0s autopkgtest [17:09:26]: starting date and time: 2025-03-15 17:09:26+0000 0s autopkgtest [17:09:26]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:09:26]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9015wedz/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-2.secgroup --name adt-plucky-arm64-tree-puzzle-20250315-170926-juju-7f2275-prod-proposed-migration-environment-15-5027be0b-3163-4054-a9f2-09a4ee632046 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 186s autopkgtest [17:12:32]: testbed dpkg architecture: arm64 186s autopkgtest [17:12:32]: testbed apt version: 2.9.33 186s autopkgtest [17:12:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 187s autopkgtest [17:12:33]: testbed release detected to be: None 188s autopkgtest [17:12:34]: updating testbed package index (apt update) 188s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 188s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 188s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 188s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 188s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 189s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 189s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 189s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 189s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 189s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 189s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 189s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 189s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 189s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 190s Fetched 1078 kB in 2s (611 kB/s) 191s Reading package lists... 191s + lsb_release --codename --short 191s + RELEASE=plucky 191s + cat 191s + [ plucky != trusty ] 191s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 191s Reading package lists... 192s Building dependency tree... 192s Reading state information... 192s Calculating upgrade... 192s Calculating upgrade... 193s The following packages will be upgraded: 193s pinentry-curses python3-jinja2 strace 193s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Need to get 647 kB of archives. 193s After this operation, 11.3 kB of additional disk space will be used. 193s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 194s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 194s Fetched 647 kB in 1s (643 kB/s) 195s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 195s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 195s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 195s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 195s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 195s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 195s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 195s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 195s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 195s Setting up strace (6.13+ds-1ubuntu1) ... 196s Processing triggers for man-db (2.13.0-1) ... 196s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 196s + /usr/lib/apt/apt-helper analyze-pattern ?true 196s + uname -r 196s + sed s/\./\\./g 196s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 196s + apt list ?obsolete 196s + tail -n+2 196s + grep -v ^linux-.*6\.14\.0-10-generic.* 196s + cut -d/ -f1 196s + obsolete_pkgs=linux-headers-6.11.0-8-generic 196s linux-headers-6.11.0-8 196s linux-image-6.11.0-8-generic 196s linux-modules-6.11.0-8-generic 196s linux-tools-6.11.0-8-generic 196s linux-tools-6.11.0-8 196s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 196s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Solving dependencies... 197s The following packages will be REMOVED: 197s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 197s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 197s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 197s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 198s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 198s After this operation, 267 MB disk space will be freed. 198s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 198s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 198s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 198s Removing libpython3.12t64:arm64 (3.12.9-1) ... 198s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 198s Removing libnsl2:arm64 (1.3.0-3build3) ... 198s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 198s Removing libunwind8:arm64 (1.6.2-3.1) ... 198s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 199s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 200s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 201s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 201s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 201s /etc/kernel/postrm.d/initramfs-tools: 201s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 201s /etc/kernel/postrm.d/zz-flash-kernel: 201s flash-kernel: Kernel 6.11.0-8-generic has been removed. 201s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 201s /etc/kernel/postrm.d/zz-update-grub: 201s Sourcing file `/etc/default/grub' 201s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 201s Generating grub configuration file ... 201s Found linux image: /boot/vmlinuz-6.14.0-10-generic 201s Found initrd image: /boot/initrd.img-6.14.0-10-generic 202s Warning: os-prober will not be executed to detect other bootable partitions. 202s Systems on them will not be added to the GRUB boot configuration. 202s Check GRUB_DISABLE_OS_PROBER documentation entry. 202s Adding boot menu entry for UEFI Firmware Settings ... 202s done 202s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 202s Processing triggers for libc-bin (2.41-1ubuntu1) ... 202s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81650 files and directories currently installed.) 202s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 202s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 202s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 202s + grep -q trusty /etc/lsb-release 202s + [ ! -d /usr/share/doc/unattended-upgrades ] 202s + [ ! -d /usr/share/doc/lxd ] 202s + [ ! -d /usr/share/doc/lxd-client ] 202s + [ ! -d /usr/share/doc/snapd ] 202s + type iptables 202s + cat 202s + chmod 755 /etc/rc.local 202s + . /etc/rc.local 202s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 202s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 202s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 202s + uname -m 202s + [ aarch64 = ppc64le ] 202s + [ -d /run/systemd/system ] 202s + systemd-detect-virt --quiet --vm 202s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 202s + cat 202s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 202s + echo COMPRESS=lz4 202s autopkgtest [17:12:48]: upgrading testbed (apt dist-upgrade and autopurge) 203s Reading package lists... 203s Building dependency tree... 203s Reading state information... 204s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 204s Starting 2 pkgProblemResolver with broken count: 0 204s Done 204s Entering ResolveByKeep 205s 205s Calculating upgrade... 205s The following packages will be upgraded: 205s libc-bin libc-dev-bin libc6 libc6-dev locales 205s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 205s Need to get 9530 kB of archives. 205s After this operation, 0 B of additional disk space will be used. 205s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 211s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 212s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 218s Preconfiguring packages ... 218s Fetched 9530 kB in 12s (783 kB/s) 218s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 218s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 218s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 218s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 218s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 218s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 218s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 218s Setting up libc6:arm64 (2.41-1ubuntu2) ... 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 219s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 219s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 219s Setting up libc-bin (2.41-1ubuntu2) ... 219s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 219s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 219s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 219s Setting up locales (2.41-1ubuntu2) ... 220s Generating locales (this might take a while)... 222s en_US.UTF-8... done 222s Generation complete. 222s Setting up libc-dev-bin (2.41-1ubuntu2) ... 222s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 222s Processing triggers for man-db (2.13.0-1) ... 223s Processing triggers for systemd (257.3-1ubuntu3) ... 224s Reading package lists... 224s Building dependency tree... 224s Reading state information... 224s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 225s Solving dependencies... 225s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 226s autopkgtest [17:13:12]: rebooting testbed after setup commands that affected boot 250s autopkgtest [17:13:36]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 255s autopkgtest [17:13:41]: @@@@@@@@@@@@@@@@@@@@ apt-source tree-puzzle 259s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (dsc) [2235 B] 259s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (tar) [591 kB] 259s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (diff) [32.4 kB] 260s gpgv: Signature made Sat Nov 30 06:14:46 2024 UTC 260s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 260s gpgv: Can't check signature: No public key 260s dpkg-source: warning: cannot verify inline signature for ./tree-puzzle_5.3~rc16+dfsg-12build1.dsc: no acceptable signature found 260s autopkgtest [17:13:46]: testing package tree-puzzle version 5.3~rc16+dfsg-12build1 261s autopkgtest [17:13:46]: build not needed 261s autopkgtest [17:13:47]: test run-unit-test: preparing testbed 261s Reading package lists... 262s Building dependency tree... 262s Reading state information... 262s Starting pkgProblemResolver with broken count: 0 262s Starting 2 pkgProblemResolver with broken count: 0 262s Done 263s The following NEW packages will be installed: 263s libamd-comgr2 libamdhip64-5 libevent-pthreads-2.1-7t64 libfabric1 libgomp1 263s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 263s libibumad3 libllvm17t64 libmunge2 libopenmpi40 libpciaccess0 libpmix2t64 263s librdmacm1t64 libsprng2 libucx0 libxnvctrl0 mpi-default-bin 263s ocl-icd-libopencl1 openmpi-bin openmpi-common tree-ppuzzle tree-puzzle 263s tree-puzzle-doc 263s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 263s Need to get 55.5 MB of archives. 263s After this operation, 233 MB of additional disk space will be used. 263s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB] 292s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 328s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 328s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 329s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB] 340s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 340s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 55.0-1ubuntu1 [71.5 kB] 340s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB] 340s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 340s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB] 340s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 340s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 340s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 340s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 341s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB] 341s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB] 341s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 55.0-1ubuntu1 [29.8 kB] 341s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 55.0-1ubuntu1 [43.3 kB] 341s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB] 343s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB] 345s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsprng2 arm64 2.0a-16 [92.5 kB] 345s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-common all 5.0.7-1 [97.9 kB] 345s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-bin arm64 5.0.7-1 [195 kB] 346s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 mpi-default-bin arm64 1.18 [2510 B] 346s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 tree-ppuzzle arm64 5.3~rc16+dfsg-12build1 [160 kB] 346s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 tree-puzzle arm64 5.3~rc16+dfsg-12build1 [144 kB] 346s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 tree-puzzle-doc all 5.3~rc16+dfsg-12build1 [409 kB] 347s Fetched 55.5 MB in 1min 24s (662 kB/s) 347s Selecting previously unselected package libllvm17t64:arm64. 347s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 347s Preparing to unpack .../00-libllvm17t64_1%3a17.0.6-21_arm64.deb ... 347s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... 348s Selecting previously unselected package libamd-comgr2:arm64. 348s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 348s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 348s Selecting previously unselected package libhsakmt1:arm64. 348s Preparing to unpack .../02-libhsakmt1_5.7.0-1build1_arm64.deb ... 348s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 348s Selecting previously unselected package libhsa-runtime64-1. 348s Preparing to unpack .../03-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 348s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 348s Selecting previously unselected package libamdhip64-5. 348s Preparing to unpack .../04-libamdhip64-5_5.7.1-5_arm64.deb ... 348s Unpacking libamdhip64-5 (5.7.1-5) ... 348s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 348s Preparing to unpack .../05-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 348s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 348s Selecting previously unselected package librdmacm1t64:arm64. 348s Preparing to unpack .../06-librdmacm1t64_55.0-1ubuntu1_arm64.deb ... 348s Unpacking librdmacm1t64:arm64 (55.0-1ubuntu1) ... 348s Selecting previously unselected package libfabric1:arm64. 349s Preparing to unpack .../07-libfabric1_1.17.0-3.1_arm64.deb ... 349s Unpacking libfabric1:arm64 (1.17.0-3.1) ... 349s Selecting previously unselected package libgomp1:arm64. 349s Preparing to unpack .../08-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 349s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 349s Selecting previously unselected package libhwloc15:arm64. 349s Preparing to unpack .../09-libhwloc15_2.12.0-1_arm64.deb ... 349s Unpacking libhwloc15:arm64 (2.12.0-1) ... 349s Selecting previously unselected package libmunge2:arm64. 349s Preparing to unpack .../10-libmunge2_0.5.16-1_arm64.deb ... 349s Unpacking libmunge2:arm64 (0.5.16-1) ... 349s Selecting previously unselected package libpciaccess0:arm64. 349s Preparing to unpack .../11-libpciaccess0_0.17-3build1_arm64.deb ... 349s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 349s Selecting previously unselected package libxnvctrl0:arm64. 349s Preparing to unpack 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.../17-libibmad5_55.0-1ubuntu1_arm64.deb ... 349s Unpacking libibmad5:arm64 (55.0-1ubuntu1) ... 349s Selecting previously unselected package libucx0:arm64. 349s Preparing to unpack .../18-libucx0_1.18.1+ds-2_arm64.deb ... 349s Unpacking libucx0:arm64 (1.18.1+ds-2) ... 349s Selecting previously unselected package libopenmpi40:arm64. 349s Preparing to unpack .../19-libopenmpi40_5.0.7-1_arm64.deb ... 349s Unpacking libopenmpi40:arm64 (5.0.7-1) ... 349s Selecting previously unselected package libsprng2. 349s Preparing to unpack .../20-libsprng2_2.0a-16_arm64.deb ... 349s Unpacking libsprng2 (2.0a-16) ... 349s Selecting previously unselected package openmpi-common. 349s Preparing to unpack .../21-openmpi-common_5.0.7-1_all.deb ... 349s Unpacking openmpi-common (5.0.7-1) ... 349s Selecting previously unselected package openmpi-bin. 349s Preparing to unpack .../22-openmpi-bin_5.0.7-1_arm64.deb ... 349s Unpacking openmpi-bin (5.0.7-1) ... 349s Selecting previously unselected package mpi-default-bin. 349s Preparing to unpack .../23-mpi-default-bin_1.18_arm64.deb ... 349s Unpacking mpi-default-bin (1.18) ... 349s Selecting previously unselected package tree-ppuzzle. 349s Preparing to unpack .../24-tree-ppuzzle_5.3~rc16+dfsg-12build1_arm64.deb ... 349s Unpacking tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 349s Selecting previously unselected package tree-puzzle. 349s Preparing to unpack .../25-tree-puzzle_5.3~rc16+dfsg-12build1_arm64.deb ... 349s Unpacking tree-puzzle (5.3~rc16+dfsg-12build1) ... 349s Selecting previously unselected package tree-puzzle-doc. 349s Preparing to unpack .../26-tree-puzzle-doc_5.3~rc16+dfsg-12build1_all.deb ... 349s Unpacking tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 349s Setting up libpciaccess0:arm64 (0.17-3build1) ... 349s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 349s Setting up libibumad3:arm64 (55.0-1ubuntu1) ... 349s Setting up libibmad5:arm64 (55.0-1ubuntu1) ... 349s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 349s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 349s Setting up libmunge2:arm64 (0.5.16-1) ... 349s Setting up libllvm17t64:arm64 (1:17.0.6-21) ... 349s Setting up libhwloc15:arm64 (2.12.0-1) ... 349s Setting up tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 349s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 349s Setting up openmpi-common (5.0.7-1) ... 349s Setting up librdmacm1t64:arm64 (55.0-1ubuntu1) ... 349s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 349s Setting up libsprng2 (2.0a-16) ... 349s Setting up libhsakmt1:arm64 (5.7.0-1build1) ... 349s Setting up libfabric1:arm64 (1.17.0-3.1) ... 349s Setting up tree-puzzle (5.3~rc16+dfsg-12build1) ... 349s Setting up libhwloc-plugins:arm64 (2.12.0-1) ... 349s Setting up libpmix2t64:arm64 (5.0.6-5) ... 349s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 349s Setting up libamdhip64-5 (5.7.1-5) ... 349s Setting up libucx0:arm64 (1.18.1+ds-2) ... 349s Setting up libopenmpi40:arm64 (5.0.7-1) ... 349s Setting up openmpi-bin (5.0.7-1) ... 349s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 349s 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 349s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 349s Setting up mpi-default-bin (1.18) ... 349s Setting up tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 349s Processing triggers for man-db (2.13.0-1) ... 350s Processing triggers for libc-bin (2.41-1ubuntu2) ... 352s autopkgtest [17:15:18]: test run-unit-test: [----------------------- 353s .: 353s EF.3trees 353s EF.phy 353s atp6.a 353s globin.a 353s globin.ctrees 353s globin.trees 353s marswolf.ctrees 353s marswolf.n 353s marswolf.trees 353s primates.b 353s primates.ctrees 353s primates.trees 353s tests 353s 353s ./tests: 353s build-puzzle.log 353s build-puzzle.trs 353s build-remark.log 353s build-remark.trs 353s check-cons-pure-prot 353s check-lm-pure-prot 353s check-qp-clock 353s check-qp-hky-clock-nucl 353s check-qp-hky-rhet-clock-nucl 353s check-qp-hky-rhet-nucl 353s check-qp-jtt-prot 353s check-qp-jtt-rhet-clock-prot 353s check-qp-jtt-rhet-prot 353s check-qp-mtrev-prot 353s check-qp-pure-bin 353s check-qp-pure-nucl 353s check-qp-pure-prot 353s check-qp-tn-nucl 353s check-qp-vt-prot 353s check-qp-wag-prot 353s check-ut-pure-prot 353s cons-pure-prot.ctrees 353s cons-pure-prot.log 353s cons-pure-prot.param 353s cons-pure-prot.prot 353s cons-pure-prot.test 353s cons-pure-prot.trs 353s generate-scripts.sh 353s lm-pure-prot.log 353s lm-pure-prot.param 353s lm-pure-prot.prot 353s lm-pure-prot.test 353s lm-pure-prot.trs 353s qp-clock.log 353s qp-clock.nucl 353s qp-clock.param 353s qp-clock.test 353s qp-clock.trs 353s qp-hky-clock-nucl.log 353s qp-hky-clock-nucl.nucl 353s qp-hky-clock-nucl.param 353s qp-hky-clock-nucl.test 353s qp-hky-clock-nucl.trs 353s qp-hky-rhet-clock-nucl.log 353s qp-hky-rhet-clock-nucl.nucl 353s qp-hky-rhet-clock-nucl.param 353s qp-hky-rhet-clock-nucl.test 353s qp-hky-rhet-clock-nucl.trs 353s qp-hky-rhet-nucl.log 353s qp-hky-rhet-nucl.nucl 353s qp-hky-rhet-nucl.param 353s qp-hky-rhet-nucl.test 353s qp-hky-rhet-nucl.trs 353s qp-jtt-prot.log 353s qp-jtt-prot.param 353s qp-jtt-prot.prot 353s qp-jtt-prot.test 353s qp-jtt-prot.trs 353s qp-jtt-rhet-clock-prot.log 353s qp-jtt-rhet-clock-prot.param 353s qp-jtt-rhet-clock-prot.prot 353s qp-jtt-rhet-clock-prot.test 353s qp-jtt-rhet-clock-prot.trs 353s qp-jtt-rhet-prot.log 353s qp-jtt-rhet-prot.param 353s qp-jtt-rhet-prot.prot 353s qp-jtt-rhet-prot.test 353s qp-jtt-rhet-prot.trs 353s qp-mtrev-prot.log 353s qp-mtrev-prot.param 353s qp-mtrev-prot.prot 353s qp-mtrev-prot.test 353s qp-mtrev-prot.trs 353s qp-pure-bin.bin 353s qp-pure-bin.log 353s qp-pure-bin.param 353s qp-pure-bin.test 353s qp-pure-bin.trs 353s qp-pure-nucl.log 353s qp-pure-nucl.nucl 353s qp-pure-nucl.param 353s qp-pure-nucl.test 353s qp-pure-nucl.trs 353s qp-pure-prot.log 353s qp-pure-prot.param 353s qp-pure-prot.prot 353s qp-pure-prot.test 353s qp-pure-prot.trs 353s qp-tn-nucl.log 353s qp-tn-nucl.nucl 353s qp-tn-nucl.param 353s qp-tn-nucl.test 353s qp-tn-nucl.trs 353s qp-vt-prot.log 353s qp-vt-prot.param 353s qp-vt-prot.prot 353s qp-vt-prot.test 353s qp-vt-prot.trs 353s qp-wag-prot.log 353s qp-wag-prot.param 353s qp-wag-prot.prot 353s qp-wag-prot.test 353s qp-wag-prot.trs 353s template-test 353s test-suite.log 353s ut-pure-prot.log 353s ut-pure-prot.param 353s ut-pure-prot.prot 353s ut-pure-prot.test 353s ut-pure-prot.trees 353s ut-pure-prot.trs 353s Test 1 353s WARNING: random seed set to 1001 for debugging! 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-pure-bin.bin' 353s Input file: tests/qp-pure-bin.bin 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-pure-bin.bin) contains 5 sequences of length 895 353s 1. Gibbon 353s 2. Human 353s 3. Chimpanzee 353s 4. Gorilla 353s 5. Orangutan 353s (consists very likely of binary state data) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Exact maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Gibbon (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Binary states 353s m Model of substitution? Two-state model (Felsenstein 1981) 353s f Binary state frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Exact maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Gibbon (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Exact maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Gibbon (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Def.: JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Exact maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Gibbon (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Binary states 353s m Model of substitution? Two-state model (Felsenstein 1981) 353s f Binary state frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Writing parameters to file tests/qp-pure-bin.bin.puzzle 353s Writing parameters to file tests/qp-pure-bin.bin.puzzle 353s Writing pairwise distances to file tests/qp-pure-bin.bin.dist 353s Writing parameters to file tests/qp-pure-bin.bin.puzzle 353s Writing parameters to file tests/qp-pure-bin.bin.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-pure-bin.bin.puzzle 353s Likelihood distances: tests/qp-pure-bin.bin.dist 353s Phylip tree file: tests/qp-pure-bin.bin.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 2 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-pure-nucl.nucl' 353s Input file: tests/qp-pure-nucl.nucl 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s WARNING: random seed set to 1001 for debugging! 353s WARNING: random seed set to 1001 for debugging! 353s WARNING: random seed set to 1001 for debugging! 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-pure-nucl.nucl) contains 8 sequences of length 116 353s 1. Thylacinus 353s 2. Sarcophilu 353s 3. Dasyurus 353s 4. Echymipera 353s 5. Trichosuru 353s 6. Phalanger 353s 7. Philander 353s 8. Bos 353s (consists very likely of nucleotides) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Optimizing missing substitution process parameters 353s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 353s Writing pairwise distances to file tests/qp-pure-nucl.nucl.dist 353s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-pure-nucl.nucl.puzzle 353s Likelihood distances: tests/qp-pure-nucl.nucl.dist 353s Phylip tree file: tests/qp-pure-nucl.nucl.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 3 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-tn-nucl.nucl' 353s Input file: tests/qp-tn-nucl.nucl 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-tn-nucl.nucl) contains 8 sequences of length 116 353s 1. Thylacinus 353s 2. Sarcophilu 353s 3. Dasyurus 353s 4. Echymipera 353s 5. Trichosuru 353s 6. Phalanger 353s 7. Philander 353s 8. Bos 353s (consists very likely of nucleotides) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? TN (Tamura-Nei 1993) 353s p Constrain TN model to F84 model? No 353s t Transition/transversion parameter? Estimate from data set 353s r Y/R transition parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Optimizing missing substitution process parameters 353s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 353s Writing pairwise distances to file tests/qp-tn-nucl.nucl.dist 353s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-tn-nucl.nucl.puzzle 353s Likelihood distances: tests/qp-tn-nucl.nucl.dist 353s Phylip tree file: tests/qp-tn-nucl.nucl.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 4 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-hky-clock-nucl.nucl' 353s Input file: tests/qp-hky-clock-nucl.nucl 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-hky-clock-nucl.nucl) contains 8 sequences of length 116 353s 1. Thylacinus 353s 2. Sarcophilu 353s 3. Dasyurus 353s 4. Echymipera 353s 5. Trichosuru 353s 6. Phalanger 353s 7. Philander 353s 8. Bos 353s (consists very likely of nucleotides) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? Yes 353s l Location of root? Best place (automatic search) 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Optimizing missing substitution process parameters 353s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 353s Writing pairwise distances to file tests/qp-hky-clock-nucl.nucl.dist 353s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s Computing maximum likelihood branch lengths (with clock) 353s WARNING: random seed set to 1001 for debugging! 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-hky-clock-nucl.nucl.puzzle 353s Likelihood distances: tests/qp-hky-clock-nucl.nucl.dist 353s Phylip tree file: tests/qp-hky-clock-nucl.nucl.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 5 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-hky-rhet-nucl.nucl' 353s Input file: tests/qp-hky-rhet-nucl.nucl 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-hky-rhet-nucl.nucl) contains 8 sequences of length 116 353s 1. Thylacinus 353s 2. Sarcophilu 353s 3. Dasyurus 353s 4. Echymipera 353s 5. Trichosuru 353s 6. Phalanger 353s 7. Philander 353s 8. Bos 353s (consists very likely of nucleotides) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Gamma distributed rates 353s a Gamma distribution parameter alpha? Estimate from data set 353s c Number of Gamma rate categories? 4 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Optimizing missing substitution process parameters 353s Optimizing missing rate heterogeneity parameters 353s Optimizing missing substitution process parameters 353s Optimizing missing rate heterogeneity parameters 353s Optimizing missing substitution process parameters 353s Optimizing missing rate heterogeneity parameters 353s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 353s Writing pairwise distances to file tests/qp-hky-rhet-nucl.nucl.dist 353s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s WARNING: random seed set to 1001 for debugging! 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-hky-rhet-nucl.nucl.puzzle 353s Likelihood distances: tests/qp-hky-rhet-nucl.nucl.dist 353s Phylip tree file: tests/qp-hky-rhet-nucl.nucl.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 6 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-hky-rhet-clock-nucl.nucl' 353s Input file: tests/qp-hky-rhet-clock-nucl.nucl 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-hky-rhet-clock-nucl.nucl) contains 8 sequences of length 116 353s 1. Thylacinus 353s 2. Sarcophilu 353s 3. Dasyurus 353s 4. Echymipera 353s 5. Trichosuru 353s 6. Phalanger 353s 7. Philander 353s 8. Bos 353s (consists very likely of nucleotides) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? Yes 353s l Location of root? Best place (automatic search) 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? Yes 353s l Location of root? Best place (automatic search) 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Gamma distributed rates 353s a Gamma distribution parameter alpha? Estimate from data set 353s c Number of Gamma rate categories? 4 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Optimizing missing substitution process parameters 353s Optimizing missing rate heterogeneity parameters 353s Optimizing missing substitution process parameters 353s Optimizing missing rate heterogeneity parameters 353s Optimizing missing substitution process parameters 353s Optimizing missing rate heterogeneity parameters 353s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 353s Writing pairwise distances to file tests/qp-hky-rhet-clock-nucl.nucl.dist 353s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 353s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s Computing maximum likelihood branch lengths (with clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-hky-rhet-clock-nucl.nucl.puzzle 353s Likelihood distances: tests/qp-hky-rhet-clock-nucl.nucl.dist 353s Phylip tree file: tests/qp-hky-rhet-clock-nucl.nucl.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 7 353s WARNING: random seed set to 1001 for debugging! 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-pure-prot.prot' 353s Input file: tests/qp-pure-prot.prot 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-pure-prot.prot) contains 7 sequences of length 128 353s 1. HBB_HUMAN 353s 2. HBB_HORSE 353s 3. HBA_HUMAN 353s 4. HBA_HORSE 353s 5. MYG_PHYCA 353s 6. GLB5_PETMA 353s 7. LGB2_LUPLU 353s (consists very likely of amino acids encoded on nuclear DNA) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Writing parameters to file tests/qp-pure-prot.prot.puzzle 353s Writing parameters to file tests/qp-pure-prot.prot.puzzle 353s Writing pairwise distances to file tests/qp-pure-prot.prot.dist 353s Writing parameters to file tests/qp-pure-prot.prot.puzzle 353s Writing parameters to file tests/qp-pure-prot.prot.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-pure-prot.prot.puzzle 353s Likelihood distances: tests/qp-pure-prot.prot.dist 353s Phylip tree file: tests/qp-pure-prot.prot.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 8 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-mtrev-prot.prot' 353s Input file: tests/qp-mtrev-prot.prot 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s WARNING: random seed set to 1001 for debugging! 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-mtrev-prot.prot) contains 7 sequences of length 128 353s 1. HBB_HUMAN 353s 2. HBB_HORSE 353s 3. HBA_HUMAN 353s 4. HBA_HORSE 353s 5. MYG_PHYCA 353s 6. GLB5_PETMA 353s 7. LGB2_LUPLU 353s (consists very likely of amino acids encoded on nuclear DNA) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 353s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 353s Writing pairwise distances to file tests/qp-mtrev-prot.prot.dist 353s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 353s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-mtrev-prot.prot.puzzle 353s Likelihood distances: tests/qp-mtrev-prot.prot.dist 353s Phylip tree file: tests/qp-mtrev-prot.prot.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 9 353s WARNING: random seed set to 1001 for debugging! 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-vt-prot.prot' 353s Input file: tests/qp-vt-prot.prot 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-vt-prot.prot) contains 7 sequences of length 128 353s 1. HBB_HUMAN 353s 2. HBB_HORSE 353s 3. HBA_HUMAN 353s 4. HBA_HORSE 353s 5. MYG_PHYCA 353s 6. GLB5_PETMA 353s 7. LGB2_LUPLU 353s (consists very likely of amino acids encoded on nuclear DNA) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? VT (Mueller-Vingron 2000) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Writing parameters to file tests/qp-vt-prot.prot.puzzle 353s Writing parameters to file tests/qp-vt-prot.prot.puzzle 353s Writing pairwise distances to file tests/qp-vt-prot.prot.dist 353s Writing parameters to file tests/qp-vt-prot.prot.puzzle 353s Writing parameters to file tests/qp-vt-prot.prot.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-vt-prot.prot.puzzle 353s Likelihood distances: tests/qp-vt-prot.prot.dist 353s Phylip tree file: tests/qp-vt-prot.prot.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 10 353s WARNING: random seed set to 1001 for debugging! 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-wag-prot.prot' 353s Input file: tests/qp-wag-prot.prot 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-wag-prot.prot) contains 7 sequences of length 128 353s 1. HBB_HUMAN 353s 2. HBB_HORSE 353s 3. HBA_HUMAN 353s 4. HBA_HORSE 353s 5. MYG_PHYCA 353s 6. GLB5_PETMA 353s 7. LGB2_LUPLU 353s (consists very likely of amino acids encoded on nuclear DNA) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? VT (Mueller-Vingron 2000) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? WAG (Whelan-Goldman 2000) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Writing parameters to file tests/qp-wag-prot.prot.puzzle 353s Writing parameters to file tests/qp-wag-prot.prot.puzzle 353s Writing pairwise distances to file tests/qp-wag-prot.prot.dist 353s Writing parameters to file tests/qp-wag-prot.prot.puzzle 353s Writing parameters to file tests/qp-wag-prot.prot.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-wag-prot.prot.puzzle 353s Likelihood distances: tests/qp-wag-prot.prot.dist 353s Phylip tree file: tests/qp-wag-prot.prot.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 11 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-clock.nucl' 353s Input file: tests/qp-clock.nucl 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s WARNING: random seed set to 1001 for debugging! 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-clock.nucl) contains 8 sequences of length 116 353s 1. Thylacinus 353s 2. Sarcophilu 353s 3. Dasyurus 353s 4. Echymipera 353s 5. Trichosuru 353s 6. Phalanger 353s 7. Philander 353s 8. Bos 353s (consists very likely of nucleotides) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? Thylacinus (1) 353s z Compute clocklike branch lengths? Yes 353s l Location of root? Best place (automatic search) 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Optimizing missing substitution process parameters 353s Writing parameters to file tests/qp-clock.nucl.puzzle 353s Writing parameters to file tests/qp-clock.nucl.puzzle 353s Writing pairwise distances to file tests/qp-clock.nucl.dist 353s Writing parameters to file tests/qp-clock.nucl.puzzle 353s Writing parameters to file tests/qp-clock.nucl.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s Computing maximum likelihood branch lengths (with clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-clock.nucl.puzzle 353s Likelihood distances: tests/qp-clock.nucl.dist 353s Phylip tree file: tests/qp-clock.nucl.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 12 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-jtt-prot.prot' 353s Input file: tests/qp-jtt-prot.prot 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s WARNING: random seed set to 1001 for debugging! 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-jtt-prot.prot) contains 7 sequences of length 128 353s 1. HBB_HUMAN 353s 2. HBB_HORSE 353s 3. HBA_HUMAN 353s 4. HBA_HORSE 353s 5. MYG_PHYCA 353s 6. GLB5_PETMA 353s 7. LGB2_LUPLU 353s (consists very likely of amino acids encoded on nuclear DNA) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 353s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 353s Writing pairwise distances to file tests/qp-jtt-prot.prot.dist 353s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 353s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-jtt-prot.prot.puzzle 353s Likelihood distances: tests/qp-jtt-prot.prot.dist 353s Phylip tree file: tests/qp-jtt-prot.prot.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 13 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-jtt-rhet-prot.prot' 353s Input file: tests/qp-jtt-rhet-prot.prot 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s WARNING: random seed set to 1001 for debugging! 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-jtt-rhet-prot.prot) contains 7 sequences of length 128 353s 1. HBB_HUMAN 353s 2. HBB_HORSE 353s 3. HBA_HUMAN 353s 4. HBA_HORSE 353s 5. MYG_PHYCA 353s 6. GLB5_PETMA 353s 7. LGB2_LUPLU 353s (consists very likely of amino acids encoded on nuclear DNA) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Gamma distributed rates 353s a Gamma distribution parameter alpha? Estimate from data set 353s c Number of Gamma rate categories? 4 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s Optimizing missing rate heterogeneity parameters 353s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 353s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 353s Writing pairwise distances to file tests/qp-jtt-rhet-prot.prot.dist 353s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 353s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s 353s All results written to disk: 353s Puzzle report file: tests/qp-jtt-rhet-prot.prot.puzzle 353s Likelihood distances: tests/qp-jtt-rhet-prot.prot.dist 353s Phylip tree file: tests/qp-jtt-rhet-prot.prot.tree 353s 353s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 353s Passed 353s 353s Test 14 353s 353s 353s 353s WELCOME TO TREE-PUZZLE 5.3.rc16! 353s 353s 353s 353s argv[1] = '-randseed1001' 353s argv[2] = 'tests/qp-jtt-rhet-clock-prot.prot' 353s Input file: tests/qp-jtt-rhet-clock-prot.prot 353s Using SPRNG -- Scalable Parallel Random Number Generator 353s RANDOM SEED: 1001 353s 353s Input data set (tests/qp-jtt-rhet-clock-prot.prot) contains 7 sequences of length 128 353s 1. HBB_HUMAN 353s 2. HBB_HORSE 353s 3. HBA_HUMAN 353s 4. HBA_HORSE 353s 5. MYG_PHYCA 353s 6. GLB5_PETMA 353s 7. LGB2_LUPLU 353s (consists very likely of amino acids encoded on nuclear DNA) 353s 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Auto: Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Nucleotides 353s m Model of substitution? HKY (Hasegawa et al. 1985) 353s t Transition/transversion parameter? Estimate from data set 353s f Nucleotide frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? No 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? Yes 353s l Location of root? Best place (automatic search) 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Uniform rate 353s 353s Quit [q], confirm [y], or change [menu] settings: 353s 353s 353s GENERAL OPTIONS 353s b Type of analysis? Tree reconstruction 353s k Tree search procedure? Quartet puzzling 353s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 353s n Number of puzzling steps? 1000 353s o Display as outgroup? HBB_HUMAN (1) 353s z Compute clocklike branch lengths? Yes 353s l Location of root? Best place (automatic search) 353s e Parameter estimates? Approximate (faster) 353s x Parameter estimation uses? Neighbor-joining tree 353s OUTPUT OPTIONS 353s 9 List puzzling trees/splits (NEXUS)? No 353s u List unresolved quartets? No 353s j List puzzling step trees? No 353s SUBSTITUTION PROCESS 353s d Type of sequence input data? Amino acids 353s m Model of substitution? JTT (Jones et al. 1992) 353s f Amino acid frequencies? Estimate from data set 353s RATE HETEROGENEITY 353s w Model of rate heterogeneity? Gamma distributed rates 353s a Gamma distribution parameter alpha? Estimate from data set 353s c Number of Gamma rate categories? 4 353s 353s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 353s 353s Optimizing missing rate heterogeneity parameters 353s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 353s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 353s Writing pairwise distances to file tests/qp-jtt-rhet-clock-prot.prot.dist 353s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 353s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 353s Computing quartet maximum likelihood trees 353s Computing quartet puzzling trees 353s Computing maximum likelihood branch lengths (without clock) 353s Computing maximum likelihood branch lengths (with clock) 354s 354s All results written to disk: 354s Puzzle report file: tests/qp-jtt-rhet-clock-prot.prot.puzzle 354s Likelihood distances: tests/qp-jtt-rhet-clock-prot.prot.dist 354s Phylip tree file: tests/qp-jtt-rhet-clock-prot.prot.tree 354s 354s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 354s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 354s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 354s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 354s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 354s Passed 354s 354s Test 15 354s 354s 354s 354s WELCOME TO TREE-PUZZLE 5.3.rc16! 354s 354s 354s 354s argv[1] = '-randseed1001' 354s argv[2] = 'tests/lm-pure-prot.prot' 354s Input file: tests/lm-pure-prot.prot 354s Using SPRNG -- Scalable Parallel Random Number Generator 354s RANDOM SEED: 1001 354s 354s Input data set (tests/lm-pure-prot.prot) contains 7 sequences of length 128 354s 1. HBB_HUMAN 354s 2. HBB_HORSE 354s 3. HBA_HUMAN 354s 4. HBA_HORSE 354s 5. MYG_PHYCA 354s 6. GLB5_PETMA 354s 7. LGB2_LUPLU 354s (consists very likely of amino acids encoded on nuclear DNA) 354s 354s 354s 354s GENERAL OPTIONS 354s b Type of analysis? Tree reconstruction 354s k Tree search procedure? Quartet puzzling 354s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 354s n Number of puzzling steps? 1000 354s o Display as outgroup? HBB_HUMAN (1) 354s z Compute clocklike branch lengths? No 354s e Parameter estimates? Approximate (faster) 354s x Parameter estimation uses? Neighbor-joining tree 354s OUTPUT OPTIONS 354s 9 List puzzling trees/splits (NEXUS)? No 354s u List unresolved quartets? No 354s j List puzzling step trees? No 354s SUBSTITUTION PROCESS 354s d Type of sequence input data? Auto: Amino acids 354s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 354s f Amino acid frequencies? Estimate from data set 354s RATE HETEROGENEITY 354s w Model of rate heterogeneity? Uniform rate 354s 354s Quit [q], confirm [y], or change [menu] settings: 354s 354s 354s GENERAL OPTIONS 354s b Type of analysis? Tree reconstruction 354s k Tree search procedure? Quartet puzzling 354s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 354s n Number of puzzling steps? 1000 354s o Display as outgroup? HBB_HUMAN (1) 354s z Compute clocklike branch lengths? No 354s e Parameter estimates? Approximate (faster) 354s x Parameter estimation uses? Neighbor-joining tree 354s OUTPUT OPTIONS 354s 9 List puzzling trees/splits (NEXUS)? No 354s u List unresolved quartets? No 354s j List puzzling step trees? No 354s SUBSTITUTION PROCESS 354s d Type of sequence input data? Nucleotides 354s m Model of substitution? HKY (Hasegawa et al. 1985) 354s t Transition/transversion parameter? Estimate from data set 354s f Nucleotide frequencies? Estimate from data set 354s RATE HETEROGENEITY 354s w Model of rate heterogeneity? Uniform rate 354s 354s Quit [q], confirm [y], or change [menu] settings: 354s 354s 354s GENERAL OPTIONS 354s b Type of analysis? Tree reconstruction 354s k Tree search procedure? Quartet puzzling 354s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 354s n Number of puzzling steps? 1000 354s o Display as outgroup? HBB_HUMAN (1) 354s z Compute clocklike branch lengths? No 354s e Parameter estimates? Approximate (faster) 354s x Parameter estimation uses? Neighbor-joining tree 354s OUTPUT OPTIONS 354s 9 List puzzling trees/splits (NEXUS)? No 354s u List unresolved quartets? No 354s j List puzzling step trees? No 354s SUBSTITUTION PROCESS 354s d Type of sequence input data? Amino acids 354s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 354s f Amino acid frequencies? Estimate from data set 354s RATE HETEROGENEITY 354s w Model of rate heterogeneity? Uniform rate 354s 354s Quit [q], confirm [y], or change [menu] settings: 354s 354s 354s GENERAL OPTIONS 354s b Type of analysis? Likelihood mapping 354s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 354s g Group sequences in clusters? No 354s n Number of quartets? 35 (all possible) 354s e Parameter estimates? Approximate (faster) 354s x Parameter estimation uses? Neighbor-joining tree 354s SUBSTITUTION PROCESS 354s d Type of sequence input data? Amino acids 354s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 354s f Amino acid frequencies? Estimate from data set 354s RATE HETEROGENEITY 354s w Model of rate heterogeneity? Uniform rate 354s 354s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 354s 354s Writing parameters to file tests/lm-pure-prot.prot.puzzle 354s Writing parameters to file tests/lm-pure-prot.prot.puzzle 354s Writing pairwise distances to file tests/lm-pure-prot.prot.dist 354s Writing parameters to file tests/lm-pure-prot.prot.puzzle 354s Writing parameters to file tests/lm-pure-prot.prot.puzzle 354s Performing likelihood mapping analysis 354s PPP1: 0 (./puzzle1.c:8696) 354s 354s All results written to disk: 354s Puzzle report file: tests/lm-pure-prot.prot.puzzle 354s Likelihood distances: tests/lm-pure-prot.prot.dist 354s Likelihood mapping diagram (EPS): tests/lm-pure-prot.prot.eps 354s Likelihood mapping diagram (SVG): tests/lm-pure-prot.prot.svg 354s 354s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 354s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 354s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 354s Passed 354s PPP1: 1 (./puzzle1.c:8702) 354s 354s autopkgtest [17:15:20]: test run-unit-test: -----------------------] 355s run-unit-test PASS 355s autopkgtest [17:15:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 355s autopkgtest [17:15:21]: @@@@@@@@@@@@@@@@@@@@ summary 355s run-unit-test PASS 377s nova [W] Using flock in prodstack6-arm64 377s Creating nova instance adt-plucky-arm64-tree-puzzle-20250315-170926-juju-7f2275-prod-proposed-migration-environment-15-5027be0b-3163-4054-a9f2-09a4ee632046 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 377s nova [W] Timed out waiting for 4e782493-ce76-435e-97b7-ead076ce1886 to get deleted.