0s autopkgtest [19:33:33]: starting date and time: 2025-03-15 19:33:33+0000 0s autopkgtest [19:33:33]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:33:33]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7f9ijb0t/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade tree-puzzle --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-2@bos03-s390x-3.secgroup --name adt-plucky-s390x-tree-puzzle-20250315-193333-juju-7f2275-prod-proposed-migration-environment-2-eb089a03-85ad-423e-8f54-5c7db3469d30 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 102s autopkgtest [19:35:15]: testbed dpkg architecture: s390x 102s autopkgtest [19:35:15]: testbed apt version: 2.9.33 103s autopkgtest [19:35:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s autopkgtest [19:35:16]: testbed release detected to be: None 104s autopkgtest [19:35:17]: updating testbed package index (apt update) 104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 104s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 104s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB] 104s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 104s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 104s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB] 104s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB] 104s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 104s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 105s Fetched 965 kB in 1s (1192 kB/s) 105s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s Calculating upgrade... 106s The following packages were automatically installed and are no longer required: 106s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 106s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 106s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 106s linux-tools-6.11.0-8-generic 106s Use 'sudo apt autoremove' to remove them. 106s The following packages will be upgraded: 106s pinentry-curses python3-jinja2 strace 107s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 652 kB of archives. 107s After this operation, 27.6 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 107s Fetched 652 kB in 1s (1098 kB/s) 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 107s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 107s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 107s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 107s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 107s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 107s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 107s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 108s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 108s Setting up strace (6.13+ds-1ubuntu1) ... 108s Processing triggers for man-db (2.13.0-1) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Solving dependencies... 108s The following packages will be REMOVED: 108s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 108s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 108s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 108s linux-tools-6.11.0-8-generic* 109s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 109s After this operation, 167 MB disk space will be freed. 109s (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.) 109s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 109s Removing libpython3.12t64:s390x (3.12.9-1) ... 109s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 109s Removing libnsl2:s390x (1.3.0-3build3) ... 109s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 109s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 110s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s Processing triggers for libc-bin (2.41-1ubuntu1) ... 110s (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.) 110s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 110s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s autopkgtest [19:35:23]: upgrading testbed (apt dist-upgrade and autopurge) 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 111s Entering ResolveByKeep 111s 111s Calculating upgrade... 111s The following packages will be upgraded: 111s libc-bin libc-dev-bin libc6 libc6-dev locales 111s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 9512 kB of archives. 111s After this operation, 8192 B of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 112s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 112s Preconfiguring packages ... 112s Fetched 9512 kB in 1s (8640 kB/s) 112s (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.) 112s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 113s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 113s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc6:s390x (2.41-1ubuntu2) ... 113s (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.) 113s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 113s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc-bin (2.41-1ubuntu2) ... 113s (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.) 113s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 113s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up locales (2.41-1ubuntu2) ... 113s Generating locales (this might take a while)... 114s en_US.UTF-8... done 114s Generation complete. 114s Setting up libc-dev-bin (2.41-1ubuntu2) ... 114s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 114s Processing triggers for man-db (2.13.0-1) ... 115s Processing triggers for systemd (257.3-1ubuntu3) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Starting pkgProblemResolver with broken count: 0 116s Starting 2 pkgProblemResolver with broken count: 0 116s Done 116s Solving dependencies... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s autopkgtest [19:35:30]: rebooting testbed after setup commands that affected boot 135s autopkgtest [19:35:48]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 137s autopkgtest [19:35:50]: @@@@@@@@@@@@@@@@@@@@ apt-source tree-puzzle 141s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (dsc) [2235 B] 141s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (tar) [591 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (diff) [32.4 kB] 141s gpgv: Signature made Sat Nov 30 06:14:46 2024 UTC 141s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 141s gpgv: Can't check signature: No public key 141s dpkg-source: warning: cannot verify inline signature for ./tree-puzzle_5.3~rc16+dfsg-12build1.dsc: no acceptable signature found 141s autopkgtest [19:35:54]: testing package tree-puzzle version 5.3~rc16+dfsg-12build1 142s autopkgtest [19:35:55]: build not needed 142s autopkgtest [19:35:55]: test run-unit-test: preparing testbed 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Starting pkgProblemResolver with broken count: 0 143s Starting 2 pkgProblemResolver with broken count: 0 143s Done 143s The following NEW packages will be installed: 143s libevent-pthreads-2.1-7t64 libfabric1 libhwloc-plugins libhwloc15 libmunge2 143s libopenmpi40 libpciaccess0 libpmix2t64 librdmacm1t64 libsprng2 libxnvctrl0 143s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common tree-ppuzzle 143s tree-puzzle tree-puzzle-doc 143s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 4983 kB of archives. 143s After this operation, 16.8 MB of additional disk space will be used. 143s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10 [7870 B] 143s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x librdmacm1t64 s390x 55.0-1ubuntu1 [73.7 kB] 143s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libfabric1 s390x 1.17.0-3.1 [558 kB] 144s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc15 s390x 2.12.0-1 [176 kB] 144s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libmunge2 s390x 0.5.16-1 [15.2 kB] 144s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libpciaccess0 s390x 0.17-3build1 [19.0 kB] 144s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 144s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1build1 [41.1 kB] 144s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc-plugins s390x 2.12.0-1 [16.1 kB] 144s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libpmix2t64 s390x 5.0.6-5 [715 kB] 144s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x libopenmpi40 s390x 5.0.7-1 [2196 kB] 144s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x libsprng2 s390x 2.0a-16 [96.2 kB] 144s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-common all 5.0.7-1 [97.9 kB] 144s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-bin s390x 5.0.7-1 [200 kB] 144s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x mpi-default-bin s390x 1.18 [2510 B] 144s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x tree-ppuzzle s390x 5.3~rc16+dfsg-12build1 [183 kB] 144s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x tree-puzzle s390x 5.3~rc16+dfsg-12build1 [164 kB] 144s Get:18 http://ftpmaster.internal/ubuntu plucky/universe s390x tree-puzzle-doc all 5.3~rc16+dfsg-12build1 [409 kB] 144s Fetched 4983 kB in 1s (5439 kB/s) 144s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 144s (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.) 144s Preparing to unpack .../00-libevent-pthreads-2.1-7t64_2.1.12-stable-10_s390x.deb ... 144s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 144s Selecting previously unselected package librdmacm1t64:s390x. 144s Preparing to unpack .../01-librdmacm1t64_55.0-1ubuntu1_s390x.deb ... 144s Unpacking librdmacm1t64:s390x (55.0-1ubuntu1) ... 144s Selecting previously unselected package libfabric1:s390x. 144s Preparing to unpack .../02-libfabric1_1.17.0-3.1_s390x.deb ... 144s Unpacking libfabric1:s390x (1.17.0-3.1) ... 144s Selecting previously unselected package libhwloc15:s390x. 144s Preparing to unpack .../03-libhwloc15_2.12.0-1_s390x.deb ... 144s Unpacking libhwloc15:s390x (2.12.0-1) ... 144s Selecting previously unselected package libmunge2:s390x. 144s Preparing to unpack .../04-libmunge2_0.5.16-1_s390x.deb ... 144s Unpacking libmunge2:s390x (0.5.16-1) ... 144s Selecting previously unselected package libpciaccess0:s390x. 144s Preparing to unpack .../05-libpciaccess0_0.17-3build1_s390x.deb ... 144s Unpacking libpciaccess0:s390x (0.17-3build1) ... 144s Selecting previously unselected package libxnvctrl0:s390x. 144s Preparing to unpack .../06-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 144s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 144s Selecting previously unselected package ocl-icd-libopencl1:s390x. 144s Preparing to unpack .../07-ocl-icd-libopencl1_2.3.2-1build1_s390x.deb ... 144s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 144s Selecting previously unselected package libhwloc-plugins:s390x. 144s Preparing to unpack .../08-libhwloc-plugins_2.12.0-1_s390x.deb ... 144s Unpacking libhwloc-plugins:s390x (2.12.0-1) ... 144s Selecting previously unselected package libpmix2t64:s390x. 144s Preparing to unpack .../09-libpmix2t64_5.0.6-5_s390x.deb ... 144s Unpacking libpmix2t64:s390x (5.0.6-5) ... 144s Selecting previously unselected package libopenmpi40:s390x. 144s Preparing to unpack .../10-libopenmpi40_5.0.7-1_s390x.deb ... 144s Unpacking libopenmpi40:s390x (5.0.7-1) ... 144s Selecting previously unselected package libsprng2. 144s Preparing to unpack .../11-libsprng2_2.0a-16_s390x.deb ... 144s Unpacking libsprng2 (2.0a-16) ... 144s Selecting previously unselected package openmpi-common. 144s Preparing to unpack .../12-openmpi-common_5.0.7-1_all.deb ... 144s Unpacking openmpi-common (5.0.7-1) ... 144s Selecting previously unselected package openmpi-bin. 144s Preparing to unpack .../13-openmpi-bin_5.0.7-1_s390x.deb ... 144s Unpacking openmpi-bin (5.0.7-1) ... 144s Selecting previously unselected package mpi-default-bin. 144s Preparing to unpack .../14-mpi-default-bin_1.18_s390x.deb ... 144s Unpacking mpi-default-bin (1.18) ... 144s Selecting previously unselected package tree-ppuzzle. 144s Preparing to unpack .../15-tree-ppuzzle_5.3~rc16+dfsg-12build1_s390x.deb ... 144s Unpacking tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 144s Selecting previously unselected package tree-puzzle. 144s Preparing to unpack .../16-tree-puzzle_5.3~rc16+dfsg-12build1_s390x.deb ... 144s Unpacking tree-puzzle (5.3~rc16+dfsg-12build1) ... 144s Selecting previously unselected package tree-puzzle-doc. 144s Preparing to unpack .../17-tree-puzzle-doc_5.3~rc16+dfsg-12build1_all.deb ... 144s Unpacking tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 145s Setting up libpciaccess0:s390x (0.17-3build1) ... 145s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 145s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 145s Setting up libmunge2:s390x (0.5.16-1) ... 145s Setting up libhwloc15:s390x (2.12.0-1) ... 145s Setting up tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 145s Setting up ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 145s Setting up openmpi-common (5.0.7-1) ... 145s Setting up librdmacm1t64:s390x (55.0-1ubuntu1) ... 145s Setting up libsprng2 (2.0a-16) ... 145s Setting up libfabric1:s390x (1.17.0-3.1) ... 145s Setting up tree-puzzle (5.3~rc16+dfsg-12build1) ... 145s Setting up libhwloc-plugins:s390x (2.12.0-1) ... 145s Setting up libpmix2t64:s390x (5.0.6-5) ... 145s Setting up libopenmpi40:s390x (5.0.7-1) ... 145s Setting up openmpi-bin (5.0.7-1) ... 145s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 145s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 145s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 145s Setting up mpi-default-bin (1.18) ... 145s Setting up tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 145s Processing triggers for man-db (2.13.0-1) ... 145s Processing triggers for libc-bin (2.41-1ubuntu2) ... 146s autopkgtest [19:35:59]: test run-unit-test: [----------------------- 147s .: 147s EF.3trees 147s EF.phy 147s atp6.a 147s globin.a 147s globin.ctrees 147s globin.trees 147s marswolf.ctrees 147s marswolf.n 147s marswolf.trees 147s primates.b 147s primates.ctrees 147s primates.trees 147s tests 147s 147s ./tests: 147s build-puzzle.log 147s build-puzzle.trs 147s build-remark.log 147s build-remark.trs 147s check-cons-pure-prot 147s check-lm-pure-prot 147s check-qp-clock 147s check-qp-hky-clock-nucl 147s check-qp-hky-rhet-clock-nucl 147s check-qp-hky-rhet-nucl 147s check-qp-jtt-prot 147s check-qp-jtt-rhet-clock-prot 147s check-qp-jtt-rhet-prot 147s check-qp-mtrev-prot 147s check-qp-pure-bin 147s check-qp-pure-nucl 147s check-qp-pure-prot 147s check-qp-tn-nucl 147s check-qp-vt-prot 147s check-qp-wag-prot 147s check-ut-pure-prot 147s cons-pure-prot.ctrees 147s cons-pure-prot.log 147s cons-pure-prot.param 147s cons-pure-prot.prot 147s cons-pure-prot.test 147s cons-pure-prot.trs 147s generate-scripts.sh 147s lm-pure-prot.log 147s lm-pure-prot.param 147s lm-pure-prot.prot 147s lm-pure-prot.test 147s lm-pure-prot.trs 147s qp-clock.log 147s qp-clock.nucl 147s qp-clock.param 147s qp-clock.test 147s qp-clock.trs 147s qp-hky-clock-nucl.log 147s qp-hky-clock-nucl.nucl 147s qp-hky-clock-nucl.param 147s qp-hky-clock-nucl.test 147s qp-hky-clock-nucl.trs 147s qp-hky-rhet-clock-nucl.log 147s qp-hky-rhet-clock-nucl.nucl 147s qp-hky-rhet-clock-nucl.param 147s qp-hky-rhet-clock-nucl.test 147s qp-hky-rhet-clock-nucl.trs 147s qp-hky-rhet-nucl.log 147s qp-hky-rhet-nucl.nucl 147s qp-hky-rhet-nucl.param 147s qp-hky-rhet-nucl.test 147s qp-hky-rhet-nucl.trs 147s qp-jtt-prot.log 147s qp-jtt-prot.param 147s qp-jtt-prot.prot 147s qp-jtt-prot.test 147s qp-jtt-prot.trs 147s qp-jtt-rhet-clock-prot.log 147s qp-jtt-rhet-clock-prot.param 147s qp-jtt-rhet-clock-prot.prot 147s qp-jtt-rhet-clock-prot.test 147s qp-jtt-rhet-clock-prot.trs 147s qp-jtt-rhet-prot.log 147s qp-jtt-rhet-prot.param 147s qp-jtt-rhet-prot.prot 147s qp-jtt-rhet-prot.test 147s qp-jtt-rhet-prot.trs 147s qp-mtrev-prot.log 147s qp-mtrev-prot.param 147s qp-mtrev-prot.prot 147s qp-mtrev-prot.test 147s qp-mtrev-prot.trs 147s qp-pure-bin.bin 147s qp-pure-bin.log 147s qp-pure-bin.param 147s qp-pure-bin.test 147s qp-pure-bin.trs 147s qp-pure-nucl.log 147s qp-pure-nucl.nucl 147s qp-pure-nucl.param 147s qp-pure-nucl.test 147s qp-pure-nucl.trs 147s qp-pure-prot.log 147s qp-pure-prot.param 147s qp-pure-prot.prot 147s qp-pure-prot.test 147s qp-pure-prot.trs 147s qp-tn-nucl.log 147s qp-tn-nucl.nucl 147s qp-tn-nucl.param 147s qp-tn-nucl.test 147s qp-tn-nucl.trs 147s qp-vt-prot.log 147s qp-vt-prot.param 147s qp-vt-prot.prot 147s qp-vt-prot.test 147s qp-vt-prot.trs 147s qp-wag-prot.log 147s qp-wag-prot.param 147s qp-wag-prot.prot 147s qp-wag-prot.test 147s qp-wag-prot.trs 147s template-test 147s test-suite.log 147s ut-pure-prot.log 147s ut-pure-prot.param 147s ut-pure-prot.prot 147s ut-pure-prot.test 147s ut-pure-prot.trees 147s ut-pure-prot.trs 147s Test 1 147s WARNING: random seed set to 1001 for debugging! 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-pure-bin.bin' 147s Input file: tests/qp-pure-bin.bin 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-pure-bin.bin) contains 5 sequences of length 895 147s 1. Gibbon 147s 2. Human 147s 3. Chimpanzee 147s 4. Gorilla 147s 5. Orangutan 147s (consists very likely of binary state data) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Exact maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Gibbon (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Binary states 147s m Model of substitution? Two-state model (Felsenstein 1981) 147s f Binary state frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Exact maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Gibbon (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Exact maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Gibbon (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Def.: JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Exact maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Gibbon (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Binary states 147s m Model of substitution? Two-state model (Felsenstein 1981) 147s f Binary state frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Writing parameters to file tests/qp-pure-bin.bin.puzzle 147s Writing parameters to file tests/qp-pure-bin.bin.puzzle 147s Writing pairwise distances to file tests/qp-pure-bin.bin.dist 147s Writing parameters to file tests/qp-pure-bin.bin.puzzle 147s Writing parameters to file tests/qp-pure-bin.bin.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-pure-bin.bin.puzzle 147s Likelihood distances: tests/qp-pure-bin.bin.dist 147s Phylip tree file: tests/qp-pure-bin.bin.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 2 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-pure-nucl.nucl' 147s Input file: tests/qp-pure-nucl.nucl 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-pure-nucl.nucl) contains 8 sequences of length 116 147s 1. Thylacinus 147s 2. Sarcophilu 147s 3. Dasyurus 147s 4. Echymipera 147s 5. Trichosuru 147s 6. Phalanger 147s 7. Philander 147s 8. Bos 147s (consists very likely of nucleotides) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Optimizing missing substitution process parameters 147s WARNING: random seed set to 1001 for debugging! 147s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 147s Writing pairwise distances to file tests/qp-pure-nucl.nucl.dist 147s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-pure-nucl.nucl.puzzle 147s Likelihood distances: tests/qp-pure-nucl.nucl.dist 147s Phylip tree file: tests/qp-pure-nucl.nucl.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 3 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-tn-nucl.nucl' 147s Input file: tests/qp-tn-nucl.nucl 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-tn-nucl.nucl) contains 8 sequences of length 116 147s 1. Thylacinus 147s 2. Sarcophilu 147s 3. Dasyurus 147s 4. Echymipera 147s 5. Trichosuru 147s 6. Phalanger 147s 7. Philander 147s 8. Bos 147s (consists very likely of nucleotides) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? TN (Tamura-Nei 1993) 147s p Constrain TN model to F84 model? No 147s t Transition/transversion parameter? Estimate from data set 147s r Y/R transition parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Optimizing missing substitution process parameters 147s WARNING: random seed set to 1001 for debugging! 147s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 147s Writing pairwise distances to file tests/qp-tn-nucl.nucl.dist 147s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-tn-nucl.nucl.puzzle 147s Likelihood distances: tests/qp-tn-nucl.nucl.dist 147s Phylip tree file: tests/qp-tn-nucl.nucl.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 4 147s WARNING: random seed set to 1001 for debugging! 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-hky-clock-nucl.nucl' 147s Input file: tests/qp-hky-clock-nucl.nucl 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-hky-clock-nucl.nucl) contains 8 sequences of length 116 147s 1. Thylacinus 147s 2. Sarcophilu 147s 3. Dasyurus 147s 4. Echymipera 147s 5. Trichosuru 147s 6. Phalanger 147s 7. Philander 147s 8. Bos 147s (consists very likely of nucleotides) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? Yes 147s l Location of root? Best place (automatic search) 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Optimizing missing substitution process parameters 147s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 147s Writing pairwise distances to file tests/qp-hky-clock-nucl.nucl.dist 147s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s Computing maximum likelihood branch lengths (with clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-hky-clock-nucl.nucl.puzzle 147s Likelihood distances: tests/qp-hky-clock-nucl.nucl.dist 147s Phylip tree file: tests/qp-hky-clock-nucl.nucl.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 5 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-hky-rhet-nucl.nucl' 147s Input file: tests/qp-hky-rhet-nucl.nucl 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-hky-rhet-nucl.nucl) contains 8 sequences of length 116 147s 1. Thylacinus 147s 2. Sarcophilu 147s 3. Dasyurus 147s 4. Echymipera 147s 5. Trichosuru 147s 6. Phalanger 147s 7. Philander 147s 8. Bos 147s (consists very likely of nucleotides) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Gamma distributed rates 147s a Gamma distribution parameter alpha? Estimate from data set 147s c Number of Gamma rate categories? 4 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Optimizing missing substitution process parameters 147s WARNING: random seed set to 1001 for debugging! 147s Optimizing missing rate heterogeneity parameters 147s Optimizing missing substitution process parameters 147s Optimizing missing rate heterogeneity parameters 147s Optimizing missing substitution process parameters 147s Optimizing missing rate heterogeneity parameters 147s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 147s Writing pairwise distances to file tests/qp-hky-rhet-nucl.nucl.dist 147s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s WARNING: random seed set to 1001 for debugging! 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-hky-rhet-nucl.nucl.puzzle 147s Likelihood distances: tests/qp-hky-rhet-nucl.nucl.dist 147s Phylip tree file: tests/qp-hky-rhet-nucl.nucl.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 6 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-hky-rhet-clock-nucl.nucl' 147s Input file: tests/qp-hky-rhet-clock-nucl.nucl 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-hky-rhet-clock-nucl.nucl) contains 8 sequences of length 116 147s 1. Thylacinus 147s 2. Sarcophilu 147s 3. Dasyurus 147s 4. Echymipera 147s 5. Trichosuru 147s 6. Phalanger 147s 7. Philander 147s 8. Bos 147s (consists very likely of nucleotides) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? Yes 147s l Location of root? Best place (automatic search) 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? Yes 147s l Location of root? Best place (automatic search) 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Gamma distributed rates 147s a Gamma distribution parameter alpha? Estimate from data set 147s c Number of Gamma rate categories? 4 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Optimizing missing substitution process parameters 147s Optimizing missing rate heterogeneity parameters 147s Optimizing missing substitution process parameters 147s Optimizing missing rate heterogeneity parameters 147s Optimizing missing substitution process parameters 147s Optimizing missing rate heterogeneity parameters 147s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 147s Writing pairwise distances to file tests/qp-hky-rhet-clock-nucl.nucl.dist 147s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 147s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s Computing maximum likelihood branch lengths (with clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-hky-rhet-clock-nucl.nucl.puzzle 147s Likelihood distances: tests/qp-hky-rhet-clock-nucl.nucl.dist 147s Phylip tree file: tests/qp-hky-rhet-clock-nucl.nucl.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 7 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-pure-prot.prot' 147s Input file: tests/qp-pure-prot.prot 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-pure-prot.prot) contains 7 sequences of length 128 147s 1. HBB_HUMAN 147s 2. HBB_HORSE 147s 3. HBA_HUMAN 147s 4. HBA_HORSE 147s 5. MYG_PHYCA 147s 6. GLB5_PETMA 147s 7. LGB2_LUPLU 147s (consists very likely of amino acids encoded on nuclear DNA) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 147s 147s Writing parameters to file tests/qp-pure-prot.prot.puzzle 147s Writing parameters to file tests/qp-pure-prot.prot.puzzle 147s Writing pairwise distances to file tests/qp-pure-prot.prot.dist 147s Writing parameters to file tests/qp-pure-prot.prot.puzzle 147s Writing parameters to file tests/qp-pure-prot.prot.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-pure-prot.prot.puzzle 147s Likelihood distances: tests/qp-pure-prot.prot.dist 147s Phylip tree file: tests/qp-pure-prot.prot.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 8 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-mtrev-prot.prot' 147s Input file: tests/qp-mtrev-prot.prot 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-mtrev-prot.prot) contains 7 sequences of length 128 147s 1. HBB_HUMAN 147s 2. HBB_HORSE 147s 3. HBA_HUMAN 147s 4. HBA_HORSE 147s 5. MYG_PHYCA 147s 6. GLB5_PETMA 147s 7. LGB2_LUPLU 147s (consists very likely of amino acids encoded on nuclear DNA) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 147s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 147s Writing pairwise distances to file tests/qp-mtrev-prot.prot.dist 147s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 147s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-mtrev-prot.prot.puzzle 147s Likelihood distances: tests/qp-mtrev-prot.prot.dist 147s Phylip tree file: tests/qp-mtrev-prot.prot.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 9 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-vt-prot.prot' 147s Input file: tests/qp-vt-prot.prot 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-vt-prot.prot) contains 7 sequences of length 128 147s 1. HBB_HUMAN 147s 2. HBB_HORSE 147s 3. HBA_HUMAN 147s 4. HBA_HORSE 147s 5. MYG_PHYCA 147s 6. GLB5_PETMA 147s 7. LGB2_LUPLU 147s (consists very likely of amino acids encoded on nuclear DNA) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? VT (Mueller-Vingron 2000) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Writing parameters to file tests/qp-vt-prot.prot.puzzle 147s Writing parameters to file tests/qp-vt-prot.prot.puzzle 147s Writing pairwise distances to file tests/qp-vt-prot.prot.dist 147s Writing parameters to file tests/qp-vt-prot.prot.puzzle 147s Writing parameters to file tests/qp-vt-prot.prot.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-vt-prot.prot.puzzle 147s Likelihood distances: tests/qp-vt-prot.prot.dist 147s Phylip tree file: tests/qp-vt-prot.prot.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 147s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 147s Passed 147s 147s Test 10 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-wag-prot.prot' 147s Input file: tests/qp-wag-prot.prot 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-wag-prot.prot) contains 7 sequences of length 128 147s 1. HBB_HUMAN 147s 2. HBB_HORSE 147s 3. HBA_HUMAN 147s 4. HBA_HORSE 147s 5. MYG_PHYCA 147s 6. GLB5_PETMA 147s 7. LGB2_LUPLU 147s (consists very likely of amino acids encoded on nuclear DNA) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? VT (Mueller-Vingron 2000) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? WAG (Whelan-Goldman 2000) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Writing parameters to file tests/qp-wag-prot.prot.puzzle 147s Writing parameters to file tests/qp-wag-prot.prot.puzzle 147s Writing pairwise distances to file tests/qp-wag-prot.prot.dist 147s Writing parameters to file tests/qp-wag-prot.prot.puzzle 147s Writing parameters to file tests/qp-wag-prot.prot.puzzle 147s Computing quartet maximum likelihood trees 147s WARNING: random seed set to 1001 for debugging! 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-wag-prot.prot.puzzle 147s Likelihood distances: tests/qp-wag-prot.prot.dist 147s Phylip tree file: tests/qp-wag-prot.prot.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 11 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-clock.nucl' 147s Input file: tests/qp-clock.nucl 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-clock.nucl) contains 8 sequences of length 116 147s 1. Thylacinus 147s 2. Sarcophilu 147s 3. Dasyurus 147s 4. Echymipera 147s 5. Trichosuru 147s 6. Phalanger 147s 7. Philander 147s 8. Bos 147s (consists very likely of nucleotides) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? Thylacinus (1) 147s z Compute clocklike branch lengths? Yes 147s l Location of root? Best place (automatic search) 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Optimizing missing substitution process parameters 147s WARNING: random seed set to 1001 for debugging! 147s Writing parameters to file tests/qp-clock.nucl.puzzle 147s Writing parameters to file tests/qp-clock.nucl.puzzle 147s Writing pairwise distances to file tests/qp-clock.nucl.dist 147s Writing parameters to file tests/qp-clock.nucl.puzzle 147s Writing parameters to file tests/qp-clock.nucl.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s Computing maximum likelihood branch lengths (with clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-clock.nucl.puzzle 147s Likelihood distances: tests/qp-clock.nucl.dist 147s Phylip tree file: tests/qp-clock.nucl.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 12 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-jtt-prot.prot' 147s Input file: tests/qp-jtt-prot.prot 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-jtt-prot.prot) contains 7 sequences of length 128 147s 1. HBB_HUMAN 147s 2. HBB_HORSE 147s 3. HBA_HUMAN 147s 4. HBA_HORSE 147s 5. MYG_PHYCA 147s 6. GLB5_PETMA 147s 7. LGB2_LUPLU 147s (consists very likely of amino acids encoded on nuclear DNA) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 147s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 147s Writing pairwise distances to file tests/qp-jtt-prot.prot.dist 147s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 147s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 147s Computing quartet maximum likelihood trees 147s WARNING: random seed set to 1001 for debugging! 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-jtt-prot.prot.puzzle 147s Likelihood distances: tests/qp-jtt-prot.prot.dist 147s Phylip tree file: tests/qp-jtt-prot.prot.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 13 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-jtt-rhet-prot.prot' 147s Input file: tests/qp-jtt-rhet-prot.prot 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-jtt-rhet-prot.prot) contains 7 sequences of length 128 147s 1. HBB_HUMAN 147s 2. HBB_HORSE 147s 3. HBA_HUMAN 147s 4. HBA_HORSE 147s 5. MYG_PHYCA 147s 6. GLB5_PETMA 147s 7. LGB2_LUPLU 147s (consists very likely of amino acids encoded on nuclear DNA) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Gamma distributed rates 147s a Gamma distribution parameter alpha? Estimate from data set 147s c Number of Gamma rate categories? 4 147s 147s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 147s 147s Optimizing missing rate heterogeneity parameters 147s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 147s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 147s Writing pairwise distances to file tests/qp-jtt-rhet-prot.prot.dist 147s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 147s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 147s Computing quartet maximum likelihood trees 147s Computing quartet puzzling trees 147s Computing maximum likelihood branch lengths (without clock) 147s 147s All results written to disk: 147s Puzzle report file: tests/qp-jtt-rhet-prot.prot.puzzle 147s Likelihood distances: tests/qp-jtt-rhet-prot.prot.dist 147s Phylip tree file: tests/qp-jtt-rhet-prot.prot.tree 147s 147s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 147s Passed 147s 147s Test 14 147s 147s 147s 147s WELCOME TO TREE-PUZZLE 5.3.rc16! 147s 147s 147s 147s argv[1] = '-randseed1001' 147s argv[2] = 'tests/qp-jtt-rhet-clock-prot.prot' 147s Input file: tests/qp-jtt-rhet-clock-prot.prot 147s Using SPRNG -- Scalable Parallel Random Number Generator 147s RANDOM SEED: 1001 147s 147s Input data set (tests/qp-jtt-rhet-clock-prot.prot) contains 7 sequences of length 128 147s 1. HBB_HUMAN 147s 2. HBB_HORSE 147s 3. HBA_HUMAN 147s 4. HBA_HORSE 147s 5. MYG_PHYCA 147s 6. GLB5_PETMA 147s 7. LGB2_LUPLU 147s (consists very likely of amino acids encoded on nuclear DNA) 147s 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Auto: Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Nucleotides 147s m Model of substitution? HKY (Hasegawa et al. 1985) 147s t Transition/transversion parameter? Estimate from data set 147s f Nucleotide frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? No 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? Yes 147s l Location of root? Best place (automatic search) 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Uniform rate 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s 147s 147s GENERAL OPTIONS 147s b Type of analysis? Tree reconstruction 147s k Tree search procedure? Quartet puzzling 147s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 147s n Number of puzzling steps? 1000 147s o Display as outgroup? HBB_HUMAN (1) 147s z Compute clocklike branch lengths? Yes 147s l Location of root? Best place (automatic search) 147s e Parameter estimates? Approximate (faster) 147s x Parameter estimation uses? Neighbor-joining tree 147s OUTPUT OPTIONS 147s 9 List puzzling trees/splits (NEXUS)? No 147s u List unresolved quartets? No 147s j List puzzling step trees? No 147s SUBSTITUTION PROCESS 147s d Type of sequence input data? Amino acids 147s m Model of substitution? JTT (Jones et al. 1992) 147s f Amino acid frequencies? Estimate from data set 147s RATE HETEROGENEITY 147s w Model of rate heterogeneity? Gamma distributed rates 147s a Gamma distribution parameter alpha? Estimate from data set 147s c Number of Gamma rate categories? 4 147s 147s Quit [q], confirm [y], or change [menu] settings: 147s Optimizing missing rate heterogeneity parameters 147s WARNING: random seed set to 1001 for debugging! 147s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 147s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 147s Writing pairwise distances to file tests/qp-jtt-rhet-clock-prot.prot.dist 147s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 147s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 147s Computing quartet maximum likelihood trees 148s Computing quartet puzzling trees 148s Computing maximum likelihood branch lengths (without clock) 148s Computing maximum likelihood branch lengths (with clock) 148s 148s All results written to disk: 148s Puzzle report file: tests/qp-jtt-rhet-clock-prot.prot.puzzle 148s Likelihood distances: tests/qp-jtt-rhet-clock-prot.prot.dist 148s Phylip tree file: tests/qp-jtt-rhet-clock-prot.prot.tree 148s 148s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s Passed 148s 148s Test 15 148s 148s 148s 148s WELCOME TO TREE-PUZZLE 5.3.rc16! 148s 148s 148s 148s argv[1] = '-randseed1001' 148s argv[2] = 'tests/lm-pure-prot.prot' 148s Input file: tests/lm-pure-prot.prot 148s Using SPRNG -- Scalable Parallel Random Number Generator 148s RANDOM SEED: 1001 148s 148s Input data set (tests/lm-pure-prot.prot) contains 7 sequences of length 128 148s 1. HBB_HUMAN 148s 2. HBB_HORSE 148s 3. HBA_HUMAN 148s 4. HBA_HORSE 148s 5. MYG_PHYCA 148s 6. GLB5_PETMA 148s 7. LGB2_LUPLU 148s (consists very likely of amino acids encoded on nuclear DNA) 148s 148s 148s 148s GENERAL OPTIONS 148s b Type of analysis? Tree reconstruction 148s k Tree search procedure? Quartet puzzling 148s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 148s n Number of puzzling steps? 1000 148s o Display as outgroup? HBB_HUMAN (1) 148s z Compute clocklike branch lengths? No 148s e Parameter estimates? Approximate (faster) 148s x Parameter estimation uses? Neighbor-joining tree 148s OUTPUT OPTIONS 148s 9 List puzzling trees/splits (NEXUS)? No 148s u List unresolved quartets? No 148s j List puzzling step trees? No 148s SUBSTITUTION PROCESS 148s d Type of sequence input data? Auto: Amino acids 148s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 148s f Amino acid frequencies? Estimate from data set 148s RATE HETEROGENEITY 148s w Model of rate heterogeneity? Uniform rate 148s 148s Quit [q], confirm [y], or change [menu] settings: 148s 148s 148s GENERAL OPTIONS 148s b Type of analysis? Tree reconstruction 148s k Tree search procedure? Quartet puzzling 148s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 148s n Number of puzzling steps? 1000 148s o Display as outgroup? HBB_HUMAN (1) 148s z Compute clocklike branch lengths? No 148s e Parameter estimates? Approximate (faster) 148s x Parameter estimation uses? Neighbor-joining tree 148s OUTPUT OPTIONS 148s 9 List puzzling trees/splits (NEXUS)? No 148s u List unresolved quartets? No 148s j List puzzling step trees? No 148s SUBSTITUTION PROCESS 148s d Type of sequence input data? Nucleotides 148s m Model of substitution? HKY (Hasegawa et al. 1985) 148s t Transition/transversion parameter? Estimate from data set 148s f Nucleotide frequencies? Estimate from data set 148s RATE HETEROGENEITY 148s w Model of rate heterogeneity? Uniform rate 148s 148s Quit [q], confirm [y], or change [menu] settings: 148s 148s 148s GENERAL OPTIONS 148s b Type of analysis? Tree reconstruction 148s k Tree search procedure? Quartet puzzling 148s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 148s n Number of puzzling steps? 1000 148s o Display as outgroup? HBB_HUMAN (1) 148s z Compute clocklike branch lengths? No 148s e Parameter estimates? Approximate (faster) 148s x Parameter estimation uses? Neighbor-joining tree 148s OUTPUT OPTIONS 148s 9 List puzzling trees/splits (NEXUS)? No 148s u List unresolved quartets? No 148s j List puzzling step trees? No 148s SUBSTITUTION PROCESS 148s d Type of sequence input data? Amino acids 148s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 148s f Amino acid frequencies? Estimate from data set 148s RATE HETEROGENEITY 148s w Model of rate heterogeneity? Uniform rate 148s 148s Quit [q], confirm [y], or change [menu] settings: 148s 148s 148s GENERAL OPTIONS 148s b Type of analysis? Likelihood mapping 148s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 148s g Group sequences in clusters? No 148s n Number of quartets? 35 (all possible) 148s e Parameter estimates? Approximate (faster) 148s x Parameter estimation uses? Neighbor-joining tree 148s SUBSTITUTION PROCESS 148s d Type of sequence input data? Amino acids 148s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 148s f Amino acid frequencies? Estimate from data set 148s RATE HETEROGENEITY 148s w Model of rate heterogeneity? Uniform rate 148s 148s Quit [q], confirm [y], or change [menu] settings: 148s Writing parameters to file tests/lm-pure-prot.prot.puzzle 148s Writing parameters to file tests/lm-pure-prot.prot.puzzle 148s Writing pairwise distances to file tests/lm-pure-prot.prot.dist 148s Writing parameters to file tests/lm-pure-prot.prot.puzzle 148s Writing parameters to file tests/lm-pure-prot.prot.puzzle 148s Performing likelihood mapping analysis 148s WARNING: random seed set to 1001 for debugging! 148s PPP1: 0 (./puzzle1.c:8696) 148s PPP1: 1 (./puzzle1.c:8702) 148s 148s All results written to disk: 148s Puzzle report file: tests/lm-pure-prot.prot.puzzle 148s Likelihood distances: tests/lm-pure-prot.prot.dist 148s Likelihood mapping diagram (EPS): tests/lm-pure-prot.prot.eps 148s Likelihood mapping diagram (SVG): tests/lm-pure-prot.prot.svg 148s 148s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 148s Passed 148s 148s autopkgtest [19:36:01]: test run-unit-test: -----------------------] 149s autopkgtest [19:36:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 149s run-unit-test PASS 149s autopkgtest [19:36:02]: @@@@@@@@@@@@@@@@@@@@ summary 149s run-unit-test PASS 155s nova [W] Using flock in prodstack6-s390x 155s flock: timeout while waiting to get lock 155s Creating nova instance adt-plucky-s390x-tree-puzzle-20250315-193333-juju-7f2275-prod-proposed-migration-environment-2-eb089a03-85ad-423e-8f54-5c7db3469d30 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 155s nova [W] Timed out waiting for 92fa242c-3499-4bd1-9c17-239e00611582 to get deleted.