0s autopkgtest [03:34:30]: starting date and time: 2024-03-26 03:34:30+0000 0s autopkgtest [03:34:30]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [03:34:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rm5xqcf7/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-2@bos02-ppc64el-17.secgroup --name adt-noble-ppc64el-physamp-20240326-033429-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 272s autopkgtest [03:39:02]: testbed dpkg architecture: ppc64el 272s autopkgtest [03:39:02]: testbed apt version: 2.7.12 272s autopkgtest [03:39:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 273s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 273s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 273s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 273s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 273s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4027 kB] 274s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [699 kB] 274s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 274s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 274s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 274s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4226 kB] 275s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 275s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 275s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 278s Fetched 9704 kB in 3s (2994 kB/s) 279s Reading package lists... 280s Reading package lists... 281s Building dependency tree... 281s Reading state information... 281s Calculating upgrade... 281s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 282s 0 upgraded, 0 newly installed, 0 to remove and 246 not upgraded. 282s sh: Attempting to set up Debian/Ubuntu apt sources automatically 282s sh: Distribution appears to be Ubuntu 283s Reading package lists... 283s Building dependency tree... 283s Reading state information... 284s eatmydata is already the newest version (131-1). 284s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 284s Reading package lists... 284s Building dependency tree... 284s Reading state information... 284s dbus is already the newest version (1.14.10-4ubuntu1). 284s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 284s Reading package lists... 284s Building dependency tree... 284s Reading state information... 285s rng-tools-debian is already the newest version (2.4). 285s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 285s Reading package lists... 285s Building dependency tree... 285s Reading state information... 285s The following packages will be REMOVED: 285s cloud-init* python3-configobj* python3-debconf* 285s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 285s After this operation, 3256 kB disk space will be freed. 285s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70156 files and directories currently installed.) 285s Removing cloud-init (24.1.2-0ubuntu1) ... 286s Removing python3-configobj (5.0.8-3) ... 286s Removing python3-debconf (1.5.86) ... 286s Processing triggers for man-db (2.12.0-3) ... 287s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69767 files and directories currently installed.) 287s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 288s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 288s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 288s invoke-rc.d: policy-rc.d denied execution of try-restart. 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 288s linux-generic is already the newest version (6.8.0-11.11+1). 288s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 288s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 289s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 289s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 292s Reading package lists... 292s Reading package lists... 292s Building dependency tree... 292s Reading state information... 292s Calculating upgrade... 292s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 292s Reading package lists... 292s Building dependency tree... 292s Reading state information... 293s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 293s autopkgtest [03:39:23]: rebooting testbed after setup commands that affected boot 332s autopkgtest [03:40:02]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 335s autopkgtest [03:40:05]: @@@@@@@@@@@@@@@@@@@@ apt-source physamp 337s Get:1 http://ftpmaster.internal/ubuntu noble/universe physamp 1.1.0-4 (dsc) [2026 B] 337s Get:2 http://ftpmaster.internal/ubuntu noble/universe physamp 1.1.0-4 (tar) [242 kB] 337s Get:3 http://ftpmaster.internal/ubuntu noble/universe physamp 1.1.0-4 (diff) [3884 B] 338s gpgv: Signature made Thu Nov 24 18:24:42 2022 UTC 338s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 338s gpgv: issuer "tille@debian.org" 338s gpgv: Can't check signature: No public key 338s dpkg-source: warning: cannot verify inline signature for ./physamp_1.1.0-4.dsc: no acceptable signature found 338s autopkgtest [03:40:08]: testing package physamp version 1.1.0-4 338s autopkgtest [03:40:08]: build not needed 338s autopkgtest [03:40:08]: test run-unit-test: preparing testbed 340s Reading package lists... 340s Building dependency tree... 340s Reading state information... 340s Starting pkgProblemResolver with broken count: 0 340s Starting 2 pkgProblemResolver with broken count: 0 340s Done 340s The following additional packages will be installed: 340s libbpp-core4 libbpp-phyl12 libbpp-seq12 physamp 340s The following NEW packages will be installed: 340s autopkgtest-satdep libbpp-core4 libbpp-phyl12 libbpp-seq12 physamp 340s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 340s Need to get 3267 kB/3268 kB of archives. 340s After this operation, 18.1 MB of additional disk space will be used. 340s Get:1 /tmp/autopkgtest.JBCkug/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 341s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbpp-core4 ppc64el 2.4.1-11 [570 kB] 341s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbpp-seq12 ppc64el 2.4.1-10 [443 kB] 341s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbpp-phyl12 ppc64el 2.4.1-9ubuntu1 [2073 kB] 342s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el physamp ppc64el 1.1.0-4 [183 kB] 342s Fetched 3267 kB in 2s (2035 kB/s) 342s Selecting previously unselected package libbpp-core4:ppc64el. 343s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69712 files and directories currently installed.) 343s Preparing to unpack .../libbpp-core4_2.4.1-11_ppc64el.deb ... 343s Unpacking libbpp-core4:ppc64el (2.4.1-11) ... 343s Selecting previously unselected package libbpp-seq12:ppc64el. 343s Preparing to unpack .../libbpp-seq12_2.4.1-10_ppc64el.deb ... 343s Unpacking libbpp-seq12:ppc64el (2.4.1-10) ... 343s Selecting previously unselected package libbpp-phyl12:ppc64el. 343s Preparing to unpack .../libbpp-phyl12_2.4.1-9ubuntu1_ppc64el.deb ... 343s Unpacking libbpp-phyl12:ppc64el (2.4.1-9ubuntu1) ... 343s Selecting previously unselected package physamp. 343s Preparing to unpack .../physamp_1.1.0-4_ppc64el.deb ... 343s Unpacking physamp (1.1.0-4) ... 343s Selecting previously unselected package autopkgtest-satdep. 343s Preparing to unpack .../1-autopkgtest-satdep.deb ... 343s Unpacking autopkgtest-satdep (0) ... 343s Setting up libbpp-core4:ppc64el (2.4.1-11) ... 343s Setting up libbpp-seq12:ppc64el (2.4.1-10) ... 343s Setting up libbpp-phyl12:ppc64el (2.4.1-9ubuntu1) ... 343s Setting up physamp (1.1.0-4) ... 343s Setting up autopkgtest-satdep (0) ... 343s Processing triggers for man-db (2.12.0-3) ... 343s Processing triggers for install-info (7.1-3) ... 343s Processing triggers for libc-bin (2.39-0ubuntu6) ... 346s (Reading database ... 69749 files and directories currently installed.) 346s Removing autopkgtest-satdep (0) ... 346s autopkgtest [03:40:16]: test run-unit-test: [----------------------- 347s ****************************************************************** 347s * Bio++ Alignment Optimizer, version 1.1.0. * 347s * Author: J. Dutheil Last Modif. 14/03/18 * 347s * E. Figuet * 347s ****************************************************************** 347s 347s Parsing options: 347s Parsing file AlnOptimFasttree.bpp for options. 347s Alphabet type .........................: Proteic 347s Sequence file .........................: PF01049_full.txt 347s Sequence format .......................: FASTA file 347s Minimum amount of data per site........: 0.7 347s Filter gap characters..................: yes 347s Filter unresolved characters...........: yes 347s Number of reference sequences..........: 0 347s Total number of sequences..............: 1652 347s Total number of sites..................: 656 347s Input tree file .......................: PF01049_fasttree.dnd 347s Input tree format .....................: Newick 347s Comparison criterion:..................: MaxSites 347s Number of sequences in alignment.......: 1652 347s Number of sites in alignment...........: 129 347s Number of chars in alignment...........: 182603 347s Mean site entropy in alignment.........: 0.394104 347s Choice Node #seq %seq #sites %sites #chars %chars 347s 1) 2030 1647 -5 131 +2 184714 2111 347s Number of sequences in alignment.......: 1647 347s Number of sites in alignment...........: 131 347s Number of chars in alignment...........: 184714 347s Mean site entropy in alignment.........: 0.394129 347s Choice Node #seq %seq #sites %sites #chars %chars 347s 1) 1930 1645 -2 132 +1 185794 1080 347s Number of sequences in alignment.......: 1645 347s Number of sites in alignment...........: 132 347s Number of chars in alignment...........: 185794 347s Mean site entropy in alignment.........: 0.394195 347s Choice Node #seq %seq #sites %sites #chars %chars 347s 1) 1882 1644 -1 133 +1 186920 1126 347s Number of sequences in alignment.......: 1644 347s Number of sites in alignment...........: 133 347s Number of chars in alignment...........: 186920 347s Mean site entropy in alignment.........: 0.394263 347s Choice Node #seq %seq #sites %sites #chars %chars 347s 1) 386 1634 -10 134 +1 187634 714 347s Number of sequences in alignment.......: 1634 347s Number of sites in alignment...........: 134 347s Number of chars in alignment...........: 187634 347s Mean site entropy in alignment.........: 0.394887 347s Choice Node #seq %seq #sites %sites #chars %chars 347s 1) 357 1627 -7 135 +1 188437 803 347s Number of sequences in alignment.......: 1627 347s Number of sites in alignment...........: 135 347s Number of chars in alignment...........: 188437 347s Mean site entropy in alignment.........: 0.394741 347s Choice Node #seq %seq #sites %sites #chars %chars 347s 1) 1736 1614 -13 136 +1 188713 276 348s Number of sequences in alignment.......: 1614 348s Number of sites in alignment...........: 136 348s Number of chars in alignment...........: 188713 348s Mean site entropy in alignment.........: 0.394145 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 1489 1527 -87 137 +1 181488 -7225 348s Number of sequences in alignment.......: 1527 348s Number of sites in alignment...........: 137 348s Number of chars in alignment...........: 181488 348s Mean site entropy in alignment.........: 0.378687 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 2247 1524 -3 138 +1 182435 947 348s Number of sequences in alignment.......: 1524 348s Number of sites in alignment...........: 138 348s Number of chars in alignment...........: 182435 348s Mean site entropy in alignment.........: 0.378731 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 408 1515 -9 139 +1 183008 573 348s Number of sequences in alignment.......: 1515 348s Number of sites in alignment...........: 139 348s Number of chars in alignment...........: 183008 348s Mean site entropy in alignment.........: 0.377294 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 1819 1488 -27 140 +1 182208 -800 348s Number of sequences in alignment.......: 1488 348s Number of sites in alignment...........: 140 348s Number of chars in alignment...........: 182208 348s Mean site entropy in alignment.........: 0.374188 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 1676 1464 -24 141 +1 180695 -1513 348s Number of sequences in alignment.......: 1464 348s Number of sites in alignment...........: 141 348s Number of chars in alignment...........: 180695 348s Mean site entropy in alignment.........: 0.371696 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 416 1457 -7 142 +1 181323 628 348s Number of sequences in alignment.......: 1457 348s Number of sites in alignment...........: 142 348s Number of chars in alignment...........: 181323 348s Mean site entropy in alignment.........: 0.36917 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 1823 1371 -86 143 +1 176415 -4908 348s Number of sequences in alignment.......: 1371 348s Number of sites in alignment...........: 143 348s Number of chars in alignment...........: 176415 348s Mean site entropy in alignment.........: 0.359961 348s Choice Node #seq %seq #sites %sites #chars %chars 348s 1) 783 1355 -16 144 +1 175237 -1178 349s Number of sequences in alignment.......: 1355 349s Number of sites in alignment...........: 144 349s Number of chars in alignment...........: 175237 349s Mean site entropy in alignment.........: 0.360644 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 953 1307 -48 145 +1 169472 -5765 349s Number of sequences in alignment.......: 1307 349s Number of sites in alignment...........: 145 349s Number of chars in alignment...........: 169472 349s Mean site entropy in alignment.........: 0.363152 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2269 476 -831 146 +1 66187 -103285 349s Number of sequences in alignment.......: 476 349s Number of sites in alignment...........: 146 349s Number of chars in alignment...........: 66187 349s Mean site entropy in alignment.........: 0.249565 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2488 413 -63 147 +1 57456 -8731 349s Number of sequences in alignment.......: 413 349s Number of sites in alignment...........: 147 349s Number of chars in alignment...........: 57456 349s Mean site entropy in alignment.........: 0.249617 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2372 411 -2 148 +1 57619 163 349s Number of sequences in alignment.......: 411 349s Number of sites in alignment...........: 148 349s Number of chars in alignment...........: 57619 349s Mean site entropy in alignment.........: 0.248169 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 179 391 -20 149 +1 55008 -2611 349s Number of sequences in alignment.......: 391 349s Number of sites in alignment...........: 149 349s Number of chars in alignment...........: 55008 349s Mean site entropy in alignment.........: 0.249151 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2697 54 -337 151 +2 7794 -47214 349s Number of sequences in alignment.......: 54 349s Number of sites in alignment...........: 151 349s Number of chars in alignment...........: 7794 349s Mean site entropy in alignment.........: 0.0871024 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2628 50 -4 152 +1 7230 -564 349s Number of sequences in alignment.......: 50 349s Number of sites in alignment...........: 152 349s Number of chars in alignment...........: 7230 349s Mean site entropy in alignment.........: 0.0864589 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2692 48 -2 153 +1 7110 -120 349s Number of sequences in alignment.......: 48 349s Number of sites in alignment...........: 153 349s Number of chars in alignment...........: 7110 349s Mean site entropy in alignment.........: 0.0765764 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2695 10 -38 154 +1 1526 -5584 349s Number of sequences in alignment.......: 10 349s Number of sites in alignment...........: 154 349s Number of chars in alignment...........: 1526 349s Mean site entropy in alignment.........: 0.0596881 349s Choice Node #seq %seq #sites %sites #chars %chars 349s 1) 2611 2 -8 156 +2 312 -1214 349s Number of sequences in alignment.......: 2 349s Number of sites in alignment...........: 156 349s Number of chars in alignment...........: 312 349s Mean site entropy in alignment.........: 0.0190193 349s Choice Node #seq %seq #sites %sites #chars %chars 349s BppAlnOpt's done. Bye. 349s Total execution time: 0.000000d, 0.000000h, 0.000000m, 3.000000s. 349s ****************************************************************** 349s * Bio++ Alignment Optimizer, version 1.1.0. * 349s * Author: J. Dutheil Last Modif. 14/03/18 * 349s * E. Figuet * 349s ****************************************************************** 349s 349s Parsing options: 349s Parsing file AlnOptimAuto.bpp for options. 349s Alphabet type .........................: Proteic 349s Sequence file .........................: PF01049_full.txt 349s Sequence format .......................: FASTA file 349s Minimum amount of data per site........: 0.7 349s Filter gap characters..................: yes 349s Filter unresolved characters...........: yes 349s Number of reference sequences..........: 0 349s Total number of sequences..............: 1652 349s Total number of sites..................: 656 349s Compressing sequences..................: 349s [ ] 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. 349s Memory required to store distances (Mb): 20 349s Computing pairwise overlap matrix......: 352s [> ] 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. 352s Clustering linkage mode................: complete 352s Computing cluster tree.................: 360s [ ] 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. 360s Comparison criterion:..................: MaxSites 360s Number of sequences in alignment.......: 1652 360s Number of sites in alignment...........: 129 360s Number of chars in alignment...........: 182603 360s Mean site entropy in alignment.........: 0.394104 360s Choice Node #seq %seq #sites %sites #chars %chars 360s 1) 3294 1647 -5 131 +2 184716 2113 361s Number of sequences in alignment.......: 1647 361s Number of sites in alignment...........: 131 361s Number of chars in alignment...........: 184716 361s Mean site entropy in alignment.........: 0.394659 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 3286 1645 -2 132 +1 185817 1101 361s Number of sequences in alignment.......: 1645 361s Number of sites in alignment...........: 132 361s Number of chars in alignment...........: 185817 361s Mean site entropy in alignment.........: 0.394872 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 536 1644 -1 133 +1 186943 1126 361s Number of sequences in alignment.......: 1644 361s Number of sites in alignment...........: 133 361s Number of chars in alignment...........: 186943 361s Mean site entropy in alignment.........: 0.39494 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 3270 1634 -10 134 +1 187657 714 361s Number of sequences in alignment.......: 1634 361s Number of sites in alignment...........: 134 361s Number of chars in alignment...........: 187657 361s Mean site entropy in alignment.........: 0.395564 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 2951 1627 -7 135 +1 188449 792 361s Number of sequences in alignment.......: 1627 361s Number of sites in alignment...........: 135 361s Number of chars in alignment...........: 188449 361s Mean site entropy in alignment.........: 0.392385 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 3021 1614 -13 136 +1 188658 209 361s Number of sequences in alignment.......: 1614 361s Number of sites in alignment...........: 136 361s Number of chars in alignment...........: 188658 361s Mean site entropy in alignment.........: 0.391197 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 3235 1545 -69 137 +1 185332 -3326 361s Number of sequences in alignment.......: 1545 361s Number of sites in alignment...........: 137 361s Number of chars in alignment...........: 185332 361s Mean site entropy in alignment.........: 0.389695 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 3249 1542 -3 138 +1 186300 968 361s Number of sequences in alignment.......: 1542 361s Number of sites in alignment...........: 138 361s Number of chars in alignment...........: 186300 361s Mean site entropy in alignment.........: 0.389735 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 3247 1537 -5 139 +1 187136 836 361s Number of sequences in alignment.......: 1537 361s Number of sites in alignment...........: 139 361s Number of chars in alignment...........: 187136 361s Mean site entropy in alignment.........: 0.389763 361s Choice Node #seq %seq #sites %sites #chars %chars 361s 1) 2816 1521 -16 140 +1 186509 -627 362s Number of sequences in alignment.......: 1521 362s Number of sites in alignment...........: 140 362s Number of chars in alignment...........: 186509 362s Mean site entropy in alignment.........: 0.38832 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 3130 1471 -50 141 +1 183898 -2611 362s Number of sequences in alignment.......: 1471 362s Number of sites in alignment...........: 141 362s Number of chars in alignment...........: 183898 362s Mean site entropy in alignment.........: 0.370103 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 1147 1470 -1 142 +1 184902 1004 362s Number of sequences in alignment.......: 1470 362s Number of sites in alignment...........: 142 362s Number of chars in alignment...........: 184902 362s Mean site entropy in alignment.........: 0.370154 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 3251 1465 -5 143 +1 185674 772 362s Number of sequences in alignment.......: 1465 362s Number of sites in alignment...........: 143 362s Number of chars in alignment...........: 185674 362s Mean site entropy in alignment.........: 0.370155 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 3280 1391 -74 144 +1 181655 -4019 362s Number of sequences in alignment.......: 1391 362s Number of sites in alignment...........: 144 362s Number of chars in alignment...........: 181655 362s Mean site entropy in alignment.........: 0.359169 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 2928 1340 -51 145 +1 177148 -4507 362s Number of sequences in alignment.......: 1340 362s Number of sites in alignment...........: 145 362s Number of chars in alignment...........: 177148 362s Mean site entropy in alignment.........: 0.351822 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 3168 1159 -181 146 +1 163916 -13232 362s Number of sequences in alignment.......: 1159 362s Number of sites in alignment...........: 146 362s Number of chars in alignment...........: 163916 362s Mean site entropy in alignment.........: 0.32945 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 2651 1117 -42 147 +1 158726 -5190 362s Number of sequences in alignment.......: 1117 362s Number of sites in alignment...........: 147 362s Number of chars in alignment...........: 158726 362s Mean site entropy in alignment.........: 0.331341 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 2242 1097 -20 148 +1 156673 -2053 362s Number of sequences in alignment.......: 1097 362s Number of sites in alignment...........: 148 362s Number of chars in alignment...........: 156673 362s Mean site entropy in alignment.........: 0.324708 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 2221 1078 -19 149 +1 154673 -2000 362s Number of sequences in alignment.......: 1078 362s Number of sites in alignment...........: 149 362s Number of chars in alignment...........: 154673 362s Mean site entropy in alignment.........: 0.326137 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 2944 993 -85 150 +1 144901 -9772 362s Number of sequences in alignment.......: 993 362s Number of sites in alignment...........: 150 362s Number of chars in alignment...........: 144901 362s Mean site entropy in alignment.........: 0.302006 362s Choice Node #seq %seq #sites %sites #chars %chars 362s 1) 2554 941 -52 151 +1 137854 -7047 363s Number of sequences in alignment.......: 941 363s Number of sites in alignment...........: 151 363s Number of chars in alignment...........: 137854 363s Mean site entropy in alignment.........: 0.304205 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 2675 234 -707 157 +6 36220 -101634 363s Number of sequences in alignment.......: 234 363s Number of sites in alignment...........: 157 363s Number of chars in alignment...........: 36220 363s Mean site entropy in alignment.........: 0.18992 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 2046 230 -4 158 +1 35777 -443 363s Number of sequences in alignment.......: 230 363s Number of sites in alignment...........: 158 363s Number of chars in alignment...........: 35777 363s Mean site entropy in alignment.........: 0.188188 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 1950 24 -206 160 +2 3795 -31982 363s Number of sequences in alignment.......: 24 363s Number of sites in alignment...........: 160 363s Number of chars in alignment...........: 3795 363s Mean site entropy in alignment.........: 0.185344 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 1896 20 -4 161 +1 3193 -602 363s Number of sequences in alignment.......: 20 363s Number of sites in alignment...........: 161 363s Number of chars in alignment...........: 3193 363s Mean site entropy in alignment.........: 0.133241 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 1795 18 -2 163 +2 2911 -282 363s Number of sequences in alignment.......: 18 363s Number of sites in alignment...........: 163 363s Number of chars in alignment...........: 2911 363s Mean site entropy in alignment.........: 0.122561 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 1718 14 -4 165 +2 2294 -617 363s Number of sequences in alignment.......: 14 363s Number of sites in alignment...........: 165 363s Number of chars in alignment...........: 2294 363s Mean site entropy in alignment.........: 0.0452968 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 1707 12 -2 166 +1 1983 -311 363s Number of sequences in alignment.......: 12 363s Number of sites in alignment...........: 166 363s Number of chars in alignment...........: 1983 363s Mean site entropy in alignment.........: 0.0379699 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 397 11 -1 168 +2 1838 -145 363s Number of sequences in alignment.......: 11 363s Number of sites in alignment...........: 168 363s Number of chars in alignment...........: 1838 363s Mean site entropy in alignment.........: 0.03305 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 1682 8 -3 169 +1 1349 -489 363s Number of sequences in alignment.......: 8 363s Number of sites in alignment...........: 169 363s Number of chars in alignment...........: 1349 363s Mean site entropy in alignment.........: 0.0183685 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 46 7 -1 172 +3 1196 -153 363s Number of sequences in alignment.......: 7 363s Number of sites in alignment...........: 172 363s Number of chars in alignment...........: 1196 363s Mean site entropy in alignment.........: 0.0178367 363s Choice Node #seq %seq #sites %sites #chars %chars 363s 1) 1664 2 -5 176 +4 352 -844 363s Number of sequences in alignment.......: 2 363s Number of sites in alignment...........: 176 363s Number of chars in alignment...........: 352 363s Mean site entropy in alignment.........: 0.010038 363s Choice Node #seq %seq #sites %sites #chars %chars 363s BppAlnOpt's done. Bye. 363s Total execution time: 0.000000d, 0.000000h, 0.000000m, 13.000000s. 363s ****************************************************************** 363s * Bio++ Alignment Optimizer, version 1.1.0. * 363s * Author: J. Dutheil Last Modif. 14/03/18 * 363s * E. Figuet * 363s ****************************************************************** 363s 363s Parsing options: 363s Parsing file AlnOptimAuto.bpp for options. 363s Alphabet type .........................: Proteic 363s Sequence file .........................: PF01049_full.txt 363s Sequence format .......................: FASTA file 363s Minimum amount of data per site........: 0.7 363s Filter gap characters..................: yes 363s Filter unresolved characters...........: yes 363s Number of reference sequences..........: 0 363s Total number of sequences..............: 1652 363s Total number of sites..................: 656 363s Compressing sequences..................: 363s [ ] 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. 363s Memory required to store distances (Mb): 20 363s Computing pairwise overlap matrix......: 366s [> ] 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. 366s Clustering linkage mode................: single 366s Computing cluster tree.................: 374s [ ] 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. 374s Comparison criterion:..................: MaxSites 374s Number of sequences in alignment.......: 1652 374s Number of sites in alignment...........: 129 374s Number of chars in alignment...........: 182603 374s Mean site entropy in alignment.........: 0.394104 374s Choice Node #seq %seq #sites %sites #chars %chars 374s 1) 3297 1647 -5 131 +2 184776 2173 374s Number of sequences in alignment.......: 1647 374s Number of sites in alignment...........: 131 374s Number of chars in alignment...........: 184776 374s Mean site entropy in alignment.........: 0.394536 374s Choice Node #seq %seq #sites %sites #chars %chars 374s 1) 3295 1645 -2 132 +1 185874 1098 374s Number of sequences in alignment.......: 1645 374s Number of sites in alignment...........: 132 374s Number of chars in alignment...........: 185874 374s Mean site entropy in alignment.........: 0.394721 374s Choice Node #seq %seq #sites %sites #chars %chars 374s 1) 181 1644 -1 133 +1 186998 1124 375s Number of sequences in alignment.......: 1644 375s Number of sites in alignment...........: 133 375s Number of chars in alignment...........: 186998 375s Mean site entropy in alignment.........: 0.394677 375s Choice Node #seq %seq #sites %sites #chars %chars 375s 1) 3285 1634 -10 134 +1 187772 774 375s Number of sequences in alignment.......: 1634 375s Number of sites in alignment...........: 134 375s Number of chars in alignment...........: 187772 375s Mean site entropy in alignment.........: 0.395614 375s Choice Node #seq %seq #sites %sites #chars %chars 375s 1) 3278 1627 -7 135 +1 188620 848 375s Number of sequences in alignment.......: 1627 375s Number of sites in alignment...........: 135 375s Number of chars in alignment...........: 188620 375s Mean site entropy in alignment.........: 0.396053 375s Choice Node #seq %seq #sites %sites #chars %chars 375s 1) 3265 1614 -13 136 +1 189192 572 375s Number of sequences in alignment.......: 1614 375s Number of sites in alignment...........: 136 375s Number of chars in alignment...........: 189192 375s Mean site entropy in alignment.........: 0.396866 375s Choice Node #seq %seq #sites %sites #chars %chars 375s 1) 3157 1505 -109 137 +1 184306 -4886 375s Number of sequences in alignment.......: 1505 375s Number of sites in alignment...........: 137 375s Number of chars in alignment...........: 184306 375s Mean site entropy in alignment.........: 0.397698 375s Choice Node #seq %seq #sites %sites #chars %chars 375s 1) 3139 1488 -17 138 +1 184277 -29 376s Number of sequences in alignment.......: 1488 376s Number of sites in alignment...........: 138 376s Number of chars in alignment...........: 184277 376s Mean site entropy in alignment.........: 0.396924 376s Choice Node #seq %seq #sites %sites #chars %chars 376s 1) 3136 1485 -3 139 +1 185134 857 376s Number of sequences in alignment.......: 1485 376s Number of sites in alignment...........: 139 376s Number of chars in alignment...........: 185134 376s Mean site entropy in alignment.........: 0.396707 376s Choice Node #seq %seq #sites %sites #chars %chars 376s 1) 3122 1471 -14 140 +1 185214 80 376s Number of sequences in alignment.......: 1471 376s Number of sites in alignment...........: 140 376s Number of chars in alignment...........: 185214 376s Mean site entropy in alignment.........: 0.396624 376s Choice Node #seq %seq #sites %sites #chars %chars 376s 1) 2848 1437 -34 141 +1 183753 -1461 376s Number of sequences in alignment.......: 1437 376s Number of sites in alignment...........: 141 376s Number of chars in alignment...........: 183753 376s Mean site entropy in alignment.........: 0.379676 376s Choice Node #seq %seq #sites %sites #chars %chars 376s 1) 3110 1425 -12 142 +1 183898 145 376s Number of sequences in alignment.......: 1425 376s Number of sites in alignment...........: 142 376s Number of chars in alignment...........: 183898 376s Mean site entropy in alignment.........: 0.379975 376s Choice Node #seq %seq #sites %sites #chars %chars 376s 1) 3073 1387 -38 143 +1 182369 -1529 376s Number of sequences in alignment.......: 1387 376s Number of sites in alignment...........: 143 376s Number of chars in alignment...........: 182369 376s Mean site entropy in alignment.........: 0.376594 376s Choice Node #seq %seq #sites %sites #chars %chars 376s 1) 2904 1380 -7 144 +1 182593 224 377s Number of sequences in alignment.......: 1380 377s Number of sites in alignment...........: 144 377s Number of chars in alignment...........: 182593 377s Mean site entropy in alignment.........: 0.375989 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2941 1206 -174 145 +1 167869 -14724 377s Number of sequences in alignment.......: 1206 377s Number of sites in alignment...........: 145 377s Number of chars in alignment...........: 167869 377s Mean site entropy in alignment.........: 0.346494 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2829 1145 -61 146 +1 162413 -5456 377s Number of sequences in alignment.......: 1145 377s Number of sites in alignment...........: 146 377s Number of chars in alignment...........: 162413 377s Mean site entropy in alignment.........: 0.332586 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2751 1071 -74 147 +1 153723 -8690 377s Number of sequences in alignment.......: 1071 377s Number of sites in alignment...........: 147 377s Number of chars in alignment...........: 153723 377s Mean site entropy in alignment.........: 0.320762 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 1751 998 -73 148 +1 144121 -9602 377s Number of sequences in alignment.......: 998 377s Number of sites in alignment...........: 148 377s Number of chars in alignment...........: 144121 377s Mean site entropy in alignment.........: 0.298818 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2100 985 -13 149 +1 142964 -1157 377s Number of sequences in alignment.......: 985 377s Number of sites in alignment...........: 149 377s Number of chars in alignment...........: 142964 377s Mean site entropy in alignment.........: 0.298279 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2427 665 -320 150 +1 97526 -45438 377s Number of sequences in alignment.......: 665 377s Number of sites in alignment...........: 150 377s Number of chars in alignment...........: 97526 377s Mean site entropy in alignment.........: 0.293825 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 1379 664 -1 151 +1 97882 356 377s Number of sequences in alignment.......: 664 377s Number of sites in alignment...........: 151 377s Number of chars in alignment...........: 97882 377s Mean site entropy in alignment.........: 0.292162 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2203 441 -223 152 +1 65487 -32395 377s Number of sequences in alignment.......: 441 377s Number of sites in alignment...........: 152 377s Number of chars in alignment...........: 65487 377s Mean site entropy in alignment.........: 0.29729 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2189 427 -14 153 +1 63726 -1761 377s Number of sequences in alignment.......: 427 377s Number of sites in alignment...........: 153 377s Number of chars in alignment...........: 63726 377s Mean site entropy in alignment.........: 0.295662 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2082 334 -93 154 +1 50320 -13406 377s Number of sequences in alignment.......: 334 377s Number of sites in alignment...........: 154 377s Number of chars in alignment...........: 50320 377s Mean site entropy in alignment.........: 0.268583 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 2006 258 -76 155 +1 39190 -11130 377s Number of sequences in alignment.......: 258 377s Number of sites in alignment...........: 155 377s Number of chars in alignment...........: 39190 377s Mean site entropy in alignment.........: 0.230649 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 1987 254 -4 156 +1 38780 -410 377s Number of sequences in alignment.......: 254 377s Number of sites in alignment...........: 156 377s Number of chars in alignment...........: 38780 377s Mean site entropy in alignment.........: 0.228398 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 1915 247 -7 157 +1 37896 -884 377s Number of sequences in alignment.......: 247 377s Number of sites in alignment...........: 157 377s Number of chars in alignment...........: 37896 377s Mean site entropy in alignment.........: 0.226904 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 1876 130 -117 158 +1 20276 -17620 377s Number of sequences in alignment.......: 130 377s Number of sites in alignment...........: 158 377s Number of chars in alignment...........: 20276 377s Mean site entropy in alignment.........: 0.134572 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 1704 3 -127 163 +5 489 -19787 377s Number of sequences in alignment.......: 3 377s Number of sites in alignment...........: 163 377s Number of chars in alignment...........: 489 377s Mean site entropy in alignment.........: 0.065727 377s Choice Node #seq %seq #sites %sites #chars %chars 377s 1) 1474 2 -1 167 +4 334 -155 377s Number of sequences in alignment.......: 2 377s Number of sites in alignment...........: 167 377s Number of chars in alignment...........: 334 377s Mean site entropy in alignment.........: 0.0338121 377s Choice Node #seq %seq #sites %sites #chars %chars 377s BppAlnOpt's done. Bye. 377s Total execution time: 0.000000d, 0.000000h, 0.000000m, 14.000000s. 377s ****************************************************************** 377s * Bio++ Alignment Optimizer, version 1.1.0. * 377s * Author: J. Dutheil Last Modif. 14/03/18 * 377s * E. Figuet * 377s ****************************************************************** 377s 377s Parsing options: 377s Parsing file AlnOptimAuto.bpp for options. 377s Alphabet type .........................: Proteic 377s Sequence file .........................: PF01049_full.txt 377s Sequence format .......................: FASTA file 378s Minimum amount of data per site........: 0.7 378s Filter gap characters..................: yes 378s Filter unresolved characters...........: yes 378s Number of reference sequences..........: 0 378s Total number of sequences..............: 1652 378s Total number of sites..................: 656 378s Compressing sequences..................: 378s [ ] 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. 378s Memory required to store distances (Mb): 20 378s Computing pairwise overlap matrix......: 381s [> ] 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. 381s Clustering linkage mode................: average 381s Computing cluster tree.................: 389s [ ] 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. 389s Comparison criterion:..................: MaxSites 389s Number of sequences in alignment.......: 1652 389s Number of sites in alignment...........: 129 389s Number of chars in alignment...........: 182603 389s Mean site entropy in alignment.........: 0.394104 389s Choice Node #seq %seq #sites %sites #chars %chars 389s 1) 3299 1647 -5 131 +2 184774 2171 390s Number of sequences in alignment.......: 1647 390s Number of sites in alignment...........: 131 390s Number of chars in alignment...........: 184774 390s Mean site entropy in alignment.........: 0.394431 390s Choice Node #seq %seq #sites %sites #chars %chars 390s 1) 3293 1645 -2 132 +1 185875 1101 390s Number of sequences in alignment.......: 1645 390s Number of sites in alignment...........: 132 390s Number of chars in alignment...........: 185875 390s Mean site entropy in alignment.........: 0.394643 390s Choice Node #seq %seq #sites %sites #chars %chars 390s 1) 181 1644 -1 133 +1 186999 1124 390s Number of sequences in alignment.......: 1644 390s Number of sites in alignment...........: 133 390s Number of chars in alignment...........: 186999 390s Mean site entropy in alignment.........: 0.394599 390s Choice Node #seq %seq #sites %sites #chars %chars 390s 1) 3287 1634 -10 134 +1 187779 780 390s Number of sequences in alignment.......: 1634 390s Number of sites in alignment...........: 134 390s Number of chars in alignment...........: 187779 390s Mean site entropy in alignment.........: 0.395631 390s Choice Node #seq %seq #sites %sites #chars %chars 390s 1) 3276 1627 -7 135 +1 188617 838 390s Number of sequences in alignment.......: 1627 390s Number of sites in alignment...........: 135 390s Number of chars in alignment...........: 188617 390s Mean site entropy in alignment.........: 0.396076 390s Choice Node #seq %seq #sites %sites #chars %chars 390s 1) 3238 1614 -13 136 +1 189013 396 390s Number of sequences in alignment.......: 1614 390s Number of sites in alignment...........: 136 390s Number of chars in alignment...........: 189013 390s Mean site entropy in alignment.........: 0.395128 390s Choice Node #seq %seq #sites %sites #chars %chars 390s 1) 3023 1533 -81 138 +2 185240 -3773 391s Number of sequences in alignment.......: 1533 391s Number of sites in alignment...........: 138 391s Number of chars in alignment...........: 185240 391s Mean site entropy in alignment.........: 0.372196 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 1629 1532 -1 139 +1 186276 1036 391s Number of sequences in alignment.......: 1532 391s Number of sites in alignment...........: 139 391s Number of chars in alignment...........: 186276 391s Mean site entropy in alignment.........: 0.372208 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 3282 1521 -11 140 +1 186867 591 391s Number of sequences in alignment.......: 1521 391s Number of sites in alignment...........: 140 391s Number of chars in alignment...........: 186867 391s Mean site entropy in alignment.........: 0.372497 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 3105 1482 -39 141 +1 185210 -1657 391s Number of sequences in alignment.......: 1482 391s Number of sites in alignment...........: 141 391s Number of chars in alignment...........: 185210 391s Mean site entropy in alignment.........: 0.368185 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 3135 1471 -11 142 +1 185562 352 391s Number of sequences in alignment.......: 1471 391s Number of sites in alignment...........: 142 391s Number of chars in alignment...........: 185562 391s Mean site entropy in alignment.........: 0.367384 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 2863 1455 -16 143 +1 184869 -693 391s Number of sequences in alignment.......: 1455 391s Number of sites in alignment...........: 143 391s Number of chars in alignment...........: 184869 391s Mean site entropy in alignment.........: 0.366056 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 3166 1413 -42 144 +1 183102 -1767 391s Number of sequences in alignment.......: 1413 391s Number of sites in alignment...........: 144 391s Number of chars in alignment...........: 183102 391s Mean site entropy in alignment.........: 0.362023 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 2996 1204 -209 145 +1 168239 -14863 391s Number of sequences in alignment.......: 1204 391s Number of sites in alignment...........: 145 391s Number of chars in alignment...........: 168239 391s Mean site entropy in alignment.........: 0.339856 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 2960 1154 -50 146 +1 163602 -4637 391s Number of sequences in alignment.......: 1154 391s Number of sites in alignment...........: 146 391s Number of chars in alignment...........: 163602 391s Mean site entropy in alignment.........: 0.330406 391s Choice Node #seq %seq #sites %sites #chars %chars 391s 1) 2809 1097 -57 147 +1 157455 -6147 392s Number of sequences in alignment.......: 1097 392s Number of sites in alignment...........: 147 392s Number of chars in alignment...........: 157455 392s Mean site entropy in alignment.........: 0.314798 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2635 1063 -34 148 +1 153359 -4096 392s Number of sequences in alignment.......: 1063 392s Number of sites in alignment...........: 148 392s Number of chars in alignment...........: 153359 392s Mean site entropy in alignment.........: 0.316144 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 1948 1048 -15 149 +1 151998 -1361 392s Number of sequences in alignment.......: 1048 392s Number of sites in alignment...........: 149 392s Number of chars in alignment...........: 151998 392s Mean site entropy in alignment.........: 0.31084 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2069 1031 -17 150 +1 150327 -1671 392s Number of sequences in alignment.......: 1031 392s Number of sites in alignment...........: 150 392s Number of chars in alignment...........: 150327 392s Mean site entropy in alignment.........: 0.303727 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2640 451 -580 151 +1 67067 -83260 392s Number of sequences in alignment.......: 451 392s Number of sites in alignment...........: 151 392s Number of chars in alignment...........: 67067 392s Mean site entropy in alignment.........: 0.278258 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2555 425 -26 152 +1 63569 -3498 392s Number of sequences in alignment.......: 425 392s Number of sites in alignment...........: 152 392s Number of chars in alignment...........: 63569 392s Mean site entropy in alignment.........: 0.276822 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2332 391 -34 153 +1 58841 -4728 392s Number of sequences in alignment.......: 391 392s Number of sites in alignment...........: 153 392s Number of chars in alignment...........: 58841 392s Mean site entropy in alignment.........: 0.269678 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2039 342 -49 154 +1 51693 -7148 392s Number of sequences in alignment.......: 342 392s Number of sites in alignment...........: 154 392s Number of chars in alignment...........: 51693 392s Mean site entropy in alignment.........: 0.250803 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2337 280 -62 155 +1 42698 -8995 392s Number of sequences in alignment.......: 280 392s Number of sites in alignment...........: 155 392s Number of chars in alignment...........: 42698 392s Mean site entropy in alignment.........: 0.230831 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 1969 277 -3 156 +1 42454 -244 392s Number of sequences in alignment.......: 277 392s Number of sites in alignment...........: 156 392s Number of chars in alignment...........: 42454 392s Mean site entropy in alignment.........: 0.228862 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 2097 246 -31 157 +1 37949 -4505 392s Number of sequences in alignment.......: 246 392s Number of sites in alignment...........: 157 392s Number of chars in alignment...........: 37949 392s Mean site entropy in alignment.........: 0.216654 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 884 245 -1 158 +1 37976 27 392s Number of sequences in alignment.......: 245 392s Number of sites in alignment...........: 158 392s Number of chars in alignment...........: 37976 392s Mean site entropy in alignment.........: 0.215946 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 1937 19 -226 163 +5 3067 -34909 392s Number of sequences in alignment.......: 19 392s Number of sites in alignment...........: 163 392s Number of chars in alignment...........: 3067 392s Mean site entropy in alignment.........: 0.115126 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 1719 14 -5 165 +2 2297 -770 392s Number of sequences in alignment.......: 14 392s Number of sites in alignment...........: 165 392s Number of chars in alignment...........: 2297 392s Mean site entropy in alignment.........: 0.0991142 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 1699 12 -2 166 +1 1983 -314 392s Number of sequences in alignment.......: 12 392s Number of sites in alignment...........: 166 392s Number of chars in alignment...........: 1983 392s Mean site entropy in alignment.........: 0.0379699 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 397 11 -1 168 +2 1838 -145 392s Number of sequences in alignment.......: 11 392s Number of sites in alignment...........: 168 392s Number of chars in alignment...........: 1838 392s Mean site entropy in alignment.........: 0.03305 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 1684 8 -3 169 +1 1349 -489 392s Number of sequences in alignment.......: 8 392s Number of sites in alignment...........: 169 392s Number of chars in alignment...........: 1349 392s Mean site entropy in alignment.........: 0.0183685 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 46 7 -1 172 +3 1196 -153 392s Number of sequences in alignment.......: 7 392s Number of sites in alignment...........: 172 392s Number of chars in alignment...........: 1196 392s Mean site entropy in alignment.........: 0.0178367 392s Choice Node #seq %seq #sites %sites #chars %chars 392s 1) 1664 2 -5 176 +4 352 -844 392s Number of sequences in alignment.......: 2 392s Number of sites in alignment...........: 176 392s Number of chars in alignment...........: 352 392s Mean site entropy in alignment.........: 0.010038 392s Choice Node #seq %seq #sites %sites #chars %chars 392s BppAlnOpt's done. Bye. 392s Total execution time: 0.000000d, 0.000000h, 0.000000m, 15.000000s. 392s ****************************************************************** 392s * Bio++ Alignment Optimizer, version 1.1.0. * 392s * Author: J. Dutheil Last Modif. 14/03/18 * 392s * E. Figuet * 392s ****************************************************************** 392s 392s Parsing options: 392s Parsing file AlnOptimAuto.bpp for options. 392s Alphabet type .........................: Proteic 392s Sequence file .........................: PF01049_full.txt 392s Sequence format .......................: FASTA file 392s Minimum amount of data per site........: 0.7 392s Filter gap characters..................: yes 392s Filter unresolved characters...........: yes 392s Number of reference sequences..........: 0 392s Total number of sequences..............: 1652 392s Total number of sites..................: 656 392s Compressing sequences..................: 392s [ ] 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. 392s Memory required to store distances (Mb): 20 392s Computing pairwise overlap matrix......: 395s [> ] 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. 395s Clustering linkage mode................: median 395s Computing cluster tree.................: 403s [ ] 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. 403s Comparison criterion:..................: MaxSites 403s Number of sequences in alignment.......: 1652 403s Number of sites in alignment...........: 129 403s Number of chars in alignment...........: 182603 403s Mean site entropy in alignment.........: 0.394104 403s Choice Node #seq %seq #sites %sites #chars %chars 403s 1) 3297 1647 -5 131 +2 184774 2171 404s Number of sequences in alignment.......: 1647 404s Number of sites in alignment...........: 131 404s Number of chars in alignment...........: 184774 404s Mean site entropy in alignment.........: 0.394431 404s Choice Node #seq %seq #sites %sites #chars %chars 404s 1) 3295 1645 -2 132 +1 185873 1099 404s Number of sequences in alignment.......: 1645 404s Number of sites in alignment...........: 132 404s Number of chars in alignment...........: 185873 404s Mean site entropy in alignment.........: 0.394618 404s Choice Node #seq %seq #sites %sites #chars %chars 404s 1) 275 1644 -1 133 +1 186998 1125 404s Number of sequences in alignment.......: 1644 404s Number of sites in alignment...........: 133 404s Number of chars in alignment...........: 186998 404s Mean site entropy in alignment.........: 0.394724 404s Choice Node #seq %seq #sites %sites #chars %chars 404s 1) 3280 1630 -14 134 +1 187559 561 404s Number of sequences in alignment.......: 1630 404s Number of sites in alignment...........: 134 404s Number of chars in alignment...........: 187559 404s Mean site entropy in alignment.........: 0.39546 404s Choice Node #seq %seq #sites %sites #chars %chars 404s 1) 3272 1622 -8 135 +1 188376 817 405s Number of sequences in alignment.......: 1622 405s Number of sites in alignment...........: 135 405s Number of chars in alignment...........: 188376 405s Mean site entropy in alignment.........: 0.396213 405s Choice Node #seq %seq #sites %sites #chars %chars 405s 1) 3261 1611 -11 136 +1 189031 655 405s Number of sequences in alignment.......: 1611 405s Number of sites in alignment...........: 136 405s Number of chars in alignment...........: 189031 405s Mean site entropy in alignment.........: 0.396902 405s Choice Node #seq %seq #sites %sites #chars %chars 405s 1) 3184 1534 -77 137 +1 185562 -3469 405s Number of sequences in alignment.......: 1534 405s Number of sites in alignment...........: 137 405s Number of chars in alignment...........: 185562 405s Mean site entropy in alignment.........: 0.396433 405s Choice Node #seq %seq #sites %sites #chars %chars 405s 1) 3182 1532 -2 138 +1 186503 941 405s Number of sequences in alignment.......: 1532 405s Number of sites in alignment...........: 138 405s Number of chars in alignment...........: 186503 405s Mean site entropy in alignment.........: 0.396422 405s Choice Node #seq %seq #sites %sites #chars %chars 405s 1) 513 1531 -1 139 +1 187535 1032 405s Number of sequences in alignment.......: 1531 405s Number of sites in alignment...........: 139 405s Number of chars in alignment...........: 187535 405s Mean site entropy in alignment.........: 0.396222 405s Choice Node #seq %seq #sites %sites #chars %chars 405s 1) 3169 1518 -13 140 +1 187760 225 406s Number of sequences in alignment.......: 1518 406s Number of sites in alignment...........: 140 406s Number of chars in alignment...........: 187760 406s Mean site entropy in alignment.........: 0.395785 406s Choice Node #seq %seq #sites %sites #chars %chars 406s 1) 3125 1475 -43 141 +1 185962 -1798 406s Number of sequences in alignment.......: 1475 406s Number of sites in alignment...........: 141 406s Number of chars in alignment...........: 185962 406s Mean site entropy in alignment.........: 0.388512 406s Choice Node #seq %seq #sites %sites #chars %chars 406s 1) 3117 1467 -8 142 +1 186502 540 406s Number of sequences in alignment.......: 1467 406s Number of sites in alignment...........: 142 406s Number of chars in alignment...........: 186502 406s Mean site entropy in alignment.........: 0.388016 406s Choice Node #seq %seq #sites %sites #chars %chars 406s 1) 3102 1452 -15 143 +1 186490 -12 406s Number of sequences in alignment.......: 1452 406s Number of sites in alignment...........: 143 406s Number of chars in alignment...........: 186490 406s Mean site entropy in alignment.........: 0.386609 406s Choice Node #seq %seq #sites %sites #chars %chars 406s 1) 3052 1402 -50 144 +1 183727 -2763 406s Number of sequences in alignment.......: 1402 406s Number of sites in alignment...........: 144 406s Number of chars in alignment...........: 183727 406s Mean site entropy in alignment.........: 0.379315 406s Choice Node #seq %seq #sites %sites #chars %chars 406s 1) 2877 1227 -175 145 +1 170235 -13492 407s Number of sequences in alignment.......: 1227 407s Number of sites in alignment...........: 145 407s Number of chars in alignment...........: 170235 407s Mean site entropy in alignment.........: 0.34859 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2788 1138 -89 146 +1 161621 -8614 407s Number of sequences in alignment.......: 1138 407s Number of sites in alignment...........: 146 407s Number of chars in alignment...........: 161621 407s Mean site entropy in alignment.........: 0.330459 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2731 1081 -57 147 +1 155136 -6485 407s Number of sequences in alignment.......: 1081 407s Number of sites in alignment...........: 147 407s Number of chars in alignment...........: 155136 407s Mean site entropy in alignment.........: 0.319787 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 1701 1030 -51 148 +1 148555 -6581 407s Number of sequences in alignment.......: 1030 407s Number of sites in alignment...........: 148 407s Number of chars in alignment...........: 148555 407s Mean site entropy in alignment.........: 0.305707 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2499 798 -232 149 +1 116805 -31750 407s Number of sequences in alignment.......: 798 407s Number of sites in alignment...........: 149 407s Number of chars in alignment...........: 116805 407s Mean site entropy in alignment.........: 0.273968 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2468 767 -31 150 +1 112894 -3911 407s Number of sequences in alignment.......: 767 407s Number of sites in alignment...........: 150 407s Number of chars in alignment...........: 112894 407s Mean site entropy in alignment.........: 0.272075 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2239 538 -229 151 +1 79674 -33220 407s Number of sequences in alignment.......: 538 407s Number of sites in alignment...........: 151 407s Number of chars in alignment...........: 79674 407s Mean site entropy in alignment.........: 0.280963 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2196 495 -43 152 +1 73702 -5972 407s Number of sequences in alignment.......: 495 407s Number of sites in alignment...........: 152 407s Number of chars in alignment...........: 73702 407s Mean site entropy in alignment.........: 0.28148 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2076 375 -120 153 +1 56316 -17386 407s Number of sequences in alignment.......: 375 407s Number of sites in alignment...........: 153 407s Number of chars in alignment...........: 56316 407s Mean site entropy in alignment.........: 0.267502 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 2018 317 -58 154 +1 47977 -8339 407s Number of sequences in alignment.......: 317 407s Number of sites in alignment...........: 154 407s Number of chars in alignment...........: 47977 407s Mean site entropy in alignment.........: 0.249671 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 1949 248 -69 155 +1 37817 -10160 407s Number of sequences in alignment.......: 248 407s Number of sites in alignment...........: 155 407s Number of chars in alignment...........: 37817 407s Mean site entropy in alignment.........: 0.215239 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 1938 237 -11 156 +1 36376 -1441 407s Number of sequences in alignment.......: 237 407s Number of sites in alignment...........: 156 407s Number of chars in alignment...........: 36376 407s Mean site entropy in alignment.........: 0.201826 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 1926 225 -12 157 +1 34752 -1624 407s Number of sequences in alignment.......: 225 407s Number of sites in alignment...........: 157 407s Number of chars in alignment...........: 34752 407s Mean site entropy in alignment.........: 0.184033 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 1779 78 -147 158 +1 12282 -22470 407s Number of sequences in alignment.......: 78 407s Number of sites in alignment...........: 158 407s Number of chars in alignment...........: 12282 407s Mean site entropy in alignment.........: 0.0830049 407s Choice Node #seq %seq #sites %sites #chars %chars 407s 1) 1703 2 -76 160 +2 320 -11962 407s Number of sequences in alignment.......: 2 407s Number of sites in alignment...........: 160 407s Number of chars in alignment...........: 320 407s Mean site entropy in alignment.........: 0 407s Choice Node #seq %seq #sites %sites #chars %chars 407s BppAlnOpt's done. Bye. 407s Total execution time: 0.000000d, 0.000000h, 0.000000m, 15.000000s. 407s ****************************************************************** 407s * Bio++ Alignment Optimizer, version 1.1.0. * 407s * Author: J. Dutheil Last Modif. 14/03/18 * 407s * E. Figuet * 407s ****************************************************************** 407s 407s Parsing options: 407s Parsing file AlnOptimAuto.bpp for options. 407s Alphabet type .........................: Proteic 407s Sequence file .........................: PF01049_full.txt 407s Sequence format .......................: FASTA file 408s Minimum amount of data per site........: 0.7 408s Filter gap characters..................: yes 408s Filter unresolved characters...........: yes 408s Number of reference sequences..........: 0 408s Total number of sequences..............: 1652 408s Total number of sites..................: 656 408s Compressing sequences..................: 408s [ ] 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. 408s Memory required to store distances (Mb): 20 408s Computing pairwise overlap matrix......: 411s [> ] 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. 411s Clustering linkage mode................: centroid 411s Computing cluster tree.................: 419s [ ] 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. 419s Comparison criterion:..................: MaxSites 419s Number of sequences in alignment.......: 1652 419s Number of sites in alignment...........: 129 419s Number of chars in alignment...........: 182603 419s Mean site entropy in alignment.........: 0.394104 419s Choice Node #seq %seq #sites %sites #chars %chars 419s 1) 3297 1647 -5 131 +2 184783 2180 419s Number of sequences in alignment.......: 1647 419s Number of sites in alignment...........: 131 419s Number of chars in alignment...........: 184783 419s Mean site entropy in alignment.........: 0.394537 419s Choice Node #seq %seq #sites %sites #chars %chars 419s 1) 3295 1645 -2 132 +1 185880 1097 420s Number of sequences in alignment.......: 1645 420s Number of sites in alignment...........: 132 420s Number of chars in alignment...........: 185880 420s Mean site entropy in alignment.........: 0.394662 420s Choice Node #seq %seq #sites %sites #chars %chars 420s 1) 181 1644 -1 133 +1 187004 1124 420s Number of sequences in alignment.......: 1644 420s Number of sites in alignment...........: 133 420s Number of chars in alignment...........: 187004 420s Mean site entropy in alignment.........: 0.394618 420s Choice Node #seq %seq #sites %sites #chars %chars 420s 1) 3284 1634 -10 134 +1 187785 781 420s Number of sequences in alignment.......: 1634 420s Number of sites in alignment...........: 134 420s Number of chars in alignment...........: 187785 420s Mean site entropy in alignment.........: 0.395449 420s Choice Node #seq %seq #sites %sites #chars %chars 420s 1) 3277 1627 -7 135 +1 188649 864 420s Number of sequences in alignment.......: 1627 420s Number of sites in alignment...........: 135 420s Number of chars in alignment...........: 188649 420s Mean site entropy in alignment.........: 0.395884 420s Choice Node #seq %seq #sites %sites #chars %chars 420s 1) 3264 1614 -13 136 +1 189270 621 420s Number of sequences in alignment.......: 1614 420s Number of sites in alignment...........: 136 420s Number of chars in alignment...........: 189270 420s Mean site entropy in alignment.........: 0.396209 420s Choice Node #seq %seq #sites %sites #chars %chars 420s 1) 3158 1508 -106 137 +1 184807 -4463 421s Number of sequences in alignment.......: 1508 421s Number of sites in alignment...........: 137 421s Number of chars in alignment...........: 184807 421s Mean site entropy in alignment.........: 0.391659 421s Choice Node #seq %seq #sites %sites #chars %chars 421s 1) 3141 1491 -17 138 +1 184810 3 421s Number of sequences in alignment.......: 1491 421s Number of sites in alignment...........: 138 421s Number of chars in alignment...........: 184810 421s Mean site entropy in alignment.........: 0.389899 421s Choice Node #seq %seq #sites %sites #chars %chars 421s 1) 3135 1485 -6 139 +1 185468 658 421s Number of sequences in alignment.......: 1485 421s Number of sites in alignment...........: 139 421s Number of chars in alignment...........: 185468 421s Mean site entropy in alignment.........: 0.389868 421s Choice Node #seq %seq #sites %sites #chars %chars 421s 1) 3124 1474 -11 140 +1 185788 320 421s Number of sequences in alignment.......: 1474 421s Number of sites in alignment...........: 140 421s Number of chars in alignment...........: 185788 421s Mean site entropy in alignment.........: 0.389071 421s Choice Node #seq %seq #sites %sites #chars %chars 421s 1) 3091 1441 -33 141 +1 184655 -1133 421s Number of sequences in alignment.......: 1441 421s Number of sites in alignment...........: 141 421s Number of chars in alignment...........: 184655 421s Mean site entropy in alignment.........: 0.38709 421s Choice Node #seq %seq #sites %sites #chars %chars 421s 1) 3077 1427 -14 142 +1 184714 59 422s Number of sequences in alignment.......: 1427 422s Number of sites in alignment...........: 142 422s Number of chars in alignment...........: 184714 422s Mean site entropy in alignment.........: 0.386526 422s Choice Node #seq %seq #sites %sites #chars %chars 422s 1) 3055 1405 -22 144 +2 185186 472 422s Number of sequences in alignment.......: 1405 422s Number of sites in alignment...........: 144 422s Number of chars in alignment...........: 185186 422s Mean site entropy in alignment.........: 0.383626 422s Choice Node #seq %seq #sites %sites #chars %chars 422s 1) 2907 1257 -148 145 +1 173927 -11259 422s Number of sequences in alignment.......: 1257 422s Number of sites in alignment...........: 145 422s Number of chars in alignment...........: 173927 422s Mean site entropy in alignment.........: 0.350796 422s Choice Node #seq %seq #sites %sites #chars %chars 422s 1) 2807 1157 -100 146 +1 163983 -9944 422s Number of sequences in alignment.......: 1157 422s Number of sites in alignment...........: 146 422s Number of chars in alignment...........: 163983 422s Mean site entropy in alignment.........: 0.329626 422s Choice Node #seq %seq #sites %sites #chars %chars 422s 1) 2748 1098 -59 147 +1 157592 -6391 422s Number of sequences in alignment.......: 1098 422s Number of sites in alignment...........: 147 422s Number of chars in alignment...........: 157592 422s Mean site entropy in alignment.........: 0.314432 422s Choice Node #seq %seq #sites %sites #chars %chars 422s 1) 1678 1070 -28 148 +1 154399 -3193 422s Number of sequences in alignment.......: 1070 422s Number of sites in alignment...........: 148 422s Number of chars in alignment...........: 154399 422s Mean site entropy in alignment.........: 0.303382 422s Choice Node #seq %seq #sites %sites #chars %chars 422s 1) 2620 942 -128 149 +1 137516 -16883 422s Number of sequences in alignment.......: 942 422s Number of sites in alignment...........: 149 422s Number of chars in alignment...........: 137516 422s Mean site entropy in alignment.........: 0.284952 422s Choice Node #seq %seq #sites %sites #chars %chars 422s 1) 2615 937 -5 150 +1 137462 -54 423s Number of sequences in alignment.......: 937 423s Number of sites in alignment...........: 150 423s Number of chars in alignment...........: 137462 423s Mean site entropy in alignment.........: 0.285064 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 2320 642 -295 151 +1 95140 -42322 423s Number of sequences in alignment.......: 642 423s Number of sites in alignment...........: 151 423s Number of chars in alignment...........: 95140 423s Mean site entropy in alignment.........: 0.276628 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 2179 501 -141 152 +1 74734 -20406 423s Number of sequences in alignment.......: 501 423s Number of sites in alignment...........: 152 423s Number of chars in alignment...........: 74734 423s Mean site entropy in alignment.........: 0.281366 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 2108 430 -71 153 +1 64604 -10130 423s Number of sequences in alignment.......: 430 423s Number of sites in alignment...........: 153 423s Number of chars in alignment...........: 64604 423s Mean site entropy in alignment.........: 0.282214 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 2038 360 -70 154 +1 54522 -10082 423s Number of sequences in alignment.......: 360 423s Number of sites in alignment...........: 154 423s Number of chars in alignment...........: 54522 423s Mean site entropy in alignment.........: 0.265356 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 1969 291 -69 155 +1 44461 -10061 423s Number of sequences in alignment.......: 291 423s Number of sites in alignment...........: 155 423s Number of chars in alignment...........: 44461 423s Mean site entropy in alignment.........: 0.240018 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 1956 278 -13 156 +1 42693 -1768 423s Number of sequences in alignment.......: 278 423s Number of sites in alignment...........: 156 423s Number of chars in alignment...........: 42693 423s Mean site entropy in alignment.........: 0.236678 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 1925 247 -31 157 +1 38195 -4498 423s Number of sequences in alignment.......: 247 423s Number of sites in alignment...........: 157 423s Number of chars in alignment...........: 38195 423s Mean site entropy in alignment.........: 0.216008 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 1923 245 -2 158 +1 38065 -130 423s Number of sequences in alignment.......: 245 423s Number of sites in alignment...........: 158 423s Number of chars in alignment...........: 38065 423s Mean site entropy in alignment.........: 0.215165 423s Choice Node #seq %seq #sites %sites #chars %chars 423s 1) 610 1 -244 177 +19 177 -37888 423s Number of sequences in alignment.......: 1 423s Number of sites in alignment...........: 177 423s Number of chars in alignment...........: 177 423s Mean site entropy in alignment.........: 0 423s Choice Node #seq %seq #sites %sites #chars %chars 423s BppAlnOpt's done. Bye. 423s Total execution time: 0.000000d, 0.000000h, 0.000000m, 16.000000s. 423s ****************************************************************** 423s * Bio++ Alignment Optimizer, version 1.1.0. * 423s * Author: J. Dutheil Last Modif. 14/03/18 * 423s * E. Figuet * 423s ****************************************************************** 423s 423s Parsing options: 423s Parsing file AlnOptimAuto.bpp for options. 423s Alphabet type .........................: Proteic 423s Sequence file .........................: PF01049_full.txt 423s Sequence format .......................: FASTA file 423s Minimum amount of data per site........: 0.7 423s Filter gap characters..................: yes 423s Filter unresolved characters...........: yes 423s Number of reference sequences..........: 0 423s Total number of sequences..............: 1652 423s Total number of sites..................: 656 423s Compressing sequences..................: 423s [ ] 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. 423s Memory required to store distances (Mb): 20 423s Computing pairwise overlap matrix......: 426s [> ] 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. 426s Clustering linkage mode................: ward 426s Computing cluster tree.................: 434s [ ] 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. 435s Comparison criterion:..................: MaxSites 435s Number of sequences in alignment.......: 1652 435s Number of sites in alignment...........: 129 435s Number of chars in alignment...........: 182603 435s Mean site entropy in alignment.........: 0.394104 435s Choice Node #seq %seq #sites %sites #chars %chars 435s 1) 3251 1647 -5 131 +2 184716 2113 435s Number of sequences in alignment.......: 1647 435s Number of sites in alignment...........: 131 435s Number of chars in alignment...........: 184716 435s Mean site entropy in alignment.........: 0.394659 435s Choice Node #seq %seq #sites %sites #chars %chars 435s 1) 3238 1645 -2 132 +1 185817 1101 435s Number of sequences in alignment.......: 1645 435s Number of sites in alignment...........: 132 435s Number of chars in alignment...........: 185817 435s Mean site entropy in alignment.........: 0.394872 435s Choice Node #seq %seq #sites %sites #chars %chars 435s 1) 626 1644 -1 133 +1 186943 1126 435s Number of sequences in alignment.......: 1644 435s Number of sites in alignment...........: 133 435s Number of chars in alignment...........: 186943 435s Mean site entropy in alignment.........: 0.394963 435s Choice Node #seq %seq #sites %sites #chars %chars 435s 1) 3225 1634 -10 134 +1 187538 595 435s Number of sequences in alignment.......: 1634 435s Number of sites in alignment...........: 134 435s Number of chars in alignment...........: 187538 435s Mean site entropy in alignment.........: 0.395167 435s Choice Node #seq %seq #sites %sites #chars %chars 435s 1) 3259 1627 -7 135 +1 188469 931 435s Number of sequences in alignment.......: 1627 435s Number of sites in alignment...........: 135 435s Number of chars in alignment...........: 188469 435s Mean site entropy in alignment.........: 0.39572 435s Choice Node #seq %seq #sites %sites #chars %chars 435s 1) 3231 1614 -13 136 +1 189043 574 435s Number of sequences in alignment.......: 1614 435s Number of sites in alignment...........: 136 435s Number of chars in alignment...........: 189043 435s Mean site entropy in alignment.........: 0.396503 435s Choice Node #seq %seq #sites %sites #chars %chars 435s 1) 3276 1530 -84 139 +3 186415 -2628 436s Number of sequences in alignment.......: 1530 436s Number of sites in alignment...........: 139 436s Number of chars in alignment...........: 186415 436s Mean site entropy in alignment.........: 0.389001 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3232 1521 -9 140 +1 187030 615 436s Number of sequences in alignment.......: 1521 436s Number of sites in alignment...........: 140 436s Number of chars in alignment...........: 187030 436s Mean site entropy in alignment.........: 0.389238 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3267 1485 -36 141 +1 185744 -1286 436s Number of sequences in alignment.......: 1485 436s Number of sites in alignment...........: 141 436s Number of chars in alignment...........: 185744 436s Mean site entropy in alignment.........: 0.389095 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3288 1470 -15 142 +1 185982 238 436s Number of sequences in alignment.......: 1470 436s Number of sites in alignment...........: 142 436s Number of chars in alignment...........: 185982 436s Mean site entropy in alignment.........: 0.38758 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3098 1457 -13 143 +1 185643 -339 436s Number of sequences in alignment.......: 1457 436s Number of sites in alignment...........: 143 436s Number of chars in alignment...........: 185643 436s Mean site entropy in alignment.........: 0.385646 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3289 1411 -46 144 +1 183758 -1885 436s Number of sequences in alignment.......: 1411 436s Number of sites in alignment...........: 144 436s Number of chars in alignment...........: 183758 436s Mean site entropy in alignment.........: 0.38204 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3273 1313 -98 145 +1 171322 -12436 436s Number of sequences in alignment.......: 1313 436s Number of sites in alignment...........: 145 436s Number of chars in alignment...........: 171322 436s Mean site entropy in alignment.........: 0.380643 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3299 1133 -180 147 +2 152385 -18937 436s Number of sequences in alignment.......: 1133 436s Number of sites in alignment...........: 147 436s Number of chars in alignment...........: 152385 436s Mean site entropy in alignment.........: 0.346351 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 2941 1121 -12 148 +1 152294 -91 436s Number of sequences in alignment.......: 1121 436s Number of sites in alignment...........: 148 436s Number of chars in alignment...........: 152294 436s Mean site entropy in alignment.........: 0.340977 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 1664 1115 -6 149 +1 152613 319 436s Number of sequences in alignment.......: 1115 436s Number of sites in alignment...........: 149 436s Number of chars in alignment...........: 152613 436s Mean site entropy in alignment.........: 0.336552 436s Choice Node #seq %seq #sites %sites #chars %chars 436s 1) 3193 1104 -11 150 +1 152591 -22 436s Number of sequences in alignment.......: 1104 436s Number of sites in alignment...........: 150 436s Number of chars in alignment...........: 152591 436s Mean site entropy in alignment.........: 0.330411 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 2891 153 -951 157 +7 23971 -128620 437s Number of sequences in alignment.......: 153 437s Number of sites in alignment...........: 157 437s Number of chars in alignment...........: 23971 437s Mean site entropy in alignment.........: 0.0601394 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 1887 120 -33 158 +1 18876 -5095 437s Number of sequences in alignment.......: 120 437s Number of sites in alignment...........: 158 437s Number of chars in alignment...........: 18876 437s Mean site entropy in alignment.........: 0.0586193 437s Choice Node #seq %seq #sites %sites #chars %chars 437s BppAlnOpt's done. Bye. 437s Total execution time: 0.000000d, 0.000000h, 0.000000m, 13.000000s. 437s ****************************************************************** 437s * Bio++ Alignment Optimizer, version 1.1.0. * 437s * Author: J. Dutheil Last Modif. 14/03/18 * 437s * E. Figuet * 437s ****************************************************************** 437s 437s Parsing options: 437s Parsing file AlnOptimFasttreeStop.bpp for options. 437s Alphabet type .........................: Proteic 437s Sequence file .........................: PF01049_full.txt 437s Sequence format .......................: FASTA file 437s Minimum amount of data per site........: 0.7 437s Filter gap characters..................: yes 437s Filter unresolved characters...........: yes 437s Number of reference sequences..........: 0 437s Total number of sequences..............: 1652 437s Total number of sites..................: 656 437s Input tree file .......................: PF01049_fasttree.dnd 437s Input tree format .....................: Newick 437s Minimum number of sequences to keep....: 826 437s Comparison criterion:..................: MaxSites 437s Number of sequences in alignment.......: 1652 437s Number of sites in alignment...........: 129 437s Number of chars in alignment...........: 182603 437s Mean site entropy in alignment.........: 0.394104 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 2030 1647 -5 131 +2 184714 2111 437s Number of sequences in alignment.......: 1647 437s Number of sites in alignment...........: 131 437s Number of chars in alignment...........: 184714 437s Mean site entropy in alignment.........: 0.394129 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 1930 1645 -2 132 +1 185794 1080 437s Number of sequences in alignment.......: 1645 437s Number of sites in alignment...........: 132 437s Number of chars in alignment...........: 185794 437s Mean site entropy in alignment.........: 0.394195 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 1882 1644 -1 133 +1 186920 1126 437s Number of sequences in alignment.......: 1644 437s Number of sites in alignment...........: 133 437s Number of chars in alignment...........: 186920 437s Mean site entropy in alignment.........: 0.394263 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 386 1634 -10 134 +1 187634 714 437s Number of sequences in alignment.......: 1634 437s Number of sites in alignment...........: 134 437s Number of chars in alignment...........: 187634 437s Mean site entropy in alignment.........: 0.394887 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 357 1627 -7 135 +1 188437 803 437s Number of sequences in alignment.......: 1627 437s Number of sites in alignment...........: 135 437s Number of chars in alignment...........: 188437 437s Mean site entropy in alignment.........: 0.394741 437s Choice Node #seq %seq #sites %sites #chars %chars 437s 1) 1736 1614 -13 136 +1 188713 276 438s Number of sequences in alignment.......: 1614 438s Number of sites in alignment...........: 136 438s Number of chars in alignment...........: 188713 438s Mean site entropy in alignment.........: 0.394145 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 1489 1527 -87 137 +1 181488 -7225 438s Number of sequences in alignment.......: 1527 438s Number of sites in alignment...........: 137 438s Number of chars in alignment...........: 181488 438s Mean site entropy in alignment.........: 0.378687 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 2247 1524 -3 138 +1 182435 947 438s Number of sequences in alignment.......: 1524 438s Number of sites in alignment...........: 138 438s Number of chars in alignment...........: 182435 438s Mean site entropy in alignment.........: 0.378731 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 408 1515 -9 139 +1 183008 573 438s Number of sequences in alignment.......: 1515 438s Number of sites in alignment...........: 139 438s Number of chars in alignment...........: 183008 438s Mean site entropy in alignment.........: 0.377294 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 1819 1488 -27 140 +1 182208 -800 438s Number of sequences in alignment.......: 1488 438s Number of sites in alignment...........: 140 438s Number of chars in alignment...........: 182208 438s Mean site entropy in alignment.........: 0.374188 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 1676 1464 -24 141 +1 180695 -1513 438s Number of sequences in alignment.......: 1464 438s Number of sites in alignment...........: 141 438s Number of chars in alignment...........: 180695 438s Mean site entropy in alignment.........: 0.371696 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 416 1457 -7 142 +1 181323 628 438s Number of sequences in alignment.......: 1457 438s Number of sites in alignment...........: 142 438s Number of chars in alignment...........: 181323 438s Mean site entropy in alignment.........: 0.36917 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 1823 1371 -86 143 +1 176415 -4908 438s Number of sequences in alignment.......: 1371 438s Number of sites in alignment...........: 143 438s Number of chars in alignment...........: 176415 438s Mean site entropy in alignment.........: 0.359961 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 783 1355 -16 144 +1 175237 -1178 438s Number of sequences in alignment.......: 1355 438s Number of sites in alignment...........: 144 438s Number of chars in alignment...........: 175237 438s Mean site entropy in alignment.........: 0.360644 438s Choice Node #seq %seq #sites %sites #chars %chars 438s 1) 953 1307 -48 145 +1 169472 -5765 439s Number of sequences in alignment.......: 1307 439s Number of sites in alignment...........: 145 439s Number of chars in alignment...........: 169472 439s Mean site entropy in alignment.........: 0.363152 439s Choice Node #seq %seq #sites %sites #chars %chars 439s Output alignment file .................: PF01049_optimized_fastml.fasta 439s Output alignment format ...............: FASTA file 439s Output tree file ......................: PF01049_optimized_fastml.dnd 439s Output tree format ....................: Newick 439s BppAlnOpt's done. Bye. 439s Total execution time: 0.000000d, 0.000000h, 0.000000m, 3.000000s. 439s PASS 439s autopkgtest [03:41:49]: test run-unit-test: -----------------------] 440s run-unit-test PASS 440s autopkgtest [03:41:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 440s autopkgtest [03:41:50]: @@@@@@@@@@@@@@@@@@@@ summary 440s run-unit-test PASS 465s Creating nova instance adt-noble-ppc64el-physamp-20240326-033429-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...