0s autopkgtest [16:41:39]: starting date and time: 2025-03-15 16:41:39+0000 0s autopkgtest [16:41:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:41:39]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rfc5ma88/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-4.secgroup --name adt-plucky-s390x-physamp-20250315-164138-juju-7f2275-prod-proposed-migration-environment-15-7de34058-d2f9-446c-93ad-2ce03e12c0d6 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/ 139s autopkgtest [16:43:58]: testbed dpkg architecture: s390x 139s autopkgtest [16:43:58]: testbed apt version: 2.9.33 140s autopkgtest [16:43:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s autopkgtest [16:43:59]: testbed release detected to be: None 140s autopkgtest [16:43:59]: updating testbed package index (apt update) 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 141s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 141s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 141s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 142s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 142s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 142s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 143s Fetched 1073 kB in 2s (626 kB/s) 143s Reading package lists... 144s + lsb_release --codename --short 144s + RELEASE=plucky 144s + cat 144s + [ plucky != trusty ] 144s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 144s Calculating upgrade... 144s The following packages were automatically installed and are no longer required: 144s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 144s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 144s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 144s linux-tools-6.11.0-8-generic 144s Use 'sudo apt autoremove' to remove them. 144s The following packages will be upgraded: 144s pinentry-curses python3-jinja2 strace 144s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 652 kB of archives. 144s After this operation, 27.6 kB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 145s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 146s Fetched 652 kB in 1s (585 kB/s) 146s (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 ... 81428 files and directories currently installed.) 146s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 146s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 146s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 146s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 146s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 146s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 146s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 146s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 146s Setting up strace (6.13+ds-1ubuntu1) ... 146s Processing triggers for man-db (2.13.0-1) ... 147s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 147s + /usr/lib/apt/apt-helper analyze-pattern ?true 147s + uname -r 147s + sed s/\./\\./g 147s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 147s + apt list ?obsolete 147s + tail -n+2 147s + grep -v ^linux-.*6\.14\.0-10-generic.* 147s + cut -d/ -f1 147s + obsolete_pkgs=linux-headers-6.11.0-8-generic 147s linux-headers-6.11.0-8 147s linux-modules-6.11.0-8-generic 147s linux-tools-6.11.0-8-generic 147s linux-tools-6.11.0-8 147s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 147s The following packages will be REMOVED: 147s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 147s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 147s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 147s linux-tools-6.11.0-8-generic* 147s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 147s After this operation, 167 MB disk space will be freed. 147s (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 ... 81428 files and directories currently installed.) 147s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 147s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 147s Removing libpython3.12t64:s390x (3.12.9-1) ... 147s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 147s Removing libnsl2:s390x (1.3.0-3build3) ... 147s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 147s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 147s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 148s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 148s Processing triggers for libc-bin (2.41-1ubuntu1) ... 148s (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 ... 56328 files and directories currently installed.) 148s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 148s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 149s + grep -q trusty /etc/lsb-release 149s + [ ! -d /usr/share/doc/unattended-upgrades ] 149s + [ ! -d /usr/share/doc/lxd ] 149s + [ ! -d /usr/share/doc/lxd-client ] 149s + [ ! -d /usr/share/doc/snapd ] 149s + type iptables 149s + cat 149s + chmod 755 /etc/rc.local 149s + . /etc/rc.local 149s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 149s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 149s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 149s + uname -m 149s + [ s390x = ppc64le ] 149s + [ -d /run/systemd/system ] 149s + systemd-detect-virt --quiet --vm 149s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 149s + cat 149s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 149s + echo COMPRESS=lz4 149s autopkgtest [16:44:08]: upgrading testbed (apt dist-upgrade and autopurge) 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 149s Entering ResolveByKeep 149s 149s Calculating upgrade... 150s The following packages will be upgraded: 150s libc-bin libc-dev-bin libc6 libc6-dev locales 150s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 9512 kB of archives. 150s After this operation, 8192 B of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 152s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 152s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 155s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 155s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 160s Preconfiguring packages ... 160s Fetched 9512 kB in 10s (944 kB/s) 160s (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 ... 56326 files and directories currently installed.) 160s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Setting up libc6:s390x (2.41-1ubuntu2) ... 160s (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 ... 56326 files and directories currently installed.) 160s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Setting up libc-bin (2.41-1ubuntu2) ... 160s (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 ... 56326 files and directories currently installed.) 160s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 160s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 161s Setting up locales (2.41-1ubuntu2) ... 161s Generating locales (this might take a while)... 162s en_US.UTF-8... done 162s Generation complete. 162s Setting up libc-dev-bin (2.41-1ubuntu2) ... 162s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 162s Processing triggers for man-db (2.13.0-1) ... 162s Processing triggers for systemd (257.3-1ubuntu3) ... 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 164s Done 164s Solving dependencies... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s autopkgtest [16:44:23]: rebooting testbed after setup commands that affected boot 183s autopkgtest [16:44:42]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 186s autopkgtest [16:44:45]: @@@@@@@@@@@@@@@@@@@@ apt-source physamp 188s Get:1 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (dsc) [2001 B] 188s Get:2 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (tar) [242 kB] 188s Get:3 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (diff) [3924 B] 188s gpgv: Signature made Mon Mar 25 18:00:09 2024 UTC 188s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 188s gpgv: Can't check signature: No public key 188s dpkg-source: warning: cannot verify inline signature for ./physamp_1.1.0-5.dsc: no acceptable signature found 188s autopkgtest [16:44:47]: testing package physamp version 1.1.0-5 188s autopkgtest [16:44:47]: build not needed 189s autopkgtest [16:44:48]: test run-unit-test: preparing testbed 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 190s The following NEW packages will be installed: 190s libbpp-core4t64 libbpp-phyl12t64 libbpp-seq12t64 physamp 190s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 190s Need to get 3173 kB of archives. 190s After this operation, 16.6 MB of additional disk space will be used. 190s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x libbpp-core4t64 s390x 2.4.1-13 [546 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libbpp-seq12t64 s390x 2.4.1-13 [440 kB] 191s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libbpp-phyl12t64 s390x 2.4.1-9.1ubuntu3 [2006 kB] 194s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x physamp s390x 1.1.0-5 [181 kB] 194s Fetched 3173 kB in 4s (752 kB/s) 194s Selecting previously unselected package libbpp-core4t64:s390x. 194s (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 ... 56326 files and directories currently installed.) 194s Preparing to unpack .../libbpp-core4t64_2.4.1-13_s390x.deb ... 194s Unpacking libbpp-core4t64:s390x (2.4.1-13) ... 194s Selecting previously unselected package libbpp-seq12t64:s390x. 194s Preparing to unpack .../libbpp-seq12t64_2.4.1-13_s390x.deb ... 194s Unpacking libbpp-seq12t64:s390x (2.4.1-13) ... 194s Selecting previously unselected package libbpp-phyl12t64:s390x. 194s Preparing to unpack .../libbpp-phyl12t64_2.4.1-9.1ubuntu3_s390x.deb ... 194s Unpacking libbpp-phyl12t64:s390x (2.4.1-9.1ubuntu3) ... 194s Selecting previously unselected package physamp. 194s Preparing to unpack .../physamp_1.1.0-5_s390x.deb ... 194s Unpacking physamp (1.1.0-5) ... 194s Setting up libbpp-core4t64:s390x (2.4.1-13) ... 194s Setting up libbpp-seq12t64:s390x (2.4.1-13) ... 194s Setting up libbpp-phyl12t64:s390x (2.4.1-9.1ubuntu3) ... 194s Setting up physamp (1.1.0-5) ... 194s Processing triggers for man-db (2.13.0-1) ... 195s Processing triggers for install-info (7.1.1-1) ... 195s Processing triggers for libc-bin (2.41-1ubuntu2) ... 196s autopkgtest [16:44:55]: test run-unit-test: [----------------------- 196s ****************************************************************** 196s * Bio++ Alignment Optimizer, version 1.1.0. * 196s * Author: J. Dutheil Last Modif. 14/03/18 * 196s * E. Figuet * 196s ****************************************************************** 196s 196s Parsing options: 196s Parsing file AlnOptimFasttree.bpp for options. 196s Alphabet type .........................: Proteic 196s Sequence file .........................: PF01049_full.txt 196s Sequence format .......................: FASTA file 196s Minimum amount of data per site........: 0.7 196s Filter gap characters..................: yes 196s Filter unresolved characters...........: yes 196s Number of reference sequences..........: 0 196s Total number of sequences..............: 1652 196s Total number of sites..................: 656 196s Input tree file .......................: PF01049_fasttree.dnd 196s Input tree format .....................: Newick 196s Comparison criterion:..................: MaxSites 196s Number of sequences in alignment.......: 1652 196s Number of sites in alignment...........: 129 196s Number of chars in alignment...........: 182603 196s Mean site entropy in alignment.........: 0.394104 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 2030 1647 -5 131 +2 184714 2111 196s Number of sequences in alignment.......: 1647 196s Number of sites in alignment...........: 131 196s Number of chars in alignment...........: 184714 196s Mean site entropy in alignment.........: 0.394129 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 1930 1645 -2 132 +1 185794 1080 196s Number of sequences in alignment.......: 1645 196s Number of sites in alignment...........: 132 196s Number of chars in alignment...........: 185794 196s Mean site entropy in alignment.........: 0.394195 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 1882 1644 -1 133 +1 186920 1126 196s Number of sequences in alignment.......: 1644 196s Number of sites in alignment...........: 133 196s Number of chars in alignment...........: 186920 196s Mean site entropy in alignment.........: 0.394263 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 386 1634 -10 134 +1 187634 714 197s Number of sequences in alignment.......: 1634 197s Number of sites in alignment...........: 134 197s Number of chars in alignment...........: 187634 197s Mean site entropy in alignment.........: 0.394887 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 357 1627 -7 135 +1 188437 803 197s Number of sequences in alignment.......: 1627 197s Number of sites in alignment...........: 135 197s Number of chars in alignment...........: 188437 197s Mean site entropy in alignment.........: 0.394741 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 1736 1614 -13 136 +1 188713 276 197s Number of sequences in alignment.......: 1614 197s Number of sites in alignment...........: 136 197s Number of chars in alignment...........: 188713 197s Mean site entropy in alignment.........: 0.394145 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 1489 1527 -87 137 +1 181488 -7225 197s Number of sequences in alignment.......: 1527 197s Number of sites in alignment...........: 137 197s Number of chars in alignment...........: 181488 197s Mean site entropy in alignment.........: 0.378687 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2247 1524 -3 138 +1 182435 947 197s Number of sequences in alignment.......: 1524 197s Number of sites in alignment...........: 138 197s Number of chars in alignment...........: 182435 197s Mean site entropy in alignment.........: 0.378731 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 408 1515 -9 139 +1 183008 573 197s Number of sequences in alignment.......: 1515 197s Number of sites in alignment...........: 139 197s Number of chars in alignment...........: 183008 197s Mean site entropy in alignment.........: 0.377294 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 1819 1488 -27 140 +1 182208 -800 197s Number of sequences in alignment.......: 1488 197s Number of sites in alignment...........: 140 197s Number of chars in alignment...........: 182208 197s Mean site entropy in alignment.........: 0.374188 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 1676 1464 -24 141 +1 180695 -1513 197s Number of sequences in alignment.......: 1464 197s Number of sites in alignment...........: 141 197s Number of chars in alignment...........: 180695 197s Mean site entropy in alignment.........: 0.371696 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 416 1457 -7 142 +1 181323 628 197s Number of sequences in alignment.......: 1457 197s Number of sites in alignment...........: 142 197s Number of chars in alignment...........: 181323 197s Mean site entropy in alignment.........: 0.36917 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 1823 1371 -86 143 +1 176415 -4908 197s Number of sequences in alignment.......: 1371 197s Number of sites in alignment...........: 143 197s Number of chars in alignment...........: 176415 197s Mean site entropy in alignment.........: 0.359961 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 783 1355 -16 144 +1 175237 -1178 197s Number of sequences in alignment.......: 1355 197s Number of sites in alignment...........: 144 197s Number of chars in alignment...........: 175237 197s Mean site entropy in alignment.........: 0.360644 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 953 1307 -48 145 +1 169472 -5765 197s Number of sequences in alignment.......: 1307 197s Number of sites in alignment...........: 145 197s Number of chars in alignment...........: 169472 197s Mean site entropy in alignment.........: 0.363152 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2269 476 -831 146 +1 66187 -103285 197s Number of sequences in alignment.......: 476 197s Number of sites in alignment...........: 146 197s Number of chars in alignment...........: 66187 197s Mean site entropy in alignment.........: 0.249565 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2488 413 -63 147 +1 57456 -8731 197s Number of sequences in alignment.......: 413 197s Number of sites in alignment...........: 147 197s Number of chars in alignment...........: 57456 197s Mean site entropy in alignment.........: 0.249617 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2372 411 -2 148 +1 57619 163 198s Number of sequences in alignment.......: 411 198s Number of sites in alignment...........: 148 198s Number of chars in alignment...........: 57619 198s Mean site entropy in alignment.........: 0.248169 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 179 391 -20 149 +1 55008 -2611 198s Number of sequences in alignment.......: 391 198s Number of sites in alignment...........: 149 198s Number of chars in alignment...........: 55008 198s Mean site entropy in alignment.........: 0.249151 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 2697 54 -337 151 +2 7794 -47214 198s Number of sequences in alignment.......: 54 198s Number of sites in alignment...........: 151 198s Number of chars in alignment...........: 7794 198s Mean site entropy in alignment.........: 0.0871024 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 2628 50 -4 152 +1 7230 -564 198s Number of sequences in alignment.......: 50 198s Number of sites in alignment...........: 152 198s Number of chars in alignment...........: 7230 198s Mean site entropy in alignment.........: 0.0864589 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 2692 48 -2 153 +1 7110 -120 198s Number of sequences in alignment.......: 48 198s Number of sites in alignment...........: 153 198s Number of chars in alignment...........: 7110 198s Mean site entropy in alignment.........: 0.0765764 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 2695 10 -38 154 +1 1526 -5584 198s Number of sequences in alignment.......: 10 198s Number of sites in alignment...........: 154 198s Number of chars in alignment...........: 1526 198s Mean site entropy in alignment.........: 0.0596881 198s Choice Node #seq %seq #sites %sites #chars %chars 198s 1) 2611 2 -8 156 +2 312 -1214 198s Number of sequences in alignment.......: 2 198s Number of sites in alignment...........: 156 198s Number of chars in alignment...........: 312 198s Mean site entropy in alignment.........: 0.0190193 198s Choice Node #seq %seq #sites %sites #chars %chars 198s BppAlnOpt's done. Bye. 198s Total execution time: 0.000000d, 0.000000h, 0.000000m, 2.000000s. 198s ****************************************************************** 198s * Bio++ Alignment Optimizer, version 1.1.0. * 198s * Author: J. Dutheil Last Modif. 14/03/18 * 198s * E. Figuet * 198s ****************************************************************** 198s 198s Parsing options: 198s Parsing file AlnOptimAuto.bpp for options. 198s Alphabet type .........................: Proteic 198s Sequence file .........................: PF01049_full.txt 198s Sequence format .......................: FASTA file 198s Minimum amount of data per site........: 0.7 198s Filter gap characters..................: yes 198s Filter unresolved characters...........: yes 198s Number of reference sequences..........: 0 198s Total number of sequences..............: 1652 198s Total number of sites..................: 656 198s Compressing sequences..................: 198s [ ] 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. 198s Memory required to store distances (Mb): 20 198s Computing pairwise overlap matrix......: 201s [> ] 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. 201s Clustering linkage mode................: complete 201s Computing cluster tree.................: 208s [ ] 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. 208s Comparison criterion:..................: MaxSites 208s Number of sequences in alignment.......: 1652 208s Number of sites in alignment...........: 129 208s Number of chars in alignment...........: 182603 208s Mean site entropy in alignment.........: 0.394104 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 3294 1647 -5 131 +2 184716 2113 208s Number of sequences in alignment.......: 1647 208s Number of sites in alignment...........: 131 208s Number of chars in alignment...........: 184716 208s Mean site entropy in alignment.........: 0.394659 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 3286 1645 -2 132 +1 185817 1101 209s Number of sequences in alignment.......: 1645 209s Number of sites in alignment...........: 132 209s Number of chars in alignment...........: 185817 209s Mean site entropy in alignment.........: 0.394872 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 536 1644 -1 133 +1 186943 1126 209s Number of sequences in alignment.......: 1644 209s Number of sites in alignment...........: 133 209s Number of chars in alignment...........: 186943 209s Mean site entropy in alignment.........: 0.39494 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 3270 1634 -10 134 +1 187657 714 209s Number of sequences in alignment.......: 1634 209s Number of sites in alignment...........: 134 209s Number of chars in alignment...........: 187657 209s Mean site entropy in alignment.........: 0.395564 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 2951 1627 -7 135 +1 188449 792 209s Number of sequences in alignment.......: 1627 209s Number of sites in alignment...........: 135 209s Number of chars in alignment...........: 188449 209s Mean site entropy in alignment.........: 0.392385 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 3021 1614 -13 136 +1 188658 209 209s Number of sequences in alignment.......: 1614 209s Number of sites in alignment...........: 136 209s Number of chars in alignment...........: 188658 209s Mean site entropy in alignment.........: 0.391197 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 3235 1545 -69 137 +1 185332 -3326 209s Number of sequences in alignment.......: 1545 209s Number of sites in alignment...........: 137 209s Number of chars in alignment...........: 185332 209s Mean site entropy in alignment.........: 0.389695 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 3249 1542 -3 138 +1 186300 968 209s Number of sequences in alignment.......: 1542 209s Number of sites in alignment...........: 138 209s Number of chars in alignment...........: 186300 209s Mean site entropy in alignment.........: 0.389735 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 3247 1537 -5 139 +1 187136 836 209s Number of sequences in alignment.......: 1537 209s Number of sites in alignment...........: 139 209s Number of chars in alignment...........: 187136 209s Mean site entropy in alignment.........: 0.389763 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 2816 1521 -16 140 +1 186509 -627 209s Number of sequences in alignment.......: 1521 209s Number of sites in alignment...........: 140 209s Number of chars in alignment...........: 186509 209s Mean site entropy in alignment.........: 0.38832 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 3130 1471 -50 141 +1 183898 -2611 209s Number of sequences in alignment.......: 1471 209s Number of sites in alignment...........: 141 209s Number of chars in alignment...........: 183898 209s Mean site entropy in alignment.........: 0.370103 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1147 1470 -1 142 +1 184902 1004 210s Number of sequences in alignment.......: 1470 210s Number of sites in alignment...........: 142 210s Number of chars in alignment...........: 184902 210s Mean site entropy in alignment.........: 0.370154 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 3251 1465 -5 143 +1 185674 772 210s Number of sequences in alignment.......: 1465 210s Number of sites in alignment...........: 143 210s Number of chars in alignment...........: 185674 210s Mean site entropy in alignment.........: 0.370155 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 3280 1391 -74 144 +1 181655 -4019 210s Number of sequences in alignment.......: 1391 210s Number of sites in alignment...........: 144 210s Number of chars in alignment...........: 181655 210s Mean site entropy in alignment.........: 0.359169 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2928 1340 -51 145 +1 177148 -4507 210s Number of sequences in alignment.......: 1340 210s Number of sites in alignment...........: 145 210s Number of chars in alignment...........: 177148 210s Mean site entropy in alignment.........: 0.351822 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 3168 1159 -181 146 +1 163916 -13232 210s Number of sequences in alignment.......: 1159 210s Number of sites in alignment...........: 146 210s Number of chars in alignment...........: 163916 210s Mean site entropy in alignment.........: 0.32945 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2651 1117 -42 147 +1 158726 -5190 210s Number of sequences in alignment.......: 1117 210s Number of sites in alignment...........: 147 210s Number of chars in alignment...........: 158726 210s Mean site entropy in alignment.........: 0.331341 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2242 1097 -20 148 +1 156673 -2053 210s Number of sequences in alignment.......: 1097 210s Number of sites in alignment...........: 148 210s Number of chars in alignment...........: 156673 210s Mean site entropy in alignment.........: 0.324708 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2221 1078 -19 149 +1 154673 -2000 210s Number of sequences in alignment.......: 1078 210s Number of sites in alignment...........: 149 210s Number of chars in alignment...........: 154673 210s Mean site entropy in alignment.........: 0.326137 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2944 993 -85 150 +1 144901 -9772 210s Number of sequences in alignment.......: 993 210s Number of sites in alignment...........: 150 210s Number of chars in alignment...........: 144901 210s Mean site entropy in alignment.........: 0.302006 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2554 941 -52 151 +1 137854 -7047 210s Number of sequences in alignment.......: 941 210s Number of sites in alignment...........: 151 210s Number of chars in alignment...........: 137854 210s Mean site entropy in alignment.........: 0.304205 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2675 234 -707 157 +6 36220 -101634 210s Number of sequences in alignment.......: 234 210s Number of sites in alignment...........: 157 210s Number of chars in alignment...........: 36220 210s Mean site entropy in alignment.........: 0.18992 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 2046 230 -4 158 +1 35777 -443 210s Number of sequences in alignment.......: 230 210s Number of sites in alignment...........: 158 210s Number of chars in alignment...........: 35777 210s Mean site entropy in alignment.........: 0.188188 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 1950 24 -206 160 +2 3795 -31982 210s Number of sequences in alignment.......: 24 210s Number of sites in alignment...........: 160 210s Number of chars in alignment...........: 3795 210s Mean site entropy in alignment.........: 0.185344 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 1896 20 -4 161 +1 3193 -602 210s Number of sequences in alignment.......: 20 210s Number of sites in alignment...........: 161 210s Number of chars in alignment...........: 3193 210s Mean site entropy in alignment.........: 0.133241 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 1795 18 -2 163 +2 2911 -282 210s Number of sequences in alignment.......: 18 210s Number of sites in alignment...........: 163 210s Number of chars in alignment...........: 2911 210s Mean site entropy in alignment.........: 0.122561 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 1718 14 -4 165 +2 2294 -617 210s Number of sequences in alignment.......: 14 210s Number of sites in alignment...........: 165 210s Number of chars in alignment...........: 2294 210s Mean site entropy in alignment.........: 0.0452968 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 1707 12 -2 166 +1 1983 -311 210s Number of sequences in alignment.......: 12 210s Number of sites in alignment...........: 166 210s Number of chars in alignment...........: 1983 210s Mean site entropy in alignment.........: 0.0379699 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 397 11 -1 168 +2 1838 -145 210s Number of sequences in alignment.......: 11 210s Number of sites in alignment...........: 168 210s Number of chars in alignment...........: 1838 210s Mean site entropy in alignment.........: 0.03305 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 1682 8 -3 169 +1 1349 -489 210s Number of sequences in alignment.......: 8 210s Number of sites in alignment...........: 169 210s Number of chars in alignment...........: 1349 210s Mean site entropy in alignment.........: 0.0183685 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 46 7 -1 172 +3 1196 -153 210s Number of sequences in alignment.......: 7 210s Number of sites in alignment...........: 172 210s Number of chars in alignment...........: 1196 210s Mean site entropy in alignment.........: 0.0178367 210s Choice Node #seq %seq #sites %sites #chars %chars 210s 1) 1664 2 -5 176 +4 352 -844 210s Number of sequences in alignment.......: 2 210s Number of sites in alignment...........: 176 210s Number of chars in alignment...........: 352 210s Mean site entropy in alignment.........: 0.010038 210s Choice Node #seq %seq #sites %sites #chars %chars 210s BppAlnOpt's done. Bye. 210s Total execution time: -1.000000d, 23.000000h, 58.000000m, 47.000000s. 210s ****************************************************************** 210s * Bio++ Alignment Optimizer, version 1.1.0. * 210s * Author: J. Dutheil Last Modif. 14/03/18 * 210s * E. Figuet * 210s ****************************************************************** 210s 210s Parsing options: 210s Parsing file AlnOptimAuto.bpp for options. 210s Alphabet type .........................: Proteic 210s Sequence file .........................: PF01049_full.txt 210s Sequence format .......................: FASTA file 210s Minimum amount of data per site........: 0.7 210s Filter gap characters..................: yes 210s Filter unresolved characters...........: yes 210s Number of reference sequences..........: 0 210s Total number of sequences..............: 1652 210s Total number of sites..................: 656 210s Compressing sequences..................: 210s [ ] 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. 210s Memory required to store distances (Mb): 20 210s Computing pairwise overlap matrix......: 213s [> ] 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. 213s Clustering linkage mode................: single 213s Computing cluster tree.................: 221s [ ] 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. 221s Comparison criterion:..................: MaxSites 221s Number of sequences in alignment.......: 1652 221s Number of sites in alignment...........: 129 221s Number of chars in alignment...........: 182603 221s Mean site entropy in alignment.........: 0.394104 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 3297 1647 -5 131 +2 184776 2173 221s Number of sequences in alignment.......: 1647 221s Number of sites in alignment...........: 131 221s Number of chars in alignment...........: 184776 221s Mean site entropy in alignment.........: 0.394536 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 3295 1645 -2 132 +1 185874 1098 221s Number of sequences in alignment.......: 1645 221s Number of sites in alignment...........: 132 221s Number of chars in alignment...........: 185874 221s Mean site entropy in alignment.........: 0.394721 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 181 1644 -1 133 +1 186998 1124 221s Number of sequences in alignment.......: 1644 221s Number of sites in alignment...........: 133 221s Number of chars in alignment...........: 186998 221s Mean site entropy in alignment.........: 0.394677 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 3285 1634 -10 134 +1 187772 774 222s Number of sequences in alignment.......: 1634 222s Number of sites in alignment...........: 134 222s Number of chars in alignment...........: 187772 222s Mean site entropy in alignment.........: 0.395614 222s Choice Node #seq %seq #sites %sites #chars %chars 222s 1) 3278 1627 -7 135 +1 188620 848 222s Number of sequences in alignment.......: 1627 222s Number of sites in alignment...........: 135 222s Number of chars in alignment...........: 188620 222s Mean site entropy in alignment.........: 0.396053 222s Choice Node #seq %seq #sites %sites #chars %chars 222s 1) 3265 1614 -13 136 +1 189192 572 222s Number of sequences in alignment.......: 1614 222s Number of sites in alignment...........: 136 222s Number of chars in alignment...........: 189192 222s Mean site entropy in alignment.........: 0.396866 222s Choice Node #seq %seq #sites %sites #chars %chars 222s 1) 3157 1505 -109 137 +1 184306 -4886 222s Number of sequences in alignment.......: 1505 222s Number of sites in alignment...........: 137 222s Number of chars in alignment...........: 184306 222s Mean site entropy in alignment.........: 0.397698 222s Choice Node #seq %seq #sites %sites #chars %chars 222s 1) 3139 1488 -17 138 +1 184277 -29 222s Number of sequences in alignment.......: 1488 222s Number of sites in alignment...........: 138 222s Number of chars in alignment...........: 184277 222s Mean site entropy in alignment.........: 0.396924 222s Choice Node #seq %seq #sites %sites #chars %chars 222s 1) 3136 1485 -3 139 +1 185134 857 222s Number of sequences in alignment.......: 1485 222s Number of sites in alignment...........: 139 222s Number of chars in alignment...........: 185134 222s Mean site entropy in alignment.........: 0.396707 222s Choice Node #seq %seq #sites %sites #chars %chars 222s 1) 3122 1471 -14 140 +1 185214 80 222s Number of sequences in alignment.......: 1471 222s Number of sites in alignment...........: 140 222s Number of chars in alignment...........: 185214 222s Mean site entropy in alignment.........: 0.396624 222s Choice Node #seq %seq #sites %sites #chars %chars 222s 1) 2848 1437 -34 141 +1 183753 -1461 223s Number of sequences in alignment.......: 1437 223s Number of sites in alignment...........: 141 223s Number of chars in alignment...........: 183753 223s Mean site entropy in alignment.........: 0.379676 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 3110 1425 -12 142 +1 183898 145 223s Number of sequences in alignment.......: 1425 223s Number of sites in alignment...........: 142 223s Number of chars in alignment...........: 183898 223s Mean site entropy in alignment.........: 0.379975 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 3073 1387 -38 143 +1 182369 -1529 223s Number of sequences in alignment.......: 1387 223s Number of sites in alignment...........: 143 223s Number of chars in alignment...........: 182369 223s Mean site entropy in alignment.........: 0.376594 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 2904 1380 -7 144 +1 182593 224 223s Number of sequences in alignment.......: 1380 223s Number of sites in alignment...........: 144 223s Number of chars in alignment...........: 182593 223s Mean site entropy in alignment.........: 0.375989 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 2941 1206 -174 145 +1 167869 -14724 223s Number of sequences in alignment.......: 1206 223s Number of sites in alignment...........: 145 223s Number of chars in alignment...........: 167869 223s Mean site entropy in alignment.........: 0.346494 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 2829 1145 -61 146 +1 162413 -5456 223s Number of sequences in alignment.......: 1145 223s Number of sites in alignment...........: 146 223s Number of chars in alignment...........: 162413 223s Mean site entropy in alignment.........: 0.332586 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 2751 1071 -74 147 +1 153723 -8690 223s Number of sequences in alignment.......: 1071 223s Number of sites in alignment...........: 147 223s Number of chars in alignment...........: 153723 223s Mean site entropy in alignment.........: 0.320762 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 1751 998 -73 148 +1 144121 -9602 223s Number of sequences in alignment.......: 998 223s Number of sites in alignment...........: 148 223s Number of chars in alignment...........: 144121 223s Mean site entropy in alignment.........: 0.298818 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 2100 985 -13 149 +1 142964 -1157 223s Number of sequences in alignment.......: 985 223s Number of sites in alignment...........: 149 223s Number of chars in alignment...........: 142964 223s Mean site entropy in alignment.........: 0.298279 223s Choice Node #seq %seq #sites %sites #chars %chars 223s 1) 2427 665 -320 150 +1 97526 -45438 224s Number of sequences in alignment.......: 665 224s Number of sites in alignment...........: 150 224s Number of chars in alignment...........: 97526 224s Mean site entropy in alignment.........: 0.293825 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 1379 664 -1 151 +1 97882 356 224s Number of sequences in alignment.......: 664 224s Number of sites in alignment...........: 151 224s Number of chars in alignment...........: 97882 224s Mean site entropy in alignment.........: 0.292162 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 2203 441 -223 152 +1 65487 -32395 224s Number of sequences in alignment.......: 441 224s Number of sites in alignment...........: 152 224s Number of chars in alignment...........: 65487 224s Mean site entropy in alignment.........: 0.29729 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 2189 427 -14 153 +1 63726 -1761 224s Number of sequences in alignment.......: 427 224s Number of sites in alignment...........: 153 224s Number of chars in alignment...........: 63726 224s Mean site entropy in alignment.........: 0.295662 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 2082 334 -93 154 +1 50320 -13406 224s Number of sequences in alignment.......: 334 224s Number of sites in alignment...........: 154 224s Number of chars in alignment...........: 50320 224s Mean site entropy in alignment.........: 0.268583 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 2006 258 -76 155 +1 39190 -11130 224s Number of sequences in alignment.......: 258 224s Number of sites in alignment...........: 155 224s Number of chars in alignment...........: 39190 224s Mean site entropy in alignment.........: 0.230649 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 1987 254 -4 156 +1 38780 -410 224s Number of sequences in alignment.......: 254 224s Number of sites in alignment...........: 156 224s Number of chars in alignment...........: 38780 224s Mean site entropy in alignment.........: 0.228398 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 1915 247 -7 157 +1 37896 -884 224s Number of sequences in alignment.......: 247 224s Number of sites in alignment...........: 157 224s Number of chars in alignment...........: 37896 224s Mean site entropy in alignment.........: 0.226904 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 1876 130 -117 158 +1 20276 -17620 224s Number of sequences in alignment.......: 130 224s Number of sites in alignment...........: 158 224s Number of chars in alignment...........: 20276 224s Mean site entropy in alignment.........: 0.134572 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 1704 3 -127 163 +5 489 -19787 224s Number of sequences in alignment.......: 3 224s Number of sites in alignment...........: 163 224s Number of chars in alignment...........: 489 224s Mean site entropy in alignment.........: 0.065727 224s Choice Node #seq %seq #sites %sites #chars %chars 224s 1) 1474 2 -1 167 +4 334 -155 224s Number of sequences in alignment.......: 2 224s Number of sites in alignment...........: 167 224s Number of chars in alignment...........: 334 224s Mean site entropy in alignment.........: 0.0338121 224s Choice Node #seq %seq #sites %sites #chars %chars 224s BppAlnOpt's done. Bye. 224s Total execution time: 0.000000d, 0.000000h, 0.000000m, 14.000000s. 224s ****************************************************************** 224s * Bio++ Alignment Optimizer, version 1.1.0. * 224s * Author: J. Dutheil Last Modif. 14/03/18 * 224s * E. Figuet * 224s ****************************************************************** 224s 224s Parsing options: 224s Parsing file AlnOptimAuto.bpp for options. 224s Alphabet type .........................: Proteic 224s Sequence file .........................: PF01049_full.txt 224s Sequence format .......................: FASTA file 224s Minimum amount of data per site........: 0.7 224s Filter gap characters..................: yes 224s Filter unresolved characters...........: yes 224s Number of reference sequences..........: 0 224s Total number of sequences..............: 1652 224s Total number of sites..................: 656 224s Compressing sequences..................: 224s [ ] 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. 224s Memory required to store distances (Mb): 20 224s Computing pairwise overlap matrix......: 227s [> ] 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. 227s Clustering linkage mode................: average 227s Computing cluster tree.................: 235s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 235s Comparison criterion:..................: MaxSites 235s Number of sequences in alignment.......: 1652 235s Number of sites in alignment...........: 129 235s Number of chars in alignment...........: 182603 235s Mean site entropy in alignment.........: 0.394104 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3299 1647 -5 131 +2 184774 2171 235s Number of sequences in alignment.......: 1647 235s Number of sites in alignment...........: 131 235s Number of chars in alignment...........: 184774 235s Mean site entropy in alignment.........: 0.394431 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3293 1645 -2 132 +1 185875 1101 235s Number of sequences in alignment.......: 1645 235s Number of sites in alignment...........: 132 235s Number of chars in alignment...........: 185875 235s Mean site entropy in alignment.........: 0.394643 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 181 1644 -1 133 +1 186999 1124 235s Number of sequences in alignment.......: 1644 235s Number of sites in alignment...........: 133 235s Number of chars in alignment...........: 186999 235s Mean site entropy in alignment.........: 0.394599 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3287 1634 -10 134 +1 187779 780 236s Number of sequences in alignment.......: 1634 236s Number of sites in alignment...........: 134 236s Number of chars in alignment...........: 187779 236s Mean site entropy in alignment.........: 0.395631 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3276 1627 -7 135 +1 188617 838 236s Number of sequences in alignment.......: 1627 236s Number of sites in alignment...........: 135 236s Number of chars in alignment...........: 188617 236s Mean site entropy in alignment.........: 0.396076 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3238 1614 -13 136 +1 189013 396 236s Number of sequences in alignment.......: 1614 236s Number of sites in alignment...........: 136 236s Number of chars in alignment...........: 189013 236s Mean site entropy in alignment.........: 0.395128 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3023 1533 -81 138 +2 185240 -3773 236s Number of sequences in alignment.......: 1533 236s Number of sites in alignment...........: 138 236s Number of chars in alignment...........: 185240 236s Mean site entropy in alignment.........: 0.372196 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1629 1532 -1 139 +1 186276 1036 236s Number of sequences in alignment.......: 1532 236s Number of sites in alignment...........: 139 236s Number of chars in alignment...........: 186276 236s Mean site entropy in alignment.........: 0.372208 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3282 1521 -11 140 +1 186867 591 236s Number of sequences in alignment.......: 1521 236s Number of sites in alignment...........: 140 236s Number of chars in alignment...........: 186867 236s Mean site entropy in alignment.........: 0.372497 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3105 1482 -39 141 +1 185210 -1657 236s Number of sequences in alignment.......: 1482 236s Number of sites in alignment...........: 141 236s Number of chars in alignment...........: 185210 236s Mean site entropy in alignment.........: 0.368185 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3135 1471 -11 142 +1 185562 352 236s Number of sequences in alignment.......: 1471 236s Number of sites in alignment...........: 142 236s Number of chars in alignment...........: 185562 236s Mean site entropy in alignment.........: 0.367384 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2863 1455 -16 143 +1 184869 -693 236s Number of sequences in alignment.......: 1455 236s Number of sites in alignment...........: 143 236s Number of chars in alignment...........: 184869 236s Mean site entropy in alignment.........: 0.366056 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3166 1413 -42 144 +1 183102 -1767 236s Number of sequences in alignment.......: 1413 236s Number of sites in alignment...........: 144 236s Number of chars in alignment...........: 183102 236s Mean site entropy in alignment.........: 0.362023 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2996 1204 -209 145 +1 168239 -14863 237s Number of sequences in alignment.......: 1204 237s Number of sites in alignment...........: 145 237s Number of chars in alignment...........: 168239 237s Mean site entropy in alignment.........: 0.339856 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2960 1154 -50 146 +1 163602 -4637 237s Number of sequences in alignment.......: 1154 237s Number of sites in alignment...........: 146 237s Number of chars in alignment...........: 163602 237s Mean site entropy in alignment.........: 0.330406 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2809 1097 -57 147 +1 157455 -6147 237s Number of sequences in alignment.......: 1097 237s Number of sites in alignment...........: 147 237s Number of chars in alignment...........: 157455 237s Mean site entropy in alignment.........: 0.314798 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2635 1063 -34 148 +1 153359 -4096 237s Number of sequences in alignment.......: 1063 237s Number of sites in alignment...........: 148 237s Number of chars in alignment...........: 153359 237s Mean site entropy in alignment.........: 0.316144 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1948 1048 -15 149 +1 151998 -1361 237s Number of sequences in alignment.......: 1048 237s Number of sites in alignment...........: 149 237s Number of chars in alignment...........: 151998 237s Mean site entropy in alignment.........: 0.31084 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2069 1031 -17 150 +1 150327 -1671 237s Number of sequences in alignment.......: 1031 237s Number of sites in alignment...........: 150 237s Number of chars in alignment...........: 150327 237s Mean site entropy in alignment.........: 0.303727 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2640 451 -580 151 +1 67067 -83260 237s Number of sequences in alignment.......: 451 237s Number of sites in alignment...........: 151 237s Number of chars in alignment...........: 67067 237s Mean site entropy in alignment.........: 0.278258 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2555 425 -26 152 +1 63569 -3498 237s Number of sequences in alignment.......: 425 237s Number of sites in alignment...........: 152 237s Number of chars in alignment...........: 63569 237s Mean site entropy in alignment.........: 0.276822 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2332 391 -34 153 +1 58841 -4728 237s Number of sequences in alignment.......: 391 237s Number of sites in alignment...........: 153 237s Number of chars in alignment...........: 58841 237s Mean site entropy in alignment.........: 0.269678 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2039 342 -49 154 +1 51693 -7148 237s Number of sequences in alignment.......: 342 237s Number of sites in alignment...........: 154 237s Number of chars in alignment...........: 51693 237s Mean site entropy in alignment.........: 0.250803 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2337 280 -62 155 +1 42698 -8995 237s Number of sequences in alignment.......: 280 237s Number of sites in alignment...........: 155 237s Number of chars in alignment...........: 42698 237s Mean site entropy in alignment.........: 0.230831 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1969 277 -3 156 +1 42454 -244 237s Number of sequences in alignment.......: 277 237s Number of sites in alignment...........: 156 237s Number of chars in alignment...........: 42454 237s Mean site entropy in alignment.........: 0.228862 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 2097 246 -31 157 +1 37949 -4505 237s Number of sequences in alignment.......: 246 237s Number of sites in alignment...........: 157 237s Number of chars in alignment...........: 37949 237s Mean site entropy in alignment.........: 0.216654 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 884 245 -1 158 +1 37976 27 237s Number of sequences in alignment.......: 245 237s Number of sites in alignment...........: 158 237s Number of chars in alignment...........: 37976 237s Mean site entropy in alignment.........: 0.215946 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1937 19 -226 163 +5 3067 -34909 237s Number of sequences in alignment.......: 19 237s Number of sites in alignment...........: 163 237s Number of chars in alignment...........: 3067 237s Mean site entropy in alignment.........: 0.115126 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1719 14 -5 165 +2 2297 -770 237s Number of sequences in alignment.......: 14 237s Number of sites in alignment...........: 165 237s Number of chars in alignment...........: 2297 237s Mean site entropy in alignment.........: 0.0991142 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1699 12 -2 166 +1 1983 -314 237s Number of sequences in alignment.......: 12 237s Number of sites in alignment...........: 166 237s Number of chars in alignment...........: 1983 237s Mean site entropy in alignment.........: 0.0379699 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 397 11 -1 168 +2 1838 -145 237s Number of sequences in alignment.......: 11 237s Number of sites in alignment...........: 168 237s Number of chars in alignment...........: 1838 237s Mean site entropy in alignment.........: 0.03305 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1684 8 -3 169 +1 1349 -489 237s Number of sequences in alignment.......: 8 237s Number of sites in alignment...........: 169 237s Number of chars in alignment...........: 1349 237s Mean site entropy in alignment.........: 0.0183685 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 46 7 -1 172 +3 1196 -153 237s Number of sequences in alignment.......: 7 237s Number of sites in alignment...........: 172 237s Number of chars in alignment...........: 1196 237s Mean site entropy in alignment.........: 0.0178367 237s Choice Node #seq %seq #sites %sites #chars %chars 237s 1) 1664 2 -5 176 +4 352 -844 237s Number of sequences in alignment.......: 2 237s Number of sites in alignment...........: 176 237s Number of chars in alignment...........: 352 237s Mean site entropy in alignment.........: 0.010038 237s Choice Node #seq %seq #sites %sites #chars %chars 237s BppAlnOpt's done. Bye. 237s Total execution time: 0.000000d, 0.000000h, 0.000000m, 13.000000s. 237s ****************************************************************** 237s * Bio++ Alignment Optimizer, version 1.1.0. * 237s * Author: J. Dutheil Last Modif. 14/03/18 * 237s * E. Figuet * 237s ****************************************************************** 237s 237s Parsing options: 237s Parsing file AlnOptimAuto.bpp for options. 237s Alphabet type .........................: Proteic 237s Sequence file .........................: PF01049_full.txt 237s Sequence format .......................: FASTA file 237s Minimum amount of data per site........: 0.7 237s Filter gap characters..................: yes 237s Filter unresolved characters...........: yes 237s Number of reference sequences..........: 0 237s Total number of sequences..............: 1652 237s Total number of sites..................: 656 237s Compressing sequences..................: 237s [ ] 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. 237s Memory required to store distances (Mb): 20 237s Computing pairwise overlap matrix......: 240s [> ] 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. 240s Clustering linkage mode................: median 240s Computing cluster tree.................: 248s [ ] 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. 248s Comparison criterion:..................: MaxSites 248s Number of sequences in alignment.......: 1652 248s Number of sites in alignment...........: 129 248s Number of chars in alignment...........: 182603 248s Mean site entropy in alignment.........: 0.394104 248s Choice Node #seq %seq #sites %sites #chars %chars 248s 1) 3297 1647 -5 131 +2 184774 2171 248s Number of sequences in alignment.......: 1647 248s Number of sites in alignment...........: 131 248s Number of chars in alignment...........: 184774 248s Mean site entropy in alignment.........: 0.394431 248s Choice Node #seq %seq #sites %sites #chars %chars 248s 1) 3295 1645 -2 132 +1 185873 1099 248s Number of sequences in alignment.......: 1645 248s Number of sites in alignment...........: 132 248s Number of chars in alignment...........: 185873 248s Mean site entropy in alignment.........: 0.394618 248s Choice Node #seq %seq #sites %sites #chars %chars 248s 1) 275 1644 -1 133 +1 186998 1125 248s Number of sequences in alignment.......: 1644 248s Number of sites in alignment...........: 133 248s Number of chars in alignment...........: 186998 248s Mean site entropy in alignment.........: 0.394724 248s Choice Node #seq %seq #sites %sites #chars %chars 248s 1) 3280 1630 -14 134 +1 187559 561 249s Number of sequences in alignment.......: 1630 249s Number of sites in alignment...........: 134 249s Number of chars in alignment...........: 187559 249s Mean site entropy in alignment.........: 0.39546 249s Choice Node #seq %seq #sites %sites #chars %chars 249s 1) 3272 1622 -8 135 +1 188376 817 249s Number of sequences in alignment.......: 1622 249s Number of sites in alignment...........: 135 249s Number of chars in alignment...........: 188376 249s Mean site entropy in alignment.........: 0.396213 249s Choice Node #seq %seq #sites %sites #chars %chars 249s 1) 3261 1611 -11 136 +1 189031 655 249s Number of sequences in alignment.......: 1611 249s Number of sites in alignment...........: 136 249s Number of chars in alignment...........: 189031 249s Mean site entropy in alignment.........: 0.396902 249s Choice Node #seq %seq #sites %sites #chars %chars 249s 1) 3184 1534 -77 137 +1 185562 -3469 249s Number of sequences in alignment.......: 1534 249s Number of sites in alignment...........: 137 249s Number of chars in alignment...........: 185562 249s Mean site entropy in alignment.........: 0.396433 249s Choice Node #seq %seq #sites %sites #chars %chars 249s 1) 3182 1532 -2 138 +1 186503 941 249s Number of sequences in alignment.......: 1532 249s Number of sites in alignment...........: 138 249s Number of chars in alignment...........: 186503 249s Mean site entropy in alignment.........: 0.396422 249s Choice Node #seq %seq #sites %sites #chars %chars 249s 1) 513 1531 -1 139 +1 187535 1032 249s Number of sequences in alignment.......: 1531 249s Number of sites in alignment...........: 139 249s Number of chars in alignment...........: 187535 249s Mean site entropy in alignment.........: 0.396222 249s Choice Node #seq %seq #sites %sites #chars %chars 249s 1) 3169 1518 -13 140 +1 187760 225 250s Number of sequences in alignment.......: 1518 250s Number of sites in alignment...........: 140 250s Number of chars in alignment...........: 187760 250s Mean site entropy in alignment.........: 0.395785 250s Choice Node #seq %seq #sites %sites #chars %chars 250s 1) 3125 1475 -43 141 +1 185962 -1798 250s Number of sequences in alignment.......: 1475 250s Number of sites in alignment...........: 141 250s Number of chars in alignment...........: 185962 250s Mean site entropy in alignment.........: 0.388512 250s Choice Node #seq %seq #sites %sites #chars %chars 250s 1) 3117 1467 -8 142 +1 186502 540 250s Number of sequences in alignment.......: 1467 250s Number of sites in alignment...........: 142 250s Number of chars in alignment...........: 186502 250s Mean site entropy in alignment.........: 0.388016 250s Choice Node #seq %seq #sites %sites #chars %chars 250s 1) 3102 1452 -15 143 +1 186490 -12 250s Number of sequences in alignment.......: 1452 250s Number of sites in alignment...........: 143 250s Number of chars in alignment...........: 186490 250s Mean site entropy in alignment.........: 0.386609 250s Choice Node #seq %seq #sites %sites #chars %chars 250s 1) 3052 1402 -50 144 +1 183727 -2763 250s Number of sequences in alignment.......: 1402 250s Number of sites in alignment...........: 144 250s Number of chars in alignment...........: 183727 250s Mean site entropy in alignment.........: 0.379315 250s Choice Node #seq %seq #sites %sites #chars %chars 250s 1) 2877 1227 -175 145 +1 170235 -13492 250s Number of sequences in alignment.......: 1227 250s Number of sites in alignment...........: 145 250s Number of chars in alignment...........: 170235 250s Mean site entropy in alignment.........: 0.34859 250s Choice Node #seq %seq #sites %sites #chars %chars 250s 1) 2788 1138 -89 146 +1 161621 -8614 250s Number of sequences in alignment.......: 1138 250s Number of sites in alignment...........: 146 250s Number of chars in alignment...........: 161621 250s Mean site entropy in alignment.........: 0.330459 250s Choice Node #seq %seq #sites %sites #chars %chars 250s 1) 2731 1081 -57 147 +1 155136 -6485 251s Number of sequences in alignment.......: 1081 251s Number of sites in alignment...........: 147 251s Number of chars in alignment...........: 155136 251s Mean site entropy in alignment.........: 0.319787 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 1701 1030 -51 148 +1 148555 -6581 251s Number of sequences in alignment.......: 1030 251s Number of sites in alignment...........: 148 251s Number of chars in alignment...........: 148555 251s Mean site entropy in alignment.........: 0.305707 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 2499 798 -232 149 +1 116805 -31750 251s Number of sequences in alignment.......: 798 251s Number of sites in alignment...........: 149 251s Number of chars in alignment...........: 116805 251s Mean site entropy in alignment.........: 0.273968 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 2468 767 -31 150 +1 112894 -3911 251s Number of sequences in alignment.......: 767 251s Number of sites in alignment...........: 150 251s Number of chars in alignment...........: 112894 251s Mean site entropy in alignment.........: 0.272075 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 2239 538 -229 151 +1 79674 -33220 251s Number of sequences in alignment.......: 538 251s Number of sites in alignment...........: 151 251s Number of chars in alignment...........: 79674 251s Mean site entropy in alignment.........: 0.280963 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 2196 495 -43 152 +1 73702 -5972 251s Number of sequences in alignment.......: 495 251s Number of sites in alignment...........: 152 251s Number of chars in alignment...........: 73702 251s Mean site entropy in alignment.........: 0.28148 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 2076 375 -120 153 +1 56316 -17386 251s Number of sequences in alignment.......: 375 251s Number of sites in alignment...........: 153 251s Number of chars in alignment...........: 56316 251s Mean site entropy in alignment.........: 0.267502 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 2018 317 -58 154 +1 47977 -8339 251s Number of sequences in alignment.......: 317 251s Number of sites in alignment...........: 154 251s Number of chars in alignment...........: 47977 251s Mean site entropy in alignment.........: 0.249671 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 1949 248 -69 155 +1 37817 -10160 251s Number of sequences in alignment.......: 248 251s Number of sites in alignment...........: 155 251s Number of chars in alignment...........: 37817 251s Mean site entropy in alignment.........: 0.215239 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 1938 237 -11 156 +1 36376 -1441 251s Number of sequences in alignment.......: 237 251s Number of sites in alignment...........: 156 251s Number of chars in alignment...........: 36376 251s Mean site entropy in alignment.........: 0.201826 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 1926 225 -12 157 +1 34752 -1624 251s Number of sequences in alignment.......: 225 251s Number of sites in alignment...........: 157 251s Number of chars in alignment...........: 34752 251s Mean site entropy in alignment.........: 0.184033 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 1779 78 -147 158 +1 12282 -22470 251s Number of sequences in alignment.......: 78 251s Number of sites in alignment...........: 158 251s Number of chars in alignment...........: 12282 251s Mean site entropy in alignment.........: 0.0830049 251s Choice Node #seq %seq #sites %sites #chars %chars 251s 1) 1703 2 -76 160 +2 320 -11962 251s Number of sequences in alignment.......: 2 251s Number of sites in alignment...........: 160 251s Number of chars in alignment...........: 320 251s Mean site entropy in alignment.........: 0 251s Choice Node #seq %seq #sites %sites #chars %chars 251s BppAlnOpt's done. Bye. 251s Total execution time: 0.000000d, 0.000000h, 0.000000m, 14.000000s. 251s ****************************************************************** 251s * Bio++ Alignment Optimizer, version 1.1.0. * 251s * Author: J. Dutheil Last Modif. 14/03/18 * 251s * E. Figuet * 251s ****************************************************************** 251s 251s Parsing options: 251s Parsing file AlnOptimAuto.bpp for options. 251s Alphabet type .........................: Proteic 251s Sequence file .........................: PF01049_full.txt 251s Sequence format .......................: FASTA file 251s Minimum amount of data per site........: 0.7 251s Filter gap characters..................: yes 251s Filter unresolved characters...........: yes 251s Number of reference sequences..........: 0 251s Total number of sequences..............: 1652 251s Total number of sites..................: 656 251s Compressing sequences..................: 251s [ ] 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. 251s Memory required to store distances (Mb): 20 251s Computing pairwise overlap matrix......: 254s [> ] 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. 254s Clustering linkage mode................: centroid 254s Computing cluster tree.................: 262s [ ] 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. 262s Comparison criterion:..................: MaxSites 262s Number of sequences in alignment.......: 1652 262s Number of sites in alignment...........: 129 262s Number of chars in alignment...........: 182603 262s Mean site entropy in alignment.........: 0.394104 262s Choice Node #seq %seq #sites %sites #chars %chars 262s 1) 3297 1647 -5 131 +2 184783 2180 262s Number of sequences in alignment.......: 1647 262s Number of sites in alignment...........: 131 262s Number of chars in alignment...........: 184783 262s Mean site entropy in alignment.........: 0.394537 262s Choice Node #seq %seq #sites %sites #chars %chars 262s 1) 3295 1645 -2 132 +1 185880 1097 262s Number of sequences in alignment.......: 1645 262s Number of sites in alignment...........: 132 262s Number of chars in alignment...........: 185880 262s Mean site entropy in alignment.........: 0.394662 262s Choice Node #seq %seq #sites %sites #chars %chars 262s 1) 181 1644 -1 133 +1 187004 1124 262s Number of sequences in alignment.......: 1644 262s Number of sites in alignment...........: 133 262s Number of chars in alignment...........: 187004 262s Mean site entropy in alignment.........: 0.394618 262s Choice Node #seq %seq #sites %sites #chars %chars 262s 1) 3284 1634 -10 134 +1 187785 781 263s Number of sequences in alignment.......: 1634 263s Number of sites in alignment...........: 134 263s Number of chars in alignment...........: 187785 263s Mean site entropy in alignment.........: 0.395449 263s Choice Node #seq %seq #sites %sites #chars %chars 263s 1) 3277 1627 -7 135 +1 188649 864 263s Number of sequences in alignment.......: 1627 263s Number of sites in alignment...........: 135 263s Number of chars in alignment...........: 188649 263s Mean site entropy in alignment.........: 0.395884 263s Choice Node #seq %seq #sites %sites #chars %chars 263s 1) 3264 1614 -13 136 +1 189270 621 263s Number of sequences in alignment.......: 1614 263s Number of sites in alignment...........: 136 263s Number of chars in alignment...........: 189270 263s Mean site entropy in alignment.........: 0.396209 263s Choice Node #seq %seq #sites %sites #chars %chars 263s 1) 3158 1508 -106 137 +1 184807 -4463 263s Number of sequences in alignment.......: 1508 263s Number of sites in alignment...........: 137 263s Number of chars in alignment...........: 184807 263s Mean site entropy in alignment.........: 0.391659 263s Choice Node #seq %seq #sites %sites #chars %chars 263s 1) 3141 1491 -17 138 +1 184810 3 263s Number of sequences in alignment.......: 1491 263s Number of sites in alignment...........: 138 263s Number of chars in alignment...........: 184810 263s Mean site entropy in alignment.........: 0.389899 263s Choice Node #seq %seq #sites %sites #chars %chars 263s 1) 3135 1485 -6 139 +1 185468 658 263s Number of sequences in alignment.......: 1485 263s Number of sites in alignment...........: 139 263s Number of chars in alignment...........: 185468 263s Mean site entropy in alignment.........: 0.389868 263s Choice Node #seq %seq #sites %sites #chars %chars 263s 1) 3124 1474 -11 140 +1 185788 320 264s Number of sequences in alignment.......: 1474 264s Number of sites in alignment...........: 140 264s Number of chars in alignment...........: 185788 264s Mean site entropy in alignment.........: 0.389071 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 3091 1441 -33 141 +1 184655 -1133 264s Number of sequences in alignment.......: 1441 264s Number of sites in alignment...........: 141 264s Number of chars in alignment...........: 184655 264s Mean site entropy in alignment.........: 0.38709 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 3077 1427 -14 142 +1 184714 59 264s Number of sequences in alignment.......: 1427 264s Number of sites in alignment...........: 142 264s Number of chars in alignment...........: 184714 264s Mean site entropy in alignment.........: 0.386526 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 3055 1405 -22 144 +2 185186 472 264s Number of sequences in alignment.......: 1405 264s Number of sites in alignment...........: 144 264s Number of chars in alignment...........: 185186 264s Mean site entropy in alignment.........: 0.383626 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 2907 1257 -148 145 +1 173927 -11259 264s Number of sequences in alignment.......: 1257 264s Number of sites in alignment...........: 145 264s Number of chars in alignment...........: 173927 264s Mean site entropy in alignment.........: 0.350796 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 2807 1157 -100 146 +1 163983 -9944 264s Number of sequences in alignment.......: 1157 264s Number of sites in alignment...........: 146 264s Number of chars in alignment...........: 163983 264s Mean site entropy in alignment.........: 0.329626 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 2748 1098 -59 147 +1 157592 -6391 264s Number of sequences in alignment.......: 1098 264s Number of sites in alignment...........: 147 264s Number of chars in alignment...........: 157592 264s Mean site entropy in alignment.........: 0.314432 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 1678 1070 -28 148 +1 154399 -3193 264s Number of sequences in alignment.......: 1070 264s Number of sites in alignment...........: 148 264s Number of chars in alignment...........: 154399 264s Mean site entropy in alignment.........: 0.303382 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 2620 942 -128 149 +1 137516 -16883 264s Number of sequences in alignment.......: 942 264s Number of sites in alignment...........: 149 264s Number of chars in alignment...........: 137516 264s Mean site entropy in alignment.........: 0.284952 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 2615 937 -5 150 +1 137462 -54 265s Number of sequences in alignment.......: 937 265s Number of sites in alignment...........: 150 265s Number of chars in alignment...........: 137462 265s Mean site entropy in alignment.........: 0.285064 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 2320 642 -295 151 +1 95140 -42322 265s Number of sequences in alignment.......: 642 265s Number of sites in alignment...........: 151 265s Number of chars in alignment...........: 95140 265s Mean site entropy in alignment.........: 0.276628 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 2179 501 -141 152 +1 74734 -20406 265s Number of sequences in alignment.......: 501 265s Number of sites in alignment...........: 152 265s Number of chars in alignment...........: 74734 265s Mean site entropy in alignment.........: 0.281366 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 2108 430 -71 153 +1 64604 -10130 265s Number of sequences in alignment.......: 430 265s Number of sites in alignment...........: 153 265s Number of chars in alignment...........: 64604 265s Mean site entropy in alignment.........: 0.282214 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 2038 360 -70 154 +1 54522 -10082 265s Number of sequences in alignment.......: 360 265s Number of sites in alignment...........: 154 265s Number of chars in alignment...........: 54522 265s Mean site entropy in alignment.........: 0.265356 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 1969 291 -69 155 +1 44461 -10061 265s Number of sequences in alignment.......: 291 265s Number of sites in alignment...........: 155 265s Number of chars in alignment...........: 44461 265s Mean site entropy in alignment.........: 0.240018 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 1956 278 -13 156 +1 42693 -1768 265s Number of sequences in alignment.......: 278 265s Number of sites in alignment...........: 156 265s Number of chars in alignment...........: 42693 265s Mean site entropy in alignment.........: 0.236678 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 1925 247 -31 157 +1 38195 -4498 265s Number of sequences in alignment.......: 247 265s Number of sites in alignment...........: 157 265s Number of chars in alignment...........: 38195 265s Mean site entropy in alignment.........: 0.216008 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 1923 245 -2 158 +1 38065 -130 265s Number of sequences in alignment.......: 245 265s Number of sites in alignment...........: 158 265s Number of chars in alignment...........: 38065 265s Mean site entropy in alignment.........: 0.215165 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 610 1 -244 177 +19 177 -37888 265s Number of sequences in alignment.......: 1 265s Number of sites in alignment...........: 177 265s Number of chars in alignment...........: 177 265s Mean site entropy in alignment.........: 0 265s Choice Node #seq %seq #sites %sites #chars %chars 265s BppAlnOpt's done. Bye. 265s Total execution time: 0.000000d, 0.000000h, 0.000000m, 14.000000s. 265s ****************************************************************** 265s * Bio++ Alignment Optimizer, version 1.1.0. * 265s * Author: J. Dutheil Last Modif. 14/03/18 * 265s * E. Figuet * 265s ****************************************************************** 265s 265s Parsing options: 265s Parsing file AlnOptimAuto.bpp for options. 265s Alphabet type .........................: Proteic 265s Sequence file .........................: PF01049_full.txt 265s Sequence format .......................: FASTA file 265s Minimum amount of data per site........: 0.7 265s Filter gap characters..................: yes 265s Filter unresolved characters...........: yes 265s Number of reference sequences..........: 0 265s Total number of sequences..............: 1652 265s Total number of sites..................: 656 265s Compressing sequences..................: 265s [ ] 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. 265s Memory required to store distances (Mb): 20 265s Computing pairwise overlap matrix......: 268s [> ] 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. 268s Clustering linkage mode................: ward 268s Computing cluster tree.................: 276s [ ] 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. 276s Comparison criterion:..................: MaxSites 276s Number of sequences in alignment.......: 1652 276s Number of sites in alignment...........: 129 276s Number of chars in alignment...........: 182603 276s Mean site entropy in alignment.........: 0.394104 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3251 1647 -5 131 +2 184716 2113 276s Number of sequences in alignment.......: 1647 276s Number of sites in alignment...........: 131 276s Number of chars in alignment...........: 184716 276s Mean site entropy in alignment.........: 0.394659 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3238 1645 -2 132 +1 185817 1101 276s Number of sequences in alignment.......: 1645 276s Number of sites in alignment...........: 132 276s Number of chars in alignment...........: 185817 276s Mean site entropy in alignment.........: 0.394872 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 626 1644 -1 133 +1 186943 1126 276s Number of sequences in alignment.......: 1644 276s Number of sites in alignment...........: 133 276s Number of chars in alignment...........: 186943 276s Mean site entropy in alignment.........: 0.394963 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3225 1634 -10 134 +1 187538 595 276s Number of sequences in alignment.......: 1634 276s Number of sites in alignment...........: 134 276s Number of chars in alignment...........: 187538 276s Mean site entropy in alignment.........: 0.395167 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3259 1627 -7 135 +1 188469 931 276s Number of sequences in alignment.......: 1627 276s Number of sites in alignment...........: 135 276s Number of chars in alignment...........: 188469 276s Mean site entropy in alignment.........: 0.39572 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3231 1614 -13 136 +1 189043 574 277s Number of sequences in alignment.......: 1614 277s Number of sites in alignment...........: 136 277s Number of chars in alignment...........: 189043 277s Mean site entropy in alignment.........: 0.396503 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3276 1530 -84 139 +3 186415 -2628 277s Number of sequences in alignment.......: 1530 277s Number of sites in alignment...........: 139 277s Number of chars in alignment...........: 186415 277s Mean site entropy in alignment.........: 0.389001 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3232 1521 -9 140 +1 187030 615 277s Number of sequences in alignment.......: 1521 277s Number of sites in alignment...........: 140 277s Number of chars in alignment...........: 187030 277s Mean site entropy in alignment.........: 0.389238 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3267 1485 -36 141 +1 185744 -1286 277s Number of sequences in alignment.......: 1485 277s Number of sites in alignment...........: 141 277s Number of chars in alignment...........: 185744 277s Mean site entropy in alignment.........: 0.389095 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3288 1470 -15 142 +1 185982 238 277s Number of sequences in alignment.......: 1470 277s Number of sites in alignment...........: 142 277s Number of chars in alignment...........: 185982 277s Mean site entropy in alignment.........: 0.38758 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3098 1457 -13 143 +1 185643 -339 277s Number of sequences in alignment.......: 1457 277s Number of sites in alignment...........: 143 277s Number of chars in alignment...........: 185643 277s Mean site entropy in alignment.........: 0.385646 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3289 1411 -46 144 +1 183758 -1885 277s Number of sequences in alignment.......: 1411 277s Number of sites in alignment...........: 144 277s Number of chars in alignment...........: 183758 277s Mean site entropy in alignment.........: 0.38204 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3273 1313 -98 145 +1 171322 -12436 277s Number of sequences in alignment.......: 1313 277s Number of sites in alignment...........: 145 277s Number of chars in alignment...........: 171322 277s Mean site entropy in alignment.........: 0.380643 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3299 1133 -180 147 +2 152385 -18937 277s Number of sequences in alignment.......: 1133 277s Number of sites in alignment...........: 147 277s Number of chars in alignment...........: 152385 277s Mean site entropy in alignment.........: 0.346351 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 2941 1121 -12 148 +1 152294 -91 277s Number of sequences in alignment.......: 1121 277s Number of sites in alignment...........: 148 277s Number of chars in alignment...........: 152294 277s Mean site entropy in alignment.........: 0.340977 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 1664 1115 -6 149 +1 152613 319 277s Number of sequences in alignment.......: 1115 277s Number of sites in alignment...........: 149 277s Number of chars in alignment...........: 152613 277s Mean site entropy in alignment.........: 0.336552 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3193 1104 -11 150 +1 152591 -22 277s Number of sequences in alignment.......: 1104 277s Number of sites in alignment...........: 150 277s Number of chars in alignment...........: 152591 277s Mean site entropy in alignment.........: 0.330411 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 2891 153 -951 157 +7 23971 -128620 277s Number of sequences in alignment.......: 153 277s Number of sites in alignment...........: 157 277s Number of chars in alignment...........: 23971 277s Mean site entropy in alignment.........: 0.0601394 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 1887 120 -33 158 +1 18876 -5095 277s Number of sequences in alignment.......: 120 277s Number of sites in alignment...........: 158 277s Number of chars in alignment...........: 18876 277s Mean site entropy in alignment.........: 0.0586193 277s Choice Node #seq %seq #sites %sites #chars %chars 277s BppAlnOpt's done. Bye. 277s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 277s ****************************************************************** 277s * Bio++ Alignment Optimizer, version 1.1.0. * 277s * Author: J. Dutheil Last Modif. 14/03/18 * 277s * E. Figuet * 277s ****************************************************************** 277s 277s Parsing options: 277s Parsing file AlnOptimFasttreeStop.bpp for options. 277s Alphabet type .........................: Proteic 277s Sequence file .........................: PF01049_full.txt 277s Sequence format .......................: FASTA file 278s Minimum amount of data per site........: 0.7 278s Filter gap characters..................: yes 278s Filter unresolved characters...........: yes 278s Number of reference sequences..........: 0 278s Total number of sequences..............: 1652 278s Total number of sites..................: 656 278s Input tree file .......................: PF01049_fasttree.dnd 278s Input tree format .....................: Newick 278s Minimum number of sequences to keep....: 826 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) 2030 1647 -5 131 +2 184714 2111 278s Number of sequences in alignment.......: 1647 278s Number of sites in alignment...........: 131 278s Number of chars in alignment...........: 184714 278s Mean site entropy in alignment.........: 0.394129 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 1930 1645 -2 132 +1 185794 1080 278s Number of sequences in alignment.......: 1645 278s Number of sites in alignment...........: 132 278s Number of chars in alignment...........: 185794 278s Mean site entropy in alignment.........: 0.394195 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 1882 1644 -1 133 +1 186920 1126 278s Number of sequences in alignment.......: 1644 278s Number of sites in alignment...........: 133 278s Number of chars in alignment...........: 186920 278s Mean site entropy in alignment.........: 0.394263 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 386 1634 -10 134 +1 187634 714 278s Number of sequences in alignment.......: 1634 278s Number of sites in alignment...........: 134 278s Number of chars in alignment...........: 187634 278s Mean site entropy in alignment.........: 0.394887 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 357 1627 -7 135 +1 188437 803 278s Number of sequences in alignment.......: 1627 278s Number of sites in alignment...........: 135 278s Number of chars in alignment...........: 188437 278s Mean site entropy in alignment.........: 0.394741 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 1736 1614 -13 136 +1 188713 276 278s Number of sequences in alignment.......: 1614 278s Number of sites in alignment...........: 136 278s Number of chars in alignment...........: 188713 278s Mean site entropy in alignment.........: 0.394145 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 1489 1527 -87 137 +1 181488 -7225 278s Number of sequences in alignment.......: 1527 278s Number of sites in alignment...........: 137 278s Number of chars in alignment...........: 181488 278s Mean site entropy in alignment.........: 0.378687 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2247 1524 -3 138 +1 182435 947 279s Number of sequences in alignment.......: 1524 279s Number of sites in alignment...........: 138 279s Number of chars in alignment...........: 182435 279s Mean site entropy in alignment.........: 0.378731 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 408 1515 -9 139 +1 183008 573 279s Number of sequences in alignment.......: 1515 279s Number of sites in alignment...........: 139 279s Number of chars in alignment...........: 183008 279s Mean site entropy in alignment.........: 0.377294 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1819 1488 -27 140 +1 182208 -800 279s Number of sequences in alignment.......: 1488 279s Number of sites in alignment...........: 140 279s Number of chars in alignment...........: 182208 279s Mean site entropy in alignment.........: 0.374188 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1676 1464 -24 141 +1 180695 -1513 279s Number of sequences in alignment.......: 1464 279s Number of sites in alignment...........: 141 279s Number of chars in alignment...........: 180695 279s Mean site entropy in alignment.........: 0.371696 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 416 1457 -7 142 +1 181323 628 279s Number of sequences in alignment.......: 1457 279s Number of sites in alignment...........: 142 279s Number of chars in alignment...........: 181323 279s Mean site entropy in alignment.........: 0.36917 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1823 1371 -86 143 +1 176415 -4908 279s Number of sequences in alignment.......: 1371 279s Number of sites in alignment...........: 143 279s Number of chars in alignment...........: 176415 279s Mean site entropy in alignment.........: 0.359961 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 783 1355 -16 144 +1 175237 -1178 279s Number of sequences in alignment.......: 1355 279s Number of sites in alignment...........: 144 279s Number of chars in alignment...........: 175237 279s Mean site entropy in alignment.........: 0.360644 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 953 1307 -48 145 +1 169472 -5765 279s Number of sequences in alignment.......: 1307 279s Number of sites in alignment...........: 145 279s Number of chars in alignment...........: 169472 279s Mean site entropy in alignment.........: 0.363152 279s Choice Node #seq %seq #sites %sites #chars %chars 279s Output alignment file .................: PF01049_optimized_fastml.fasta 279s Output alignment format ...............: FASTA file 279s Output tree file ......................: PF01049_optimized_fastml.dnd 279s Output tree format ....................: Newick 280s BppAlnOpt's done. Bye. 280s Total execution time: 0.000000d, 0.000000h, 0.000000m, 3.000000s. 280s PASS 280s autopkgtest [16:46:19]: test run-unit-test: -----------------------] 281s run-unit-test PASS 281s autopkgtest [16:46:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 281s autopkgtest [16:46:20]: @@@@@@@@@@@@@@@@@@@@ summary 281s run-unit-test PASS 287s nova [W] Using flock in prodstack6-s390x 287s flock: timeout while waiting to get lock 287s Creating nova instance adt-plucky-s390x-physamp-20250315-164138-juju-7f2275-prod-proposed-migration-environment-15-7de34058-d2f9-446c-93ad-2ce03e12c0d6 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 287s nova [W] Timed out waiting for 9c648e15-d28e-4150-a61f-94037b341bb0 to get deleted.