s Computing pairwise overlap matrix......: 225s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 225s Clustering linkage mode................: ward 225s Computing cluster tree.................: 235s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 235s Comparison criterion:..................: MaxSites 235s Number of sequences in alignment.......: 1652 235s Number of sites in alignment...........: 129 235s Number of chars in alignment...........: 182603 235s Mean site entropy in alignment.........: 0.394104 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3251 1647 -5 131 +2 184716 2113 235s Number of sequences in alignment.......: 1647 235s Number of sites in alignment...........: 131 235s Number of chars in alignment...........: 184716 235s Mean site entropy in alignment.........: 0.394659 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3238 1645 -2 132 +1 185817 1101 236s Number of sequences in alignment.......: 1645 236s Number of sites in alignment...........: 132 236s Number of chars in alignment...........: 185817 236s Mean site entropy in alignment.........: 0.394872 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 626 1644 -1 133 +1 186943 1126 236s Number of sequences in alignment.......: 1644 236s Number of sites in alignment...........: 133 236s Number of chars in alignment...........: 186943 236s Mean site entropy in alignment.........: 0.394963 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3225 1634 -10 134 +1 187538 595 236s Number of sequences in alignment.......: 1634 236s Number of sites in alignment...........: 134 236s Number of chars in alignment...........: 187538 236s Mean site entropy in alignment.........: 0.395167 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3259 1627 -7 135 +1 188469 931 236s Number of sequences in alignment.......: 1627 236s Number of sites in alignment...........: 135 236s Number of chars in alignment...........: 188469 236s Mean site entropy in alignment.........: 0.39572 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3231 1614 -13 136 +1 189043 574 236s Number of sequences in alignment.......: 1614 236s Number of sites in alignment...........: 136 236s Number of chars in alignment...........: 189043 236s Mean site entropy in alignment.........: 0.396503 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3276 1530 -84 139 +3 186415 -2628 236s Number of sequences in alignment.......: 1530 236s Number of sites in alignment...........: 139 236s Number of chars in alignment...........: 186415 236s Mean site entropy in alignment.........: 0.389001 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3232 1521 -9 140 +1 187030 615 236s Number of sequences in alignment.......: 1521 236s Number of sites in alignment...........: 140 236s Number of chars in alignment...........: 187030 236s Mean site entropy in alignment.........: 0.389238 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3267 1485 -36 141 +1 185744 -1286 237s Number of sequences in alignment.......: 1485 237s Number of sites in alignment...........: 141 237s Number of chars in alignment...........: 185744 237s Mean site entropy in alignment.........: 0.389095 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 3288 1470 -15 142 +1 185982 238 237s Number of sequences in alignment.......: 1470 237s Number of sites in alignment...........: 142 237s Number of chars in alignment...........: 185982 237s Mean site entropy in alignment.........: 0.38758 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 3098 1457 -13 143 +1 185643 -339 237s Number of sequences in alignment.......: 1457 237s Number of sites in alignment...........: 143 237s Number of chars in alignment...........: 185643 237s Mean site entropy in alignment.........: 0.385646 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 3289 1411 -46 144 +1 183758 -1885 237s Number of sequences in alignment.......: 1411 237s Number of sites in alignment...........: 144 237s Number of chars in alignment...........: 183758 237s Mean site entropy in alignment.........: 0.38204 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 3273 1313 -98 145 +1 171322 -12436 237s Number of sequences in alignment.......: 1313 237s Number of sites in alignment...........: 145 237s Number of chars in alignment...........: 171322 237s Mean site entropy in alignment.........: 0.380643 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 3299 1133 -180 147 +2 152385 -18937 237s Number of sequences in alignment.......: 1133 237s Number of sites in alignment...........: 147 237s Number of chars in alignment...........: 152385 237s Mean site entropy in alignment.........: 0.346351 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2941 1121 -12 148 +1 152294 -91 237s Number of sequences in alignment.......: 1121 237s Number of sites in alignment...........: 148 237s Number of chars in alignment...........: 152294 237s Mean site entropy in alignment.........: 0.340977 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1664 1115 -6 149 +1 152613 319 237s Number of sequences in alignment.......: 1115 237s Number of sites in alignment...........: 149 237s Number of chars in alignment...........: 152613 237s Mean site entropy in alignment.........: 0.336552 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 3193 1104 -11 150 +1 152591 -22 237s Number of sequences in alignment.......: 1104 237s Number of sites in alignment...........: 150 237s Number of chars in alignment...........: 152591 237s Mean site entropy in alignment.........: 0.330411 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2891 153 -951 157 +7 23971 -128620 237s Number of sequences in alignment.......: 153 237s Number of sites in alignment...........: 157 237s Number of chars in alignment...........: 23971 237s Mean site entropy in alignment.........: 0.0601394 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1887 120 -33 158 +1 18876 -5095 237s Number of sequences in alignment.......: 120 237s Number of sites in alignment...........: 158 237s Number of chars in alignment...........: 18876 237s Mean site entropy in alignment.........: 0.0586193 237s Choice Node #seq %seq #sites %sites #chars %chars 237s BppAlnOpt's done. Bye. 237s Total execution time: 0.000000d, 0.000000h, 0.000000m, 17.000000s. 238s ****************************************************************** 238s * Bio++ Alignment Optimizer, version 1.1.0. * 238s * Author: J. Dutheil Last Modif. 14/03/18 * 238s * E. Figuet * 238s ****************************************************************** 238s 238s Parsing options: 238s Parsing file AlnOptimFasttreeStop.bpp for options. 238s Alphabet type .........................: Proteic 238s Sequence file .........................: PF01049_full.txt 238s Sequence format .......................: FASTA file 238s Minimum amount of data per site........: 0.7 238s Filter gap characters..................: yes 238s Filter unresolved characters...........: yes 238s Number of reference sequences..........: 0 238s Total number of sequences..............: 1652 238s Total number of sites..................: 656 238s Input tree file .......................: PF01049_fasttree.dnd 238s Input tree format .....................: Newick 238s Minimum number of sequences to keep....: 826 238s Comparison criterion:..................: MaxSites 238s Number of sequences in alignment.......: 1652 238s Number of sites in alignment...........: 129 238s Number of chars in alignment...........: 182603 238s Mean site entropy in alignment.........: 0.394104 238s Choice Node #seq %seq #sites %sites #chars %chars 238s 1) 2030 1647 -5 131 +2 184714 2111 238s Number of sequences in alignment.......: 1647 238s Number of sites in alignment...........: 131 238s Number of chars in alignment...........: 184714 238s Mean site entropy in alignment.........: 0.394129 238s Choice Node #seq %seq #sites %sites #chars %chars 238s 1) 1930 1645 -2 132 +1 185794 1080 238s Number of sequences in alignment.......: 1645 238s Number of sites in alignment...........: 132 238s Number of chars in alignment...........: 185794 238s Mean site entropy in alignment.........: 0.394195 238s Choice Node #seq %seq #sites %sites #chars %chars 238s 1) 1882 1644 -1 133 +1 186920 1126 238s Number of sequences in alignment.......: 1644 238s Number of sites in alignment...........: 133 238s Number of chars in alignment...........: 186920 238s Mean site entropy in alignment.........: 0.394263 238s Choice Node #seq %seq #sites %sites #chars %chars 238s 1) 386 1634 -10 134 +1 187634 714 238s Number of sequences in alignment.......: 1634 238s Number of sites in alignment...........: 134 238s Number of chars in alignment...........: 187634 238s Mean site entropy in alignment.........: 0.394887 238s Choice Node #seq %seq #sites %sites #chars %chars 238s 1) 357 1627 -7 135 +1 188437 803 238s Number of sequences in alignment.......: 1627 238s Number of sites in alignment...........: 135 238s Number of chars in alignment...........: 188437 238s Mean site entropy in alignment.........: 0.394741 238s Choice Node #seq %seq #sites %sites #chars %chars 238s 1) 1736 1614 -13 136 +1 188713 276 239s Number of sequences in alignment.......: 1614 239s Number of sites in alignment...........: 136 239s Number of chars in alignment...........: 188713 239s Mean site entropy in alignment.........: 0.394145 239s Choice Node #seq %seq #sites %sites #chars %chars 239s 1) 1489 1527 -87 137 +1 181488 -7225 239s Number of sequences in alignment.......: 1527 239s Number of sites in alignment...........: 137 239s Number of chars in alignment...........: 181488 239s Mean site entropy in alignment.........: 0.378687 239s Choice Node #seq %seq #sites %sites #chars %chars 239s 1) 2247 1524 -3 138 +1 182435 947 239s Number of sequences in alignment.......: 1524 239s Number of sites in alignment...........: 138 239s Number of chars in alignment...........: 182435 239s Mean site entropy in alignment.........: 0.378731 239s Choice Node #seq %seq #sites %sites #chars %chars 239s 1) 408 1515 -9 139 +1 183008 573 239s Number of sequences in alignment.......: 1515 239s Number of sites in alignment...........: 139 239s Number of chars in alignment...........: 183008 239s Mean site entropy in alignment.........: 0.377294 239s Choice Node #seq %seq #sites %sites #chars %chars 239s 1) 1819 1488 -27 140 +1 182208 -800 239s Number of sequences in alignment.......: 1488 239s Number of sites in alignment...........: 140 239s Number of chars in alignment...........: 182208 239s Mean site entropy in alignment.........: 0.374188 239s Choice Node #seq %seq #sites %sites #chars %chars 239s 1) 1676 1464 -24 141 +1 180695 -1513 239s Number of sequences in alignment.......: 1464 239s Number of sites in alignment...........: 141 239s Number of chars in alignment...........: 180695 239s Mean site entropy in alignment.........: 0.371696 239s Choice Node #seq %seq #sites %sites #chars %chars 239s 1) 416 1457 -7 142 +1 181323 628 239s Number of sequences in alignment.......: 1457 239s Number of sites in alignment...........: 142 239s Number of chars in alignment...........: 181323 239s Mean site entropy in alignment.........: 0.36917 239s Choice Node #seq %seq #sites %sites #chars %chars 239s 1) 1823 1371 -86 143 +1 176415 -4908 240s Number of sequences in alignment.......: 1371 240s Number of sites in alignment...........: 143 240s Number of chars in alignment...........: 176415 240s Mean site entropy in alignment.........: 0.359961 240s Choice Node #seq %seq #sites %sites #chars %chars 240s 1) 783 1355 -16 144 +1 175237 -1178 240s Number of sequences in alignment.......: 1355 240s Number of sites in alignment...........: 144 240s Number of chars in alignment...........: 175237 240s Mean site entropy in alignment.........: 0.360644 240s Choice Node #seq %seq #sites %sites #chars %chars 240s 1) 953 1307 -48 145 +1 169472 -5765 240s Number of sequences in alignment.......: 1307 240s Number of sites in alignment...........: 145 240s Number of chars in alignment...........: 169472 240s Mean site entropy in alignment.........: 0.363152 240s Choice Node #seq %seq #sites %sites #chars %chars 240s Output alignment file .................: PF01049_optimized_fastml.fasta 240s Output alignment format ...............: FASTA file 240s Output tree file ......................: PF01049_optimized_fastml.dnd 240s Output tree format ....................: Newick 240s BppAlnOpt's done. Bye. 240s Total execution time: 0.000000d, 0.000000h, 0.000000m, 3.000000s. 240s PASS 240s autopkgtest [03:38:27]: test run-unit-test: -----------------------] 241s run-unit-test PASS 241s autopkgtest [03:38:28]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 241s autopkgtest [03:38:28]: @@@@@@@@@@@@@@@@@@@@ summary 241s run-unit-test PASS 252s Creating nova instance adt-noble-s390x-physamp-20240326-033426-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...