0s autopkgtest [14:21:19]: starting date and time: 2025-03-15 14:21:19+0000 0s autopkgtest [14:21:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:21:19]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8cihsh5n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade physamp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-6.secgroup --name adt-plucky-arm64-physamp-20250315-142119-juju-7f2275-prod-proposed-migration-environment-20-7f450bd9-190f-4c85-8b05-58687ba8ec6e --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 191s autopkgtest [14:24:30]: testbed dpkg architecture: arm64 191s autopkgtest [14:24:30]: testbed apt version: 2.9.33 192s autopkgtest [14:24:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 192s autopkgtest [14:24:31]: testbed release detected to be: None 193s autopkgtest [14:24:32]: updating testbed package index (apt update) 193s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 193s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 193s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 194s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 194s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 194s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 194s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 194s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 194s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 194s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 194s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 195s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 195s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 195s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 195s Fetched 1094 kB in 2s (647 kB/s) 196s Reading package lists... 197s Reading package lists... 198s Building dependency tree... 198s Reading state information... 199s Calculating upgrade... 199s Calculating upgrade... 200s The following packages will be upgraded: 200s python3-jinja2 strace 200s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 608 kB of archives. 200s After this operation, 11.3 kB of additional disk space will be used. 200s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 201s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 201s Fetched 608 kB in 1s (680 kB/s) 202s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 202s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 202s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 202s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 202s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 202s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 202s Setting up strace (6.13+ds-1ubuntu1) ... 202s Processing triggers for man-db (2.13.0-1) ... 203s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Solving dependencies... 205s The following packages will be REMOVED: 205s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 205s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 205s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 205s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 205s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 205s After this operation, 267 MB disk space will be freed. 205s (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 ... 117701 files and directories currently installed.) 205s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 205s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 205s Removing libpython3.12t64:arm64 (3.12.9-1) ... 205s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 205s Removing libnsl2:arm64 (1.3.0-3build3) ... 205s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 205s Removing libunwind8:arm64 (1.6.2-3.1) ... 205s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 206s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 208s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 208s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 208s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 208s /etc/kernel/postrm.d/initramfs-tools: 208s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 208s /etc/kernel/postrm.d/zz-flash-kernel: 208s flash-kernel: Kernel 6.11.0-8-generic has been removed. 208s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 209s /etc/kernel/postrm.d/zz-update-grub: 209s Sourcing file `/etc/default/grub' 209s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 209s Generating grub configuration file ... 209s Found linux image: /boot/vmlinuz-6.14.0-10-generic 209s Found initrd image: /boot/initrd.img-6.14.0-10-generic 209s Warning: os-prober will not be executed to detect other bootable partitions. 209s Systems on them will not be added to the GRUB boot configuration. 209s Check GRUB_DISABLE_OS_PROBER documentation entry. 209s Adding boot menu entry for UEFI Firmware Settings ... 209s done 209s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 209s Processing triggers for libc-bin (2.41-1ubuntu1) ... 210s (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 ... 81650 files and directories currently installed.) 210s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 210s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 210s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 210s autopkgtest [14:24:49]: upgrading testbed (apt dist-upgrade and autopurge) 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 211s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 212s Entering ResolveByKeep 212s 212s Calculating upgrade... 213s The following packages will be upgraded: 213s libc-bin libc-dev-bin libc6 libc6-dev locales 213s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 213s Need to get 9530 kB of archives. 213s After this operation, 0 B of additional disk space will be used. 213s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 215s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 215s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 217s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 218s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 222s Preconfiguring packages ... 222s Fetched 9530 kB in 9s (1090 kB/s) 222s (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 ... 81647 files and directories currently installed.) 222s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 222s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 222s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 222s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 222s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 222s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 223s Setting up libc6:arm64 (2.41-1ubuntu2) ... 223s (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 ... 81647 files and directories currently installed.) 223s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 223s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 223s Setting up libc-bin (2.41-1ubuntu2) ... 223s (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 ... 81647 files and directories currently installed.) 223s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 223s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 223s Setting up locales (2.41-1ubuntu2) ... 224s Generating locales (this might take a while)... 226s en_US.UTF-8... done 226s Generation complete. 226s Setting up libc-dev-bin (2.41-1ubuntu2) ... 226s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 226s Processing triggers for man-db (2.13.0-1) ... 227s Processing triggers for systemd (257.3-1ubuntu3) ... 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s Starting pkgProblemResolver with broken count: 0 228s Starting 2 pkgProblemResolver with broken count: 0 228s Done 229s Solving dependencies... 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 230s autopkgtest [14:25:09]: rebooting testbed after setup commands that affected boot 253s autopkgtest [14:25:32]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 255s autopkgtest [14:25:34]: @@@@@@@@@@@@@@@@@@@@ apt-source physamp 258s Get:1 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (dsc) [2001 B] 258s Get:2 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (tar) [242 kB] 258s Get:3 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (diff) [3924 B] 258s gpgv: Signature made Mon Mar 25 18:00:09 2024 UTC 258s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 258s gpgv: Can't check signature: No public key 258s dpkg-source: warning: cannot verify inline signature for ./physamp_1.1.0-5.dsc: no acceptable signature found 258s autopkgtest [14:25:37]: testing package physamp version 1.1.0-5 258s autopkgtest [14:25:37]: build not needed 259s autopkgtest [14:25:38]: test run-unit-test: preparing testbed 259s Reading package lists... 260s Building dependency tree... 260s Reading state information... 260s Starting pkgProblemResolver with broken count: 0 260s Starting 2 pkgProblemResolver with broken count: 0 260s Done 261s The following NEW packages will be installed: 261s libbpp-core4t64 libbpp-phyl12t64 libbpp-seq12t64 physamp 261s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 261s Need to get 2864 kB of archives. 261s After this operation, 15.9 MB of additional disk space will be used. 261s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbpp-core4t64 arm64 2.4.1-13 [509 kB] 262s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbpp-seq12t64 arm64 2.4.1-13 [409 kB] 262s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbpp-phyl12t64 arm64 2.4.1-9.1ubuntu3 [1771 kB] 264s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 physamp arm64 1.1.0-5 [175 kB] 264s Fetched 2864 kB in 3s (923 kB/s) 264s Selecting previously unselected package libbpp-core4t64:arm64. 265s (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 ... 81647 files and directories currently installed.) 265s Preparing to unpack .../libbpp-core4t64_2.4.1-13_arm64.deb ... 265s Unpacking libbpp-core4t64:arm64 (2.4.1-13) ... 265s Selecting previously unselected package libbpp-seq12t64:arm64. 265s Preparing to unpack .../libbpp-seq12t64_2.4.1-13_arm64.deb ... 265s Unpacking libbpp-seq12t64:arm64 (2.4.1-13) ... 265s Selecting previously unselected package libbpp-phyl12t64:arm64. 265s Preparing to unpack .../libbpp-phyl12t64_2.4.1-9.1ubuntu3_arm64.deb ... 265s Unpacking libbpp-phyl12t64:arm64 (2.4.1-9.1ubuntu3) ... 265s Selecting previously unselected package physamp. 265s Preparing to unpack .../physamp_1.1.0-5_arm64.deb ... 265s Unpacking physamp (1.1.0-5) ... 265s Setting up libbpp-core4t64:arm64 (2.4.1-13) ... 265s Setting up libbpp-seq12t64:arm64 (2.4.1-13) ... 265s Setting up libbpp-phyl12t64:arm64 (2.4.1-9.1ubuntu3) ... 265s Setting up physamp (1.1.0-5) ... 265s Processing triggers for man-db (2.13.0-1) ... 265s Processing triggers for install-info (7.1.1-1) ... 265s Processing triggers for libc-bin (2.41-1ubuntu2) ... 267s autopkgtest [14:25:46]: test run-unit-test: [----------------------- 267s ****************************************************************** 267s * Bio++ Alignment Optimizer, version 1.1.0. * 267s * Author: J. Dutheil Last Modif. 14/03/18 * 267s * E. Figuet * 267s ****************************************************************** 267s 267s Parsing options: 267s Parsing file AlnOptimFasttree.bpp for options. 267s Alphabet type .........................: Proteic 267s Sequence file .........................: PF01049_full.txt 267s Sequence format .......................: FASTA file 267s Minimum amount of data per site........: 0.7 267s Filter gap characters..................: yes 267s Filter unresolved characters...........: yes 267s Number of reference sequences..........: 0 267s Total number of sequences..............: 1652 267s Total number of sites..................: 656 267s Input tree file .......................: PF01049_fasttree.dnd 267s Input tree format .....................: Newick 267s Comparison criterion:..................: MaxSites 267s Number of sequences in alignment.......: 1652 267s Number of sites in alignment...........: 129 267s Number of chars in alignment...........: 182603 267s Mean site entropy in alignment.........: 0.394104 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2030 1647 -5 131 +2 184714 2111 267s Number of sequences in alignment.......: 1647 267s Number of sites in alignment...........: 131 267s Number of chars in alignment...........: 184714 267s Mean site entropy in alignment.........: 0.394129 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 1930 1645 -2 132 +1 185794 1080 268s Number of sequences in alignment.......: 1645 268s Number of sites in alignment...........: 132 268s Number of chars in alignment...........: 185794 268s Mean site entropy in alignment.........: 0.394195 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1882 1644 -1 133 +1 186920 1126 268s Number of sequences in alignment.......: 1644 268s Number of sites in alignment...........: 133 268s Number of chars in alignment...........: 186920 268s Mean site entropy in alignment.........: 0.394263 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 386 1634 -10 134 +1 187634 714 268s Number of sequences in alignment.......: 1634 268s Number of sites in alignment...........: 134 268s Number of chars in alignment...........: 187634 268s Mean site entropy in alignment.........: 0.394887 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 357 1627 -7 135 +1 188437 803 268s Number of sequences in alignment.......: 1627 268s Number of sites in alignment...........: 135 268s Number of chars in alignment...........: 188437 268s Mean site entropy in alignment.........: 0.394741 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1736 1614 -13 136 +1 188713 276 268s Number of sequences in alignment.......: 1614 268s Number of sites in alignment...........: 136 268s Number of chars in alignment...........: 188713 268s Mean site entropy in alignment.........: 0.394145 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1489 1527 -87 137 +1 181488 -7225 268s Number of sequences in alignment.......: 1527 268s Number of sites in alignment...........: 137 268s Number of chars in alignment...........: 181488 268s Mean site entropy in alignment.........: 0.378687 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 2247 1524 -3 138 +1 182435 947 268s Number of sequences in alignment.......: 1524 268s Number of sites in alignment...........: 138 268s Number of chars in alignment...........: 182435 268s Mean site entropy in alignment.........: 0.378731 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 408 1515 -9 139 +1 183008 573 268s Number of sequences in alignment.......: 1515 268s Number of sites in alignment...........: 139 268s Number of chars in alignment...........: 183008 268s Mean site entropy in alignment.........: 0.377294 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1819 1488 -27 140 +1 182208 -800 268s Number of sequences in alignment.......: 1488 268s Number of sites in alignment...........: 140 268s Number of chars in alignment...........: 182208 268s Mean site entropy in alignment.........: 0.374188 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1676 1464 -24 141 +1 180695 -1513 268s Number of sequences in alignment.......: 1464 268s Number of sites in alignment...........: 141 268s Number of chars in alignment...........: 180695 268s Mean site entropy in alignment.........: 0.371696 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 416 1457 -7 142 +1 181323 628 268s Number of sequences in alignment.......: 1457 268s Number of sites in alignment...........: 142 268s Number of chars in alignment...........: 181323 268s Mean site entropy in alignment.........: 0.36917 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1823 1371 -86 143 +1 176415 -4908 269s Number of sequences in alignment.......: 1371 269s Number of sites in alignment...........: 143 269s Number of chars in alignment...........: 176415 269s Mean site entropy in alignment.........: 0.359961 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 783 1355 -16 144 +1 175237 -1178 269s Number of sequences in alignment.......: 1355 269s Number of sites in alignment...........: 144 269s Number of chars in alignment...........: 175237 269s Mean site entropy in alignment.........: 0.360644 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 953 1307 -48 145 +1 169472 -5765 269s Number of sequences in alignment.......: 1307 269s Number of sites in alignment...........: 145 269s Number of chars in alignment...........: 169472 269s Mean site entropy in alignment.........: 0.363152 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2269 476 -831 146 +1 66187 -103285 269s Number of sequences in alignment.......: 476 269s Number of sites in alignment...........: 146 269s Number of chars in alignment...........: 66187 269s Mean site entropy in alignment.........: 0.249565 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2488 413 -63 147 +1 57456 -8731 269s Number of sequences in alignment.......: 413 269s Number of sites in alignment...........: 147 269s Number of chars in alignment...........: 57456 269s Mean site entropy in alignment.........: 0.249617 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2372 411 -2 148 +1 57619 163 269s Number of sequences in alignment.......: 411 269s Number of sites in alignment...........: 148 269s Number of chars in alignment...........: 57619 269s Mean site entropy in alignment.........: 0.248169 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 179 391 -20 149 +1 55008 -2611 269s Number of sequences in alignment.......: 391 269s Number of sites in alignment...........: 149 269s Number of chars in alignment...........: 55008 269s Mean site entropy in alignment.........: 0.249151 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2697 54 -337 151 +2 7794 -47214 269s Number of sequences in alignment.......: 54 269s Number of sites in alignment...........: 151 269s Number of chars in alignment...........: 7794 269s Mean site entropy in alignment.........: 0.0871024 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2628 50 -4 152 +1 7230 -564 269s Number of sequences in alignment.......: 50 269s Number of sites in alignment...........: 152 269s Number of chars in alignment...........: 7230 269s Mean site entropy in alignment.........: 0.0864589 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2692 48 -2 153 +1 7110 -120 269s Number of sequences in alignment.......: 48 269s Number of sites in alignment...........: 153 269s Number of chars in alignment...........: 7110 269s Mean site entropy in alignment.........: 0.0765764 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2695 10 -38 154 +1 1526 -5584 269s Number of sequences in alignment.......: 10 269s Number of sites in alignment...........: 154 269s Number of chars in alignment...........: 1526 269s Mean site entropy in alignment.........: 0.0596881 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2611 2 -8 156 +2 312 -1214 269s Number of sequences in alignment.......: 2 269s Number of sites in alignment...........: 156 269s Number of chars in alignment...........: 312 269s Mean site entropy in alignment.........: 0.0190193 269s Choice Node #seq %seq #sites %sites #chars %chars 269s BppAlnOpt's done. Bye. 269s Total execution time: 0.000000d, 0.000000h, 0.000000m, 1.000000s. 269s ****************************************************************** 269s * Bio++ Alignment Optimizer, version 1.1.0. * 269s * Author: J. Dutheil Last Modif. 14/03/18 * 269s * E. Figuet * 269s ****************************************************************** 269s 269s Parsing options: 269s Parsing file AlnOptimAuto.bpp for options. 269s Alphabet type .........................: Proteic 269s Sequence file .........................: PF01049_full.txt 269s Sequence format .......................: FASTA file 269s Minimum amount of data per site........: 0.7 269s Filter gap characters..................: yes 269s Filter unresolved characters...........: yes 269s Number of reference sequences..........: 0 269s Total number of sequences..............: 1652 269s Total number of sites..................: 656 269s Compressing sequences..................: 269s [ ] 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. 269s Memory required to store distances (Mb): 20 269s Computing pairwise overlap matrix......: 272s [> ] 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. 272s Clustering linkage mode................: complete 272s Computing cluster tree.................: 278s [ ] 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. 278s Comparison criterion:..................: MaxSites 278s Number of sequences in alignment.......: 1652 278s Number of sites in alignment...........: 129 278s Number of chars in alignment...........: 182603 278s Mean site entropy in alignment.........: 0.394104 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3294 1647 -5 131 +2 184716 2113 278s Number of sequences in alignment.......: 1647 278s Number of sites in alignment...........: 131 278s Number of chars in alignment...........: 184716 278s Mean site entropy in alignment.........: 0.394659 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3286 1645 -2 132 +1 185817 1101 278s Number of sequences in alignment.......: 1645 278s Number of sites in alignment...........: 132 278s Number of chars in alignment...........: 185817 278s Mean site entropy in alignment.........: 0.394872 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 536 1644 -1 133 +1 186943 1126 278s Number of sequences in alignment.......: 1644 278s Number of sites in alignment...........: 133 278s Number of chars in alignment...........: 186943 278s Mean site entropy in alignment.........: 0.39494 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3270 1634 -10 134 +1 187657 714 278s Number of sequences in alignment.......: 1634 278s Number of sites in alignment...........: 134 278s Number of chars in alignment...........: 187657 278s Mean site entropy in alignment.........: 0.395564 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2951 1627 -7 135 +1 188449 792 278s Number of sequences in alignment.......: 1627 278s Number of sites in alignment...........: 135 278s Number of chars in alignment...........: 188449 278s Mean site entropy in alignment.........: 0.392385 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3021 1614 -13 136 +1 188658 209 278s Number of sequences in alignment.......: 1614 278s Number of sites in alignment...........: 136 278s Number of chars in alignment...........: 188658 278s Mean site entropy in alignment.........: 0.391197 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3235 1545 -69 137 +1 185332 -3326 278s Number of sequences in alignment.......: 1545 278s Number of sites in alignment...........: 137 278s Number of chars in alignment...........: 185332 278s Mean site entropy in alignment.........: 0.389695 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3249 1542 -3 138 +1 186300 968 278s Number of sequences in alignment.......: 1542 278s Number of sites in alignment...........: 138 278s Number of chars in alignment...........: 186300 278s Mean site entropy in alignment.........: 0.389735 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3247 1537 -5 139 +1 187136 836 278s Number of sequences in alignment.......: 1537 278s Number of sites in alignment...........: 139 278s Number of chars in alignment...........: 187136 278s Mean site entropy in alignment.........: 0.389763 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2816 1521 -16 140 +1 186509 -627 279s Number of sequences in alignment.......: 1521 279s Number of sites in alignment...........: 140 279s Number of chars in alignment...........: 186509 279s Mean site entropy in alignment.........: 0.38832 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 3130 1471 -50 141 +1 183898 -2611 279s Number of sequences in alignment.......: 1471 279s Number of sites in alignment...........: 141 279s Number of chars in alignment...........: 183898 279s Mean site entropy in alignment.........: 0.370103 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1147 1470 -1 142 +1 184902 1004 279s Number of sequences in alignment.......: 1470 279s Number of sites in alignment...........: 142 279s Number of chars in alignment...........: 184902 279s Mean site entropy in alignment.........: 0.370154 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 3251 1465 -5 143 +1 185674 772 279s Number of sequences in alignment.......: 1465 279s Number of sites in alignment...........: 143 279s Number of chars in alignment...........: 185674 279s Mean site entropy in alignment.........: 0.370155 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 3280 1391 -74 144 +1 181655 -4019 279s Number of sequences in alignment.......: 1391 279s Number of sites in alignment...........: 144 279s Number of chars in alignment...........: 181655 279s Mean site entropy in alignment.........: 0.359169 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2928 1340 -51 145 +1 177148 -4507 279s Number of sequences in alignment.......: 1340 279s Number of sites in alignment...........: 145 279s Number of chars in alignment...........: 177148 279s Mean site entropy in alignment.........: 0.351822 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 3168 1159 -181 146 +1 163916 -13232 279s Number of sequences in alignment.......: 1159 279s Number of sites in alignment...........: 146 279s Number of chars in alignment...........: 163916 279s Mean site entropy in alignment.........: 0.32945 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2651 1117 -42 147 +1 158726 -5190 279s Number of sequences in alignment.......: 1117 279s Number of sites in alignment...........: 147 279s Number of chars in alignment...........: 158726 279s Mean site entropy in alignment.........: 0.331341 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2242 1097 -20 148 +1 156673 -2053 279s Number of sequences in alignment.......: 1097 279s Number of sites in alignment...........: 148 279s Number of chars in alignment...........: 156673 279s Mean site entropy in alignment.........: 0.324708 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2221 1078 -19 149 +1 154673 -2000 279s Number of sequences in alignment.......: 1078 279s Number of sites in alignment...........: 149 279s Number of chars in alignment...........: 154673 279s Mean site entropy in alignment.........: 0.326137 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2944 993 -85 150 +1 144901 -9772 279s Number of sequences in alignment.......: 993 279s Number of sites in alignment...........: 150 279s Number of chars in alignment...........: 144901 279s Mean site entropy in alignment.........: 0.302006 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2554 941 -52 151 +1 137854 -7047 279s Number of sequences in alignment.......: 941 279s Number of sites in alignment...........: 151 279s Number of chars in alignment...........: 137854 279s Mean site entropy in alignment.........: 0.304205 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2675 234 -707 157 +6 36220 -101634 279s Number of sequences in alignment.......: 234 279s Number of sites in alignment...........: 157 279s Number of chars in alignment...........: 36220 279s Mean site entropy in alignment.........: 0.18992 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2046 230 -4 158 +1 35777 -443 279s Number of sequences in alignment.......: 230 279s Number of sites in alignment...........: 158 279s Number of chars in alignment...........: 35777 279s Mean site entropy in alignment.........: 0.188188 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1950 24 -206 160 +2 3795 -31982 279s Number of sequences in alignment.......: 24 279s Number of sites in alignment...........: 160 279s Number of chars in alignment...........: 3795 279s Mean site entropy in alignment.........: 0.185344 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1896 20 -4 161 +1 3193 -602 279s Number of sequences in alignment.......: 20 279s Number of sites in alignment...........: 161 279s Number of chars in alignment...........: 3193 279s Mean site entropy in alignment.........: 0.133241 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1795 18 -2 163 +2 2911 -282 279s Number of sequences in alignment.......: 18 279s Number of sites in alignment...........: 163 279s Number of chars in alignment...........: 2911 279s Mean site entropy in alignment.........: 0.122561 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1718 14 -4 165 +2 2294 -617 279s Number of sequences in alignment.......: 14 279s Number of sites in alignment...........: 165 279s Number of chars in alignment...........: 2294 279s Mean site entropy in alignment.........: 0.0452968 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1707 12 -2 166 +1 1983 -311 279s Number of sequences in alignment.......: 12 279s Number of sites in alignment...........: 166 279s Number of chars in alignment...........: 1983 279s Mean site entropy in alignment.........: 0.0379699 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 397 11 -1 168 +2 1838 -145 279s Number of sequences in alignment.......: 11 279s Number of sites in alignment...........: 168 279s Number of chars in alignment...........: 1838 279s Mean site entropy in alignment.........: 0.03305 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1682 8 -3 169 +1 1349 -489 279s Number of sequences in alignment.......: 8 279s Number of sites in alignment...........: 169 279s Number of chars in alignment...........: 1349 279s Mean site entropy in alignment.........: 0.0183685 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 46 7 -1 172 +3 1196 -153 279s Number of sequences in alignment.......: 7 279s Number of sites in alignment...........: 172 279s Number of chars in alignment...........: 1196 279s Mean site entropy in alignment.........: 0.0178367 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1664 2 -5 176 +4 352 -844 279s Number of sequences in alignment.......: 2 279s Number of sites in alignment...........: 176 279s Number of chars in alignment...........: 352 279s Mean site entropy in alignment.........: 0.010038 279s Choice Node #seq %seq #sites %sites #chars %chars 279s BppAlnOpt's done. Bye. 279s Total execution time: 0.000000d, 0.000000h, 0.000000m, 10.000000s. 279s ****************************************************************** 279s * Bio++ Alignment Optimizer, version 1.1.0. * 279s * Author: J. Dutheil Last Modif. 14/03/18 * 279s * E. Figuet * 279s ****************************************************************** 279s 279s Parsing options: 279s Parsing file AlnOptimAuto.bpp for options. 279s Alphabet type .........................: Proteic 279s Sequence file .........................: PF01049_full.txt 279s Sequence format .......................: FASTA file 279s Minimum amount of data per site........: 0.7 279s Filter gap characters..................: yes 279s Filter unresolved characters...........: yes 279s Number of reference sequences..........: 0 279s Total number of sequences..............: 1652 279s Total number of sites..................: 656 279s Compressing sequences..................: 280s [ ] 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. 280s Memory required to store distances (Mb): 20 280s Computing pairwise overlap matrix......: 282s [> ] 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. 282s Clustering linkage mode................: single 282s Computing cluster tree.................: 288s [ ] 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. 288s Comparison criterion:..................: MaxSites 288s Number of sequences in alignment.......: 1652 288s Number of sites in alignment...........: 129 288s Number of chars in alignment...........: 182603 288s Mean site entropy in alignment.........: 0.394104 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3297 1647 -5 131 +2 184776 2173 288s Number of sequences in alignment.......: 1647 288s Number of sites in alignment...........: 131 288s Number of chars in alignment...........: 184776 288s Mean site entropy in alignment.........: 0.394536 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3295 1645 -2 132 +1 185874 1098 288s Number of sequences in alignment.......: 1645 288s Number of sites in alignment...........: 132 288s Number of chars in alignment...........: 185874 288s Mean site entropy in alignment.........: 0.394721 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 181 1644 -1 133 +1 186998 1124 289s Number of sequences in alignment.......: 1644 289s Number of sites in alignment...........: 133 289s Number of chars in alignment...........: 186998 289s Mean site entropy in alignment.........: 0.394677 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 3285 1634 -10 134 +1 187772 774 289s Number of sequences in alignment.......: 1634 289s Number of sites in alignment...........: 134 289s Number of chars in alignment...........: 187772 289s Mean site entropy in alignment.........: 0.395614 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 3278 1627 -7 135 +1 188620 848 289s Number of sequences in alignment.......: 1627 289s Number of sites in alignment...........: 135 289s Number of chars in alignment...........: 188620 289s Mean site entropy in alignment.........: 0.396053 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 3265 1614 -13 136 +1 189192 572 289s Number of sequences in alignment.......: 1614 289s Number of sites in alignment...........: 136 289s Number of chars in alignment...........: 189192 289s Mean site entropy in alignment.........: 0.396866 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 3157 1505 -109 137 +1 184306 -4886 289s Number of sequences in alignment.......: 1505 289s Number of sites in alignment...........: 137 289s Number of chars in alignment...........: 184306 289s Mean site entropy in alignment.........: 0.397698 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 3139 1488 -17 138 +1 184277 -29 289s Number of sequences in alignment.......: 1488 289s Number of sites in alignment...........: 138 289s Number of chars in alignment...........: 184277 289s Mean site entropy in alignment.........: 0.396924 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 3136 1485 -3 139 +1 185134 857 290s Number of sequences in alignment.......: 1485 290s Number of sites in alignment...........: 139 290s Number of chars in alignment...........: 185134 290s Mean site entropy in alignment.........: 0.396707 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 3122 1471 -14 140 +1 185214 80 290s Number of sequences in alignment.......: 1471 290s Number of sites in alignment...........: 140 290s Number of chars in alignment...........: 185214 290s Mean site entropy in alignment.........: 0.396624 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 2848 1437 -34 141 +1 183753 -1461 290s Number of sequences in alignment.......: 1437 290s Number of sites in alignment...........: 141 290s Number of chars in alignment...........: 183753 290s Mean site entropy in alignment.........: 0.379676 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 3110 1425 -12 142 +1 183898 145 290s Number of sequences in alignment.......: 1425 290s Number of sites in alignment...........: 142 290s Number of chars in alignment...........: 183898 290s Mean site entropy in alignment.........: 0.379975 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 3073 1387 -38 143 +1 182369 -1529 290s Number of sequences in alignment.......: 1387 290s Number of sites in alignment...........: 143 290s Number of chars in alignment...........: 182369 290s Mean site entropy in alignment.........: 0.376594 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 2904 1380 -7 144 +1 182593 224 290s Number of sequences in alignment.......: 1380 290s Number of sites in alignment...........: 144 290s Number of chars in alignment...........: 182593 290s Mean site entropy in alignment.........: 0.375989 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 2941 1206 -174 145 +1 167869 -14724 290s Number of sequences in alignment.......: 1206 290s Number of sites in alignment...........: 145 290s Number of chars in alignment...........: 167869 290s Mean site entropy in alignment.........: 0.346494 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 2829 1145 -61 146 +1 162413 -5456 290s Number of sequences in alignment.......: 1145 290s Number of sites in alignment...........: 146 290s Number of chars in alignment...........: 162413 290s Mean site entropy in alignment.........: 0.332586 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 2751 1071 -74 147 +1 153723 -8690 291s Number of sequences in alignment.......: 1071 291s Number of sites in alignment...........: 147 291s Number of chars in alignment...........: 153723 291s Mean site entropy in alignment.........: 0.320762 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 1751 998 -73 148 +1 144121 -9602 291s Number of sequences in alignment.......: 998 291s Number of sites in alignment...........: 148 291s Number of chars in alignment...........: 144121 291s Mean site entropy in alignment.........: 0.298818 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 2100 985 -13 149 +1 142964 -1157 291s Number of sequences in alignment.......: 985 291s Number of sites in alignment...........: 149 291s Number of chars in alignment...........: 142964 291s Mean site entropy in alignment.........: 0.298279 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 2427 665 -320 150 +1 97526 -45438 291s Number of sequences in alignment.......: 665 291s Number of sites in alignment...........: 150 291s Number of chars in alignment...........: 97526 291s Mean site entropy in alignment.........: 0.293825 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 1379 664 -1 151 +1 97882 356 291s Number of sequences in alignment.......: 664 291s Number of sites in alignment...........: 151 291s Number of chars in alignment...........: 97882 291s Mean site entropy in alignment.........: 0.292162 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 2203 441 -223 152 +1 65487 -32395 291s Number of sequences in alignment.......: 441 291s Number of sites in alignment...........: 152 291s Number of chars in alignment...........: 65487 291s Mean site entropy in alignment.........: 0.29729 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 2189 427 -14 153 +1 63726 -1761 291s Number of sequences in alignment.......: 427 291s Number of sites in alignment...........: 153 291s Number of chars in alignment...........: 63726 291s Mean site entropy in alignment.........: 0.295662 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 2082 334 -93 154 +1 50320 -13406 291s Number of sequences in alignment.......: 334 291s Number of sites in alignment...........: 154 291s Number of chars in alignment...........: 50320 291s Mean site entropy in alignment.........: 0.268583 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 2006 258 -76 155 +1 39190 -11130 291s Number of sequences in alignment.......: 258 291s Number of sites in alignment...........: 155 291s Number of chars in alignment...........: 39190 291s Mean site entropy in alignment.........: 0.230649 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 1987 254 -4 156 +1 38780 -410 291s Number of sequences in alignment.......: 254 291s Number of sites in alignment...........: 156 291s Number of chars in alignment...........: 38780 291s Mean site entropy in alignment.........: 0.228398 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 1915 247 -7 157 +1 37896 -884 291s Number of sequences in alignment.......: 247 291s Number of sites in alignment...........: 157 291s Number of chars in alignment...........: 37896 291s Mean site entropy in alignment.........: 0.226904 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 1876 130 -117 158 +1 20276 -17620 291s Number of sequences in alignment.......: 130 291s Number of sites in alignment...........: 158 291s Number of chars in alignment...........: 20276 291s Mean site entropy in alignment.........: 0.134572 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 1704 3 -127 163 +5 489 -19787 291s Number of sequences in alignment.......: 3 291s Number of sites in alignment...........: 163 291s Number of chars in alignment...........: 489 291s Mean site entropy in alignment.........: 0.065727 291s Choice Node #seq %seq #sites %sites #chars %chars 291s 1) 1474 2 -1 167 +4 334 -155 291s Number of sequences in alignment.......: 2 291s Number of sites in alignment...........: 167 291s Number of chars in alignment...........: 334 291s Mean site entropy in alignment.........: 0.0338121 291s Choice Node #seq %seq #sites %sites #chars %chars 291s BppAlnOpt's done. Bye. 291s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 291s ****************************************************************** 291s * Bio++ Alignment Optimizer, version 1.1.0. * 291s * Author: J. Dutheil Last Modif. 14/03/18 * 291s * E. Figuet * 291s ****************************************************************** 291s 291s Parsing options: 291s Parsing file AlnOptimAuto.bpp for options. 291s Alphabet type .........................: Proteic 291s Sequence file .........................: PF01049_full.txt 291s Sequence format .......................: FASTA file 291s Minimum amount of data per site........: 0.7 291s Filter gap characters..................: yes 291s Filter unresolved characters...........: yes 291s Number of reference sequences..........: 0 291s Total number of sequences..............: 1652 291s Total number of sites..................: 656 291s Compressing sequences..................: 291s [ ] 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. 291s Memory required to store distances (Mb): 20 291s Computing pairwise overlap matrix......: 294s [> ] 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. 294s Clustering linkage mode................: average 294s Computing cluster tree.................: 299s [ ] 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. 299s Comparison criterion:..................: MaxSites 299s Number of sequences in alignment.......: 1652 299s Number of sites in alignment...........: 129 299s Number of chars in alignment...........: 182603 299s Mean site entropy in alignment.........: 0.394104 299s Choice Node #seq %seq #sites %sites #chars %chars 299s 1) 3299 1647 -5 131 +2 184774 2171 300s Number of sequences in alignment.......: 1647 300s Number of sites in alignment...........: 131 300s Number of chars in alignment...........: 184774 300s Mean site entropy in alignment.........: 0.394431 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3293 1645 -2 132 +1 185875 1101 300s Number of sequences in alignment.......: 1645 300s Number of sites in alignment...........: 132 300s Number of chars in alignment...........: 185875 300s Mean site entropy in alignment.........: 0.394643 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 181 1644 -1 133 +1 186999 1124 300s Number of sequences in alignment.......: 1644 300s Number of sites in alignment...........: 133 300s Number of chars in alignment...........: 186999 300s Mean site entropy in alignment.........: 0.394599 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3287 1634 -10 134 +1 187779 780 300s Number of sequences in alignment.......: 1634 300s Number of sites in alignment...........: 134 300s Number of chars in alignment...........: 187779 300s Mean site entropy in alignment.........: 0.395631 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3276 1627 -7 135 +1 188617 838 300s Number of sequences in alignment.......: 1627 300s Number of sites in alignment...........: 135 300s Number of chars in alignment...........: 188617 300s Mean site entropy in alignment.........: 0.396076 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3238 1614 -13 136 +1 189013 396 300s Number of sequences in alignment.......: 1614 300s Number of sites in alignment...........: 136 300s Number of chars in alignment...........: 189013 300s Mean site entropy in alignment.........: 0.395128 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3023 1533 -81 138 +2 185240 -3773 300s Number of sequences in alignment.......: 1533 300s Number of sites in alignment...........: 138 300s Number of chars in alignment...........: 185240 300s Mean site entropy in alignment.........: 0.372196 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 1629 1532 -1 139 +1 186276 1036 300s Number of sequences in alignment.......: 1532 300s Number of sites in alignment...........: 139 300s Number of chars in alignment...........: 186276 300s Mean site entropy in alignment.........: 0.372208 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3282 1521 -11 140 +1 186867 591 300s Number of sequences in alignment.......: 1521 300s Number of sites in alignment...........: 140 300s Number of chars in alignment...........: 186867 300s Mean site entropy in alignment.........: 0.372497 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3105 1482 -39 141 +1 185210 -1657 300s Number of sequences in alignment.......: 1482 300s Number of sites in alignment...........: 141 300s Number of chars in alignment...........: 185210 300s Mean site entropy in alignment.........: 0.368185 300s Choice Node #seq %seq #sites %sites #chars %chars 300s 1) 3135 1471 -11 142 +1 185562 352 300s Number of sequences in alignment.......: 1471 300s Number of sites in alignment...........: 142 300s Number of chars in alignment...........: 185562 301s Mean site entropy in alignment.........: 0.367384 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2863 1455 -16 143 +1 184869 -693 301s Number of sequences in alignment.......: 1455 301s Number of sites in alignment...........: 143 301s Number of chars in alignment...........: 184869 301s Mean site entropy in alignment.........: 0.366056 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 3166 1413 -42 144 +1 183102 -1767 301s Number of sequences in alignment.......: 1413 301s Number of sites in alignment...........: 144 301s Number of chars in alignment...........: 183102 301s Mean site entropy in alignment.........: 0.362023 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2996 1204 -209 145 +1 168239 -14863 301s Number of sequences in alignment.......: 1204 301s Number of sites in alignment...........: 145 301s Number of chars in alignment...........: 168239 301s Mean site entropy in alignment.........: 0.339856 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2960 1154 -50 146 +1 163602 -4637 301s Number of sequences in alignment.......: 1154 301s Number of sites in alignment...........: 146 301s Number of chars in alignment...........: 163602 301s Mean site entropy in alignment.........: 0.330406 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2809 1097 -57 147 +1 157455 -6147 301s Number of sequences in alignment.......: 1097 301s Number of sites in alignment...........: 147 301s Number of chars in alignment...........: 157455 301s Mean site entropy in alignment.........: 0.314798 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2635 1063 -34 148 +1 153359 -4096 301s Number of sequences in alignment.......: 1063 301s Number of sites in alignment...........: 148 301s Number of chars in alignment...........: 153359 301s Mean site entropy in alignment.........: 0.316144 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 1948 1048 -15 149 +1 151998 -1361 301s Number of sequences in alignment.......: 1048 301s Number of sites in alignment...........: 149 301s Number of chars in alignment...........: 151998 301s Mean site entropy in alignment.........: 0.31084 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2069 1031 -17 150 +1 150327 -1671 301s Number of sequences in alignment.......: 1031 301s Number of sites in alignment...........: 150 301s Number of chars in alignment...........: 150327 301s Mean site entropy in alignment.........: 0.303727 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2640 451 -580 151 +1 67067 -83260 301s Number of sequences in alignment.......: 451 301s Number of sites in alignment...........: 151 301s Number of chars in alignment...........: 67067 301s Mean site entropy in alignment.........: 0.278258 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2555 425 -26 152 +1 63569 -3498 301s Number of sequences in alignment.......: 425 301s Number of sites in alignment...........: 152 301s Number of chars in alignment...........: 63569 301s Mean site entropy in alignment.........: 0.276822 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2332 391 -34 153 +1 58841 -4728 301s Number of sequences in alignment.......: 391 301s Number of sites in alignment...........: 153 301s Number of chars in alignment...........: 58841 301s Mean site entropy in alignment.........: 0.269678 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2039 342 -49 154 +1 51693 -7148 301s Number of sequences in alignment.......: 342 301s Number of sites in alignment...........: 154 301s Number of chars in alignment...........: 51693 301s Mean site entropy in alignment.........: 0.250803 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2337 280 -62 155 +1 42698 -8995 301s Number of sequences in alignment.......: 280 301s Number of sites in alignment...........: 155 301s Number of chars in alignment...........: 42698 301s Mean site entropy in alignment.........: 0.230831 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 1969 277 -3 156 +1 42454 -244 301s Number of sequences in alignment.......: 277 301s Number of sites in alignment...........: 156 301s Number of chars in alignment...........: 42454 301s Mean site entropy in alignment.........: 0.228862 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 2097 246 -31 157 +1 37949 -4505 301s Number of sequences in alignment.......: 246 301s Number of sites in alignment...........: 157 301s Number of chars in alignment...........: 37949 301s Mean site entropy in alignment.........: 0.216654 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 884 245 -1 158 +1 37976 27 301s Number of sequences in alignment.......: 245 301s Number of sites in alignment...........: 158 301s Number of chars in alignment...........: 37976 301s Mean site entropy in alignment.........: 0.215946 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 1937 19 -226 163 +5 3067 -34909 301s Number of sequences in alignment.......: 19 301s Number of sites in alignment...........: 163 301s Number of chars in alignment...........: 3067 301s Mean site entropy in alignment.........: 0.115126 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 1719 14 -5 165 +2 2297 -770 301s Number of sequences in alignment.......: 14 301s Number of sites in alignment...........: 165 301s Number of chars in alignment...........: 2297 301s Mean site entropy in alignment.........: 0.0991142 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 1699 12 -2 166 +1 1983 -314 301s Number of sequences in alignment.......: 12 301s Number of sites in alignment...........: 166 301s Number of chars in alignment...........: 1983 301s Mean site entropy in alignment.........: 0.0379699 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 397 11 -1 168 +2 1838 -145 301s Number of sequences in alignment.......: 11 301s Number of sites in alignment...........: 168 301s Number of chars in alignment...........: 1838 301s Mean site entropy in alignment.........: 0.03305 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 1684 8 -3 169 +1 1349 -489 301s Number of sequences in alignment.......: 8 301s Number of sites in alignment...........: 169 301s Number of chars in alignment...........: 1349 301s Mean site entropy in alignment.........: 0.0183685 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 46 7 -1 172 +3 1196 -153 301s Number of sequences in alignment.......: 7 301s Number of sites in alignment...........: 172 301s Number of chars in alignment...........: 1196 301s Mean site entropy in alignment.........: 0.0178367 301s Choice Node #seq %seq #sites %sites #chars %chars 301s 1) 1664 2 -5 176 +4 352 -844 301s Number of sequences in alignment.......: 2 301s Number of sites in alignment...........: 176 301s Number of chars in alignment...........: 352 301s Mean site entropy in alignment.........: 0.010038 301s Choice Node #seq %seq #sites %sites #chars %chars 301s BppAlnOpt's done. Bye. 301s Total execution time: 0.000000d, 0.000000h, 0.000000m, 10.000000s. 301s ****************************************************************** 301s * Bio++ Alignment Optimizer, version 1.1.0. * 301s * Author: J. Dutheil Last Modif. 14/03/18 * 301s * E. Figuet * 301s ****************************************************************** 301s 301s Parsing options: 301s Parsing file AlnOptimAuto.bpp for options. 301s Alphabet type .........................: Proteic 301s Sequence file .........................: PF01049_full.txt 301s Sequence format .......................: FASTA file 301s Minimum amount of data per site........: 0.7 301s Filter gap characters..................: yes 301s Filter unresolved characters...........: yes 301s Number of reference sequences..........: 0 301s Total number of sequences..............: 1652 301s Total number of sites..................: 656 301s Compressing sequences..................: 301s [ ] 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. 301s Memory required to store distances (Mb): 20 301s Computing pairwise overlap matrix......: 304s [> ] 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. 304s Clustering linkage mode................: median 304s Computing cluster tree.................: 310s [ ] 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. 310s Comparison criterion:..................: MaxSites 310s Number of sequences in alignment.......: 1652 310s Number of sites in alignment...........: 129 310s Number of chars in alignment...........: 182603 310s Mean site entropy in alignment.........: 0.394104 310s Choice Node #seq %seq #sites %sites #chars %chars 310s 1) 3297 1647 -5 131 +2 184774 2171 310s Number of sequences in alignment.......: 1647 310s Number of sites in alignment...........: 131 310s Number of chars in alignment...........: 184774 310s Mean site entropy in alignment.........: 0.394431 310s Choice Node #seq %seq #sites %sites #chars %chars 310s 1) 3295 1645 -2 132 +1 185873 1099 311s Number of sequences in alignment.......: 1645 311s Number of sites in alignment...........: 132 311s Number of chars in alignment...........: 185873 311s Mean site entropy in alignment.........: 0.394618 311s Choice Node #seq %seq #sites %sites #chars %chars 311s 1) 275 1644 -1 133 +1 186998 1125 311s Number of sequences in alignment.......: 1644 311s Number of sites in alignment...........: 133 311s Number of chars in alignment...........: 186998 311s Mean site entropy in alignment.........: 0.394724 311s Choice Node #seq %seq #sites %sites #chars %chars 311s 1) 3280 1630 -14 134 +1 187559 561 311s Number of sequences in alignment.......: 1630 311s Number of sites in alignment...........: 134 311s Number of chars in alignment...........: 187559 311s Mean site entropy in alignment.........: 0.39546 311s Choice Node #seq %seq #sites %sites #chars %chars 311s 1) 3272 1622 -8 135 +1 188376 817 311s Number of sequences in alignment.......: 1622 311s Number of sites in alignment...........: 135 311s Number of chars in alignment...........: 188376 311s Mean site entropy in alignment.........: 0.396213 311s Choice Node #seq %seq #sites %sites #chars %chars 311s 1) 3261 1611 -11 136 +1 189031 655 311s Number of sequences in alignment.......: 1611 311s Number of sites in alignment...........: 136 311s Number of chars in alignment...........: 189031 311s Mean site entropy in alignment.........: 0.396902 311s Choice Node #seq %seq #sites %sites #chars %chars 311s 1) 3184 1534 -77 137 +1 185562 -3469 312s Number of sequences in alignment.......: 1534 312s Number of sites in alignment...........: 137 312s Number of chars in alignment...........: 185562 312s Mean site entropy in alignment.........: 0.396433 312s Choice Node #seq %seq #sites %sites #chars %chars 312s 1) 3182 1532 -2 138 +1 186503 941 312s Number of sequences in alignment.......: 1532 312s Number of sites in alignment...........: 138 312s Number of chars in alignment...........: 186503 312s Mean site entropy in alignment.........: 0.396422 312s Choice Node #seq %seq #sites %sites #chars %chars 312s 1) 513 1531 -1 139 +1 187535 1032 312s Number of sequences in alignment.......: 1531 312s Number of sites in alignment...........: 139 312s Number of chars in alignment...........: 187535 312s Mean site entropy in alignment.........: 0.396222 312s Choice Node #seq %seq #sites %sites #chars %chars 312s 1) 3169 1518 -13 140 +1 187760 225 312s Number of sequences in alignment.......: 1518 312s Number of sites in alignment...........: 140 312s Number of chars in alignment...........: 187760 312s Mean site entropy in alignment.........: 0.395785 312s Choice Node #seq %seq #sites %sites #chars %chars 312s 1) 3125 1475 -43 141 +1 185962 -1798 312s Number of sequences in alignment.......: 1475 312s Number of sites in alignment...........: 141 312s Number of chars in alignment...........: 185962 312s Mean site entropy in alignment.........: 0.388512 312s Choice Node #seq %seq #sites %sites #chars %chars 312s 1) 3117 1467 -8 142 +1 186502 540 312s Number of sequences in alignment.......: 1467 312s Number of sites in alignment...........: 142 312s Number of chars in alignment...........: 186502 312s Mean site entropy in alignment.........: 0.388016 312s Choice Node #seq %seq #sites %sites #chars %chars 312s 1) 3102 1452 -15 143 +1 186490 -12 312s Number of sequences in alignment.......: 1452 312s Number of sites in alignment...........: 143 312s Number of chars in alignment...........: 186490 312s Mean site entropy in alignment.........: 0.386609 312s Choice Node #seq %seq #sites %sites #chars %chars 312s 1) 3052 1402 -50 144 +1 183727 -2763 313s Number of sequences in alignment.......: 1402 313s Number of sites in alignment...........: 144 313s Number of chars in alignment...........: 183727 313s Mean site entropy in alignment.........: 0.379315 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2877 1227 -175 145 +1 170235 -13492 313s Number of sequences in alignment.......: 1227 313s Number of sites in alignment...........: 145 313s Number of chars in alignment...........: 170235 313s Mean site entropy in alignment.........: 0.34859 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2788 1138 -89 146 +1 161621 -8614 313s Number of sequences in alignment.......: 1138 313s Number of sites in alignment...........: 146 313s Number of chars in alignment...........: 161621 313s Mean site entropy in alignment.........: 0.330459 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2731 1081 -57 147 +1 155136 -6485 313s Number of sequences in alignment.......: 1081 313s Number of sites in alignment...........: 147 313s Number of chars in alignment...........: 155136 313s Mean site entropy in alignment.........: 0.319787 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 1701 1030 -51 148 +1 148555 -6581 313s Number of sequences in alignment.......: 1030 313s Number of sites in alignment...........: 148 313s Number of chars in alignment...........: 148555 313s Mean site entropy in alignment.........: 0.305707 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2499 798 -232 149 +1 116805 -31750 313s Number of sequences in alignment.......: 798 313s Number of sites in alignment...........: 149 313s Number of chars in alignment...........: 116805 313s Mean site entropy in alignment.........: 0.273968 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2468 767 -31 150 +1 112894 -3911 313s Number of sequences in alignment.......: 767 313s Number of sites in alignment...........: 150 313s Number of chars in alignment...........: 112894 313s Mean site entropy in alignment.........: 0.272075 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2239 538 -229 151 +1 79674 -33220 313s Number of sequences in alignment.......: 538 313s Number of sites in alignment...........: 151 313s Number of chars in alignment...........: 79674 313s Mean site entropy in alignment.........: 0.280963 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2196 495 -43 152 +1 73702 -5972 313s Number of sequences in alignment.......: 495 313s Number of sites in alignment...........: 152 313s Number of chars in alignment...........: 73702 313s Mean site entropy in alignment.........: 0.28148 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2076 375 -120 153 +1 56316 -17386 313s Number of sequences in alignment.......: 375 313s Number of sites in alignment...........: 153 313s Number of chars in alignment...........: 56316 313s Mean site entropy in alignment.........: 0.267502 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 2018 317 -58 154 +1 47977 -8339 313s Number of sequences in alignment.......: 317 313s Number of sites in alignment...........: 154 313s Number of chars in alignment...........: 47977 313s Mean site entropy in alignment.........: 0.249671 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 1949 248 -69 155 +1 37817 -10160 313s Number of sequences in alignment.......: 248 313s Number of sites in alignment...........: 155 313s Number of chars in alignment...........: 37817 313s Mean site entropy in alignment.........: 0.215239 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 1938 237 -11 156 +1 36376 -1441 313s Number of sequences in alignment.......: 237 313s Number of sites in alignment...........: 156 313s Number of chars in alignment...........: 36376 313s Mean site entropy in alignment.........: 0.201826 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 1926 225 -12 157 +1 34752 -1624 313s Number of sequences in alignment.......: 225 313s Number of sites in alignment...........: 157 313s Number of chars in alignment...........: 34752 313s Mean site entropy in alignment.........: 0.184033 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 1779 78 -147 158 +1 12282 -22470 313s Number of sequences in alignment.......: 78 313s Number of sites in alignment...........: 158 313s Number of chars in alignment...........: 12282 313s Mean site entropy in alignment.........: 0.0830049 313s Choice Node #seq %seq #sites %sites #chars %chars 313s 1) 1703 2 -76 160 +2 320 -11962 313s Number of sequences in alignment.......: 2 313s Number of sites in alignment...........: 160 313s Number of chars in alignment...........: 320 313s Mean site entropy in alignment.........: 0 313s Choice Node #seq %seq #sites %sites #chars %chars 313s BppAlnOpt's done. Bye. 313s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 313s ****************************************************************** 313s * Bio++ Alignment Optimizer, version 1.1.0. * 313s * Author: J. Dutheil Last Modif. 14/03/18 * 313s * E. Figuet * 313s ****************************************************************** 313s 313s Parsing options: 313s Parsing file AlnOptimAuto.bpp for options. 313s Alphabet type .........................: Proteic 313s Sequence file .........................: PF01049_full.txt 313s Sequence format .......................: FASTA file 313s Minimum amount of data per site........: 0.7 313s Filter gap characters..................: yes 313s Filter unresolved characters...........: yes 313s Number of reference sequences..........: 0 313s Total number of sequences..............: 1652 313s Total number of sites..................: 656 313s Compressing sequences..................: 313s [ ] 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. 313s Memory required to store distances (Mb): 20 313s Computing pairwise overlap matrix......: 316s [> ] 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. 316s Clustering linkage mode................: centroid 316s Computing cluster tree.................: 321s [ ] 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. 322s Comparison criterion:..................: MaxSites 322s Number of sequences in alignment.......: 1652 322s Number of sites in alignment...........: 129 322s Number of chars in alignment...........: 182603 322s Mean site entropy in alignment.........: 0.394104 322s Choice Node #seq %seq #sites %sites #chars %chars 322s 1) 3297 1647 -5 131 +2 184783 2180 322s Number of sequences in alignment.......: 1647 322s Number of sites in alignment...........: 131 322s Number of chars in alignment...........: 184783 322s Mean site entropy in alignment.........: 0.394537 322s Choice Node #seq %seq #sites %sites #chars %chars 322s 1) 3295 1645 -2 132 +1 185880 1097 322s Number of sequences in alignment.......: 1645 322s Number of sites in alignment...........: 132 322s Number of chars in alignment...........: 185880 322s Mean site entropy in alignment.........: 0.394662 322s Choice Node #seq %seq #sites %sites #chars %chars 322s 1) 181 1644 -1 133 +1 187004 1124 322s Number of sequences in alignment.......: 1644 322s Number of sites in alignment...........: 133 322s Number of chars in alignment...........: 187004 322s Mean site entropy in alignment.........: 0.394618 322s Choice Node #seq %seq #sites %sites #chars %chars 322s 1) 3284 1634 -10 134 +1 187785 781 322s Number of sequences in alignment.......: 1634 322s Number of sites in alignment...........: 134 322s Number of chars in alignment...........: 187785 322s Mean site entropy in alignment.........: 0.395449 322s Choice Node #seq %seq #sites %sites #chars %chars 322s 1) 3277 1627 -7 135 +1 188649 864 323s Number of sequences in alignment.......: 1627 323s Number of sites in alignment...........: 135 323s Number of chars in alignment...........: 188649 323s Mean site entropy in alignment.........: 0.395884 323s Choice Node #seq %seq #sites %sites #chars %chars 323s 1) 3264 1614 -13 136 +1 189270 621 323s Number of sequences in alignment.......: 1614 323s Number of sites in alignment...........: 136 323s Number of chars in alignment...........: 189270 323s Mean site entropy in alignment.........: 0.396209 323s Choice Node #seq %seq #sites %sites #chars %chars 323s 1) 3158 1508 -106 137 +1 184807 -4463 323s Number of sequences in alignment.......: 1508 323s Number of sites in alignment...........: 137 323s Number of chars in alignment...........: 184807 323s Mean site entropy in alignment.........: 0.391659 323s Choice Node #seq %seq #sites %sites #chars %chars 323s 1) 3141 1491 -17 138 +1 184810 3 323s Number of sequences in alignment.......: 1491 323s Number of sites in alignment...........: 138 323s Number of chars in alignment...........: 184810 323s Mean site entropy in alignment.........: 0.389899 323s Choice Node #seq %seq #sites %sites #chars %chars 323s 1) 3135 1485 -6 139 +1 185468 658 323s Number of sequences in alignment.......: 1485 323s Number of sites in alignment...........: 139 323s Number of chars in alignment...........: 185468 323s Mean site entropy in alignment.........: 0.389868 323s Choice Node #seq %seq #sites %sites #chars %chars 323s 1) 3124 1474 -11 140 +1 185788 320 323s Number of sequences in alignment.......: 1474 323s Number of sites in alignment...........: 140 323s Number of chars in alignment...........: 185788 323s Mean site entropy in alignment.........: 0.389071 323s Choice Node #seq %seq #sites %sites #chars %chars 323s 1) 3091 1441 -33 141 +1 184655 -1133 323s Number of sequences in alignment.......: 1441 323s Number of sites in alignment...........: 141 323s Number of chars in alignment...........: 184655 323s Mean site entropy in alignment.........: 0.38709 323s Choice Node #seq %seq #sites %sites #chars %chars 323s 1) 3077 1427 -14 142 +1 184714 59 324s Number of sequences in alignment.......: 1427 324s Number of sites in alignment...........: 142 324s Number of chars in alignment...........: 184714 324s Mean site entropy in alignment.........: 0.386526 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 3055 1405 -22 144 +2 185186 472 324s Number of sequences in alignment.......: 1405 324s Number of sites in alignment...........: 144 324s Number of chars in alignment...........: 185186 324s Mean site entropy in alignment.........: 0.383626 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2907 1257 -148 145 +1 173927 -11259 324s Number of sequences in alignment.......: 1257 324s Number of sites in alignment...........: 145 324s Number of chars in alignment...........: 173927 324s Mean site entropy in alignment.........: 0.350796 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2807 1157 -100 146 +1 163983 -9944 324s Number of sequences in alignment.......: 1157 324s Number of sites in alignment...........: 146 324s Number of chars in alignment...........: 163983 324s Mean site entropy in alignment.........: 0.329626 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2748 1098 -59 147 +1 157592 -6391 324s Number of sequences in alignment.......: 1098 324s Number of sites in alignment...........: 147 324s Number of chars in alignment...........: 157592 324s Mean site entropy in alignment.........: 0.314432 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 1678 1070 -28 148 +1 154399 -3193 324s Number of sequences in alignment.......: 1070 324s Number of sites in alignment...........: 148 324s Number of chars in alignment...........: 154399 324s Mean site entropy in alignment.........: 0.303382 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2620 942 -128 149 +1 137516 -16883 324s Number of sequences in alignment.......: 942 324s Number of sites in alignment...........: 149 324s Number of chars in alignment...........: 137516 324s Mean site entropy in alignment.........: 0.284952 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2615 937 -5 150 +1 137462 -54 324s Number of sequences in alignment.......: 937 324s Number of sites in alignment...........: 150 324s Number of chars in alignment...........: 137462 324s Mean site entropy in alignment.........: 0.285064 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2320 642 -295 151 +1 95140 -42322 324s Number of sequences in alignment.......: 642 324s Number of sites in alignment...........: 151 324s Number of chars in alignment...........: 95140 324s Mean site entropy in alignment.........: 0.276628 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2179 501 -141 152 +1 74734 -20406 324s Number of sequences in alignment.......: 501 324s Number of sites in alignment...........: 152 324s Number of chars in alignment...........: 74734 324s Mean site entropy in alignment.........: 0.281366 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2108 430 -71 153 +1 64604 -10130 324s Number of sequences in alignment.......: 430 324s Number of sites in alignment...........: 153 324s Number of chars in alignment...........: 64604 324s Mean site entropy in alignment.........: 0.282214 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 2038 360 -70 154 +1 54522 -10082 324s Number of sequences in alignment.......: 360 324s Number of sites in alignment...........: 154 324s Number of chars in alignment...........: 54522 324s Mean site entropy in alignment.........: 0.265356 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 1969 291 -69 155 +1 44461 -10061 324s Number of sequences in alignment.......: 291 324s Number of sites in alignment...........: 155 324s Number of chars in alignment...........: 44461 324s Mean site entropy in alignment.........: 0.240018 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 1956 278 -13 156 +1 42693 -1768 324s Number of sequences in alignment.......: 278 324s Number of sites in alignment...........: 156 324s Number of chars in alignment...........: 42693 324s Mean site entropy in alignment.........: 0.236678 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 1925 247 -31 157 +1 38195 -4498 324s Number of sequences in alignment.......: 247 324s Number of sites in alignment...........: 157 324s Number of chars in alignment...........: 38195 324s Mean site entropy in alignment.........: 0.216008 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 1923 245 -2 158 +1 38065 -130 324s Number of sequences in alignment.......: 245 324s Number of sites in alignment...........: 158 324s Number of chars in alignment...........: 38065 324s Mean site entropy in alignment.........: 0.215165 324s Choice Node #seq %seq #sites %sites #chars %chars 324s 1) 610 1 -244 177 +19 177 -37888 324s Number of sequences in alignment.......: 1 324s Number of sites in alignment...........: 177 324s Number of chars in alignment...........: 177 324s Mean site entropy in alignment.........: 0 324s Choice Node #seq %seq #sites %sites #chars %chars 324s BppAlnOpt's done. Bye. 324s Total execution time: 0.000000d, 0.000000h, 0.000000m, 11.000000s. 324s ****************************************************************** 324s * Bio++ Alignment Optimizer, version 1.1.0. * 324s * Author: J. Dutheil Last Modif. 14/03/18 * 324s * E. Figuet * 324s ****************************************************************** 324s 324s Parsing options: 324s Parsing file AlnOptimAuto.bpp for options. 324s Alphabet type .........................: Proteic 324s Sequence file .........................: PF01049_full.txt 324s Sequence format .......................: FASTA file 325s Minimum amount of data per site........: 0.7 325s Filter gap characters..................: yes 325s Filter unresolved characters...........: yes 325s Number of reference sequences..........: 0 325s Total number of sequences..............: 1652 325s Total number of sites..................: 656 325s Compressing sequences..................: 325s [ ] 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. 325s Memory required to store distances (Mb): 20 325s Computing pairwise overlap matrix......: 327s [> ] 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. 327s Clustering linkage mode................: ward 327s Computing cluster tree.................: 333s [ ] 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. 333s Comparison criterion:..................: MaxSites 333s Number of sequences in alignment.......: 1652 333s Number of sites in alignment...........: 129 333s Number of chars in alignment...........: 182603 333s Mean site entropy in alignment.........: 0.394104 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3251 1647 -5 131 +2 184716 2113 333s Number of sequences in alignment.......: 1647 333s Number of sites in alignment...........: 131 333s Number of chars in alignment...........: 184716 333s Mean site entropy in alignment.........: 0.394659 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3238 1645 -2 132 +1 185817 1101 333s Number of sequences in alignment.......: 1645 333s Number of sites in alignment...........: 132 333s Number of chars in alignment...........: 185817 333s Mean site entropy in alignment.........: 0.394872 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 626 1644 -1 133 +1 186943 1126 333s Number of sequences in alignment.......: 1644 333s Number of sites in alignment...........: 133 333s Number of chars in alignment...........: 186943 333s Mean site entropy in alignment.........: 0.394963 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3225 1634 -10 134 +1 187538 595 333s Number of sequences in alignment.......: 1634 333s Number of sites in alignment...........: 134 333s Number of chars in alignment...........: 187538 333s Mean site entropy in alignment.........: 0.395167 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3259 1627 -7 135 +1 188469 931 333s Number of sequences in alignment.......: 1627 333s Number of sites in alignment...........: 135 333s Number of chars in alignment...........: 188469 333s Mean site entropy in alignment.........: 0.39572 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3231 1614 -13 136 +1 189043 574 333s Number of sequences in alignment.......: 1614 333s Number of sites in alignment...........: 136 333s Number of chars in alignment...........: 189043 333s Mean site entropy in alignment.........: 0.396503 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3276 1530 -84 139 +3 186415 -2628 333s Number of sequences in alignment.......: 1530 333s Number of sites in alignment...........: 139 333s Number of chars in alignment...........: 186415 333s Mean site entropy in alignment.........: 0.389001 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3232 1521 -9 140 +1 187030 615 333s Number of sequences in alignment.......: 1521 333s Number of sites in alignment...........: 140 333s Number of chars in alignment...........: 187030 333s Mean site entropy in alignment.........: 0.389238 333s Choice Node #seq %seq #sites %sites #chars %chars 333s 1) 3267 1485 -36 141 +1 185744 -1286 334s Number of sequences in alignment.......: 1485 334s Number of sites in alignment...........: 141 334s Number of chars in alignment...........: 185744 334s Mean site entropy in alignment.........: 0.389095 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 3288 1470 -15 142 +1 185982 238 334s Number of sequences in alignment.......: 1470 334s Number of sites in alignment...........: 142 334s Number of chars in alignment...........: 185982 334s Mean site entropy in alignment.........: 0.38758 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 3098 1457 -13 143 +1 185643 -339 334s Number of sequences in alignment.......: 1457 334s Number of sites in alignment...........: 143 334s Number of chars in alignment...........: 185643 334s Mean site entropy in alignment.........: 0.385646 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 3289 1411 -46 144 +1 183758 -1885 334s Number of sequences in alignment.......: 1411 334s Number of sites in alignment...........: 144 334s Number of chars in alignment...........: 183758 334s Mean site entropy in alignment.........: 0.38204 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 3273 1313 -98 145 +1 171322 -12436 334s Number of sequences in alignment.......: 1313 334s Number of sites in alignment...........: 145 334s Number of chars in alignment...........: 171322 334s Mean site entropy in alignment.........: 0.380643 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 3299 1133 -180 147 +2 152385 -18937 334s Number of sequences in alignment.......: 1133 334s Number of sites in alignment...........: 147 334s Number of chars in alignment...........: 152385 334s Mean site entropy in alignment.........: 0.346351 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 2941 1121 -12 148 +1 152294 -91 334s Number of sequences in alignment.......: 1121 334s Number of sites in alignment...........: 148 334s Number of chars in alignment...........: 152294 334s Mean site entropy in alignment.........: 0.340977 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 1664 1115 -6 149 +1 152613 319 334s Number of sequences in alignment.......: 1115 334s Number of sites in alignment...........: 149 334s Number of chars in alignment...........: 152613 334s Mean site entropy in alignment.........: 0.336552 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 3193 1104 -11 150 +1 152591 -22 334s Number of sequences in alignment.......: 1104 334s Number of sites in alignment...........: 150 334s Number of chars in alignment...........: 152591 334s Mean site entropy in alignment.........: 0.330411 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 2891 153 -951 157 +7 23971 -128620 334s Number of sequences in alignment.......: 153 334s Number of sites in alignment...........: 157 334s Number of chars in alignment...........: 23971 334s Mean site entropy in alignment.........: 0.0601394 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 1887 120 -33 158 +1 18876 -5095 334s Number of sequences in alignment.......: 120 334s Number of sites in alignment...........: 158 334s Number of chars in alignment...........: 18876 334s Mean site entropy in alignment.........: 0.0586193 334s Choice Node #seq %seq #sites %sites #chars %chars 334s BppAlnOpt's done. Bye. 334s Total execution time: 0.000000d, 0.000000h, 0.000000m, 10.000000s. 334s ****************************************************************** 334s * Bio++ Alignment Optimizer, version 1.1.0. * 334s * Author: J. Dutheil Last Modif. 14/03/18 * 334s * E. Figuet * 334s ****************************************************************** 334s 334s Parsing options: 334s Parsing file AlnOptimFasttreeStop.bpp for options. 334s Alphabet type .........................: Proteic 334s Sequence file .........................: PF01049_full.txt 334s Sequence format .......................: FASTA file 334s Minimum amount of data per site........: 0.7 334s Filter gap characters..................: yes 334s Filter unresolved characters...........: yes 334s Number of reference sequences..........: 0 334s Total number of sequences..............: 1652 334s Total number of sites..................: 656 334s Input tree file .......................: PF01049_fasttree.dnd 334s Input tree format .....................: Newick 334s Minimum number of sequences to keep....: 826 334s Comparison criterion:..................: MaxSites 334s Number of sequences in alignment.......: 1652 334s Number of sites in alignment...........: 129 334s Number of chars in alignment...........: 182603 334s Mean site entropy in alignment.........: 0.394104 334s Choice Node #seq %seq #sites %sites #chars %chars 334s 1) 2030 1647 -5 131 +2 184714 2111 335s Number of sequences in alignment.......: 1647 335s Number of sites in alignment...........: 131 335s Number of chars in alignment...........: 184714 335s Mean site entropy in alignment.........: 0.394129 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 1930 1645 -2 132 +1 185794 1080 335s Number of sequences in alignment.......: 1645 335s Number of sites in alignment...........: 132 335s Number of chars in alignment...........: 185794 335s Mean site entropy in alignment.........: 0.394195 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 1882 1644 -1 133 +1 186920 1126 335s Number of sequences in alignment.......: 1644 335s Number of sites in alignment...........: 133 335s Number of chars in alignment...........: 186920 335s Mean site entropy in alignment.........: 0.394263 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 386 1634 -10 134 +1 187634 714 335s Number of sequences in alignment.......: 1634 335s Number of sites in alignment...........: 134 335s Number of chars in alignment...........: 187634 335s Mean site entropy in alignment.........: 0.394887 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 357 1627 -7 135 +1 188437 803 335s Number of sequences in alignment.......: 1627 335s Number of sites in alignment...........: 135 335s Number of chars in alignment...........: 188437 335s Mean site entropy in alignment.........: 0.394741 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 1736 1614 -13 136 +1 188713 276 335s Number of sequences in alignment.......: 1614 335s Number of sites in alignment...........: 136 335s Number of chars in alignment...........: 188713 335s Mean site entropy in alignment.........: 0.394145 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 1489 1527 -87 137 +1 181488 -7225 335s Number of sequences in alignment.......: 1527 335s Number of sites in alignment...........: 137 335s Number of chars in alignment...........: 181488 335s Mean site entropy in alignment.........: 0.378687 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 2247 1524 -3 138 +1 182435 947 335s Number of sequences in alignment.......: 1524 335s Number of sites in alignment...........: 138 335s Number of chars in alignment...........: 182435 335s Mean site entropy in alignment.........: 0.378731 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 408 1515 -9 139 +1 183008 573 335s Number of sequences in alignment.......: 1515 335s Number of sites in alignment...........: 139 335s Number of chars in alignment...........: 183008 335s Mean site entropy in alignment.........: 0.377294 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 1819 1488 -27 140 +1 182208 -800 335s Number of sequences in alignment.......: 1488 335s Number of sites in alignment...........: 140 335s Number of chars in alignment...........: 182208 335s Mean site entropy in alignment.........: 0.374188 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 1676 1464 -24 141 +1 180695 -1513 335s Number of sequences in alignment.......: 1464 335s Number of sites in alignment...........: 141 335s Number of chars in alignment...........: 180695 335s Mean site entropy in alignment.........: 0.371696 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 416 1457 -7 142 +1 181323 628 335s Number of sequences in alignment.......: 1457 335s Number of sites in alignment...........: 142 335s Number of chars in alignment...........: 181323 335s Mean site entropy in alignment.........: 0.36917 335s Choice Node #seq %seq #sites %sites #chars %chars 335s 1) 1823 1371 -86 143 +1 176415 -4908 336s Number of sequences in alignment.......: 1371 336s Number of sites in alignment...........: 143 336s Number of chars in alignment...........: 176415 336s Mean site entropy in alignment.........: 0.359961 336s Choice Node #seq %seq #sites %sites #chars %chars 336s 1) 783 1355 -16 144 +1 175237 -1178 336s Number of sequences in alignment.......: 1355 336s Number of sites in alignment...........: 144 336s Number of chars in alignment...........: 175237 336s Mean site entropy in alignment.........: 0.360644 336s Choice Node #seq %seq #sites %sites #chars %chars 336s 1) 953 1307 -48 145 +1 169472 -5765 336s Number of sequences in alignment.......: 1307 336s Number of sites in alignment...........: 145 336s Number of chars in alignment...........: 169472 336s Mean site entropy in alignment.........: 0.363152 336s Choice Node #seq %seq #sites %sites #chars %chars 336s Output alignment file .................: PF01049_optimized_fastml.fasta 336s Output alignment format ...............: FASTA file 336s Output tree file ......................: PF01049_optimized_fastml.dnd 336s Output tree format ....................: Newick 336s BppAlnOpt's done. Bye. 336s Total execution time: 0.000000d, 0.000000h, 0.000000m, 2.000000s. 336s PASS 336s autopkgtest [14:26:55]: test run-unit-test: -----------------------] 337s autopkgtest [14:26:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 337s run-unit-test PASS 337s autopkgtest [14:26:56]: @@@@@@@@@@@@@@@@@@@@ summary 337s run-unit-test PASS 354s nova [W] Using flock in prodstack6-arm64 354s Creating nova instance adt-plucky-arm64-physamp-20250315-142119-juju-7f2275-prod-proposed-migration-environment-20-7f450bd9-190f-4c85-8b05-58687ba8ec6e from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 354s nova [W] Timed out waiting for 8310b1b8-f03c-4819-9723-f4952c70a1ab to get deleted.