0s autopkgtest [12:37:23]: starting date and time: 2024-03-18 12:37:23+0000 0s autopkgtest [12:37:23]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [12:37:23]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z83k7bx1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade tree-puzzle --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-7.secgroup --name adt-noble-arm64-tree-puzzle-20240318-123723-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 138s autopkgtest [12:39:41]: testbed dpkg architecture: arm64 138s autopkgtest [12:39:41]: testbed apt version: 2.7.12 138s autopkgtest [12:39:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 141s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 142s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 142s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 142s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3727 kB] 142s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 142s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 142s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 142s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 142s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4102 kB] 142s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 142s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 142s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 144s Fetched 9245 kB in 3s (3086 kB/s) 144s Reading package lists... 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s sh: Attempting to set up Debian/Ubuntu apt sources automatically 149s sh: Distribution appears to be Ubuntu 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s eatmydata is already the newest version (131-1). 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s dbus is already the newest version (1.14.10-4ubuntu1). 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s rng-tools-debian is already the newest version (2.4). 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 153s The following packages will be REMOVED: 153s cloud-init* python3-configobj* python3-debconf* 153s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 153s After this operation, 3252 kB disk space will be freed. 153s (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 ... 75850 files and directories currently installed.) 153s Removing cloud-init (24.1.1-0ubuntu1) ... 154s Removing python3-configobj (5.0.8-3) ... 154s Removing python3-debconf (1.5.86) ... 154s Processing triggers for man-db (2.12.0-3) ... 154s (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 ... 75461 files and directories currently installed.) 154s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 155s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 155s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 155s invoke-rc.d: policy-rc.d denied execution of try-restart. 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s linux-generic is already the newest version (6.8.0-11.11+1). 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 156s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 158s Reading package lists... 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s Calculating upgrade... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s autopkgtest [12:40:03]: rebooting testbed after setup commands that affected boot 207s autopkgtest [12:40:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 209s autopkgtest [12:40:52]: @@@@@@@@@@@@@@@@@@@@ apt-source tree-puzzle 212s Get:1 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (dsc) [2231 B] 212s Get:2 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (tar) [591 kB] 212s Get:3 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (diff) [31.2 kB] 212s gpgv: Signature made Thu Feb 17 06:17:13 2022 UTC 212s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 212s gpgv: issuer "tille@debian.org" 212s gpgv: Can't check signature: No public key 212s dpkg-source: warning: cannot verify inline signature for ./tree-puzzle_5.3~rc16+dfsg-9.dsc: no acceptable signature found 213s autopkgtest [12:40:56]: testing package tree-puzzle version 5.3~rc16+dfsg-9 213s autopkgtest [12:40:56]: build not needed 214s autopkgtest [12:40:57]: test run-unit-test: preparing testbed 228s Reading package lists... 228s Building dependency tree... 231s Reading state information... 232s Starting pkgProblemResolver with broken count: 0 232s Starting 2 pkgProblemResolver with broken count: 0 232s Done 232s The following additional packages will be installed: 232s libamd-comgr2 libamdhip64-5 libatomic1 libdrm-amdgpu1 232s libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 libhsakmt1 232s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libopenmpi3 libpciaccess0 232s libpmix2 librdmacm1t64 libsprng2 libucx0 libxnvctrl0 ocl-icd-libopencl1 232s openmpi-bin openmpi-common tree-ppuzzle tree-puzzle tree-puzzle-doc 232s Suggested packages: 232s opencl-icd gfortran | fortran-compiler phylip treetool 232s The following NEW packages will be installed: 232s autopkgtest-satdep libamd-comgr2 libamdhip64-5 libatomic1 libdrm-amdgpu1 232s libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 libhsakmt1 232s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libopenmpi3 libpciaccess0 232s libpmix2 librdmacm1t64 libsprng2 libucx0 libxnvctrl0 ocl-icd-libopencl1 232s openmpi-bin openmpi-common tree-ppuzzle tree-puzzle tree-puzzle-doc 232s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 232s Need to get 51.5 MB/51.5 MB of archives. 232s After this operation, 225 MB of additional disk space will be used. 232s Get:1 /tmp/autopkgtest.OorcG0/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 233s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 238s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 238s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 238s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 238s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 238s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 238s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 238s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 238s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 238s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 238s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 263s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 263s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 263s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 263s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 263s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 263s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 263s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 263s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 263s Ign:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 263s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 libsprng2 arm64 2.0a-13 [74.8 kB] 263s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 264s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-bin arm64 4.1.6-5ubuntu1 [123 kB] 264s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 tree-ppuzzle arm64 5.3~rc16+dfsg-9 [159 kB] 264s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 tree-puzzle arm64 5.3~rc16+dfsg-9 [145 kB] 264s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 tree-puzzle-doc all 5.3~rc16+dfsg-9 [421 kB] 264s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 265s Fetched 48.7 MB in 32s (1521 kB/s) 265s Selecting previously unselected package libllvm17:arm64. 265s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75406 files and directories currently installed.) 265s Preparing to unpack .../00-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 265s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 266s Selecting previously unselected package libamd-comgr2:arm64. 266s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 266s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 266s Selecting previously unselected package libdrm-amdgpu1:arm64. 266s Preparing to unpack .../02-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 266s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 266s Selecting previously unselected package libhsakmt1:arm64. 266s Preparing to unpack .../03-libhsakmt1_5.7.0-1_arm64.deb ... 266s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 266s Selecting previously unselected package libhsa-runtime64-1. 266s Preparing to unpack .../04-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 266s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 266s Selecting previously unselected package libamdhip64-5. 266s Preparing to unpack .../05-libamdhip64-5_5.2.3-12_arm64.deb ... 266s Unpacking libamdhip64-5 (5.2.3-12) ... 266s Selecting previously unselected package libatomic1:arm64. 266s Preparing to unpack .../06-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 266s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 266s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 266s Preparing to unpack .../07-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 266s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 266s Selecting previously unselected package librdmacm1t64:arm64. 266s Preparing to unpack .../08-librdmacm1t64_50.0-2_arm64.deb ... 266s Unpacking librdmacm1t64:arm64 (50.0-2) ... 266s Selecting previously unselected package libfabric1:arm64. 266s Preparing to unpack .../09-libfabric1_1.17.0-3_arm64.deb ... 266s Unpacking libfabric1:arm64 (1.17.0-3) ... 266s Selecting previously unselected package libhwloc15:arm64. 266s Preparing to unpack .../10-libhwloc15_2.10.0-1_arm64.deb ... 266s Unpacking libhwloc15:arm64 (2.10.0-1) ... 266s Selecting previously unselected package libmunge2:arm64. 266s Preparing to unpack .../11-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 266s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 266s Selecting previously unselected package libpciaccess0:arm64. 266s Preparing to unpack .../12-libpciaccess0_0.17-3_arm64.deb ... 266s Unpacking libpciaccess0:arm64 (0.17-3) ... 266s Selecting previously unselected package libxnvctrl0:arm64. 266s Preparing to unpack .../13-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 266s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 266s Selecting previously unselected package ocl-icd-libopencl1:arm64. 266s Preparing to unpack .../14-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 266s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 266s Selecting previously unselected package libhwloc-plugins:arm64. 266s Preparing to unpack .../15-libhwloc-plugins_2.10.0-1_arm64.deb ... 266s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 266s Selecting previously unselected package libpmix2:arm64. 266s Preparing to unpack .../16-libpmix2_5.0.1-4_arm64.deb ... 266s Unpacking libpmix2:arm64 (5.0.1-4) ... 266s Selecting previously unselected package libucx0:arm64. 266s Preparing to unpack .../17-libucx0_1.16.0+ds-4_arm64.deb ... 266s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 266s Selecting previously unselected package libopenmpi3:arm64. 266s Preparing to unpack .../18-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 266s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 267s Selecting previously unselected package libsprng2. 267s Preparing to unpack .../19-libsprng2_2.0a-13_arm64.deb ... 267s Unpacking libsprng2 (2.0a-13) ... 267s Selecting previously unselected package openmpi-common. 267s Preparing to unpack .../20-openmpi-common_4.1.6-5ubuntu1_all.deb ... 267s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 267s Selecting previously unselected package openmpi-bin. 267s Preparing to unpack .../21-openmpi-bin_4.1.6-5ubuntu1_arm64.deb ... 267s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 267s Selecting previously unselected package tree-ppuzzle. 267s Preparing to unpack .../22-tree-ppuzzle_5.3~rc16+dfsg-9_arm64.deb ... 267s Unpacking tree-ppuzzle (5.3~rc16+dfsg-9) ... 267s Selecting previously unselected package tree-puzzle. 267s Preparing to unpack .../23-tree-puzzle_5.3~rc16+dfsg-9_arm64.deb ... 267s Unpacking tree-puzzle (5.3~rc16+dfsg-9) ... 267s Selecting previously unselected package tree-puzzle-doc. 267s Preparing to unpack .../24-tree-puzzle-doc_5.3~rc16+dfsg-9_all.deb ... 267s Unpacking tree-puzzle-doc (5.3~rc16+dfsg-9) ... 267s Selecting previously unselected package autopkgtest-satdep. 267s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 267s Unpacking autopkgtest-satdep (0) ... 267s Setting up libpciaccess0:arm64 (0.17-3) ... 267s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 267s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 267s Setting up libhwloc15:arm64 (2.10.0-1) ... 267s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 267s Setting up tree-puzzle-doc (5.3~rc16+dfsg-9) ... 267s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 267s Setting up openmpi-common (4.1.6-5ubuntu1) ... 267s Setting up librdmacm1t64:arm64 (50.0-2) ... 267s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 267s Setting up libsprng2 (2.0a-13) ... 267s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 267s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 267s Setting up libfabric1:arm64 (1.17.0-3) ... 267s Setting up tree-puzzle (5.3~rc16+dfsg-9) ... 267s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 267s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 267s Setting up libhsakmt1:arm64 (5.7.0-1) ... 267s Setting up libpmix2:arm64 (5.0.1-4) ... 267s Setting up libhsa-runtime64-1 (5.7.1-1) ... 267s Setting up libamdhip64-5 (5.2.3-12) ... 267s Setting up libucx0:arm64 (1.16.0+ds-4) ... 267s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 267s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 267s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 267s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 267s Setting up tree-ppuzzle (5.3~rc16+dfsg-9) ... 267s Setting up autopkgtest-satdep (0) ... 267s Processing triggers for man-db (2.12.0-3) ... 267s Processing triggers for libc-bin (2.39-0ubuntu2) ... 271s (Reading database ... 76146 files and directories currently installed.) 271s Removing autopkgtest-satdep (0) ... 272s autopkgtest [12:41:55]: test run-unit-test: [----------------------- 272s .: 272s EF.3trees 272s EF.phy 272s atp6.a 272s globin.a 272s globin.ctrees 272s globin.trees 272s marswolf.ctrees 272s marswolf.n 272s marswolf.trees 272s primates.b 272s primates.ctrees 272s primates.trees 272s tests 272s 272s ./tests: 272s check-cons-pure-prot 272s check-lm-pure-prot 272s check-qp-clock 272s check-qp-hky-clock-nucl 272s check-qp-hky-rhet-clock-nucl 272s check-qp-hky-rhet-nucl 272s check-qp-jtt-prot 272s check-qp-jtt-rhet-clock-prot 272s check-qp-jtt-rhet-prot 272s check-qp-mtrev-prot 272s check-qp-pure-bin 272s check-qp-pure-nucl 272s check-qp-pure-prot 272s check-qp-tn-nucl 272s check-qp-vt-prot 272s check-qp-wag-prot 272s check-ut-pure-prot 272s cons-pure-prot.ctrees 272s cons-pure-prot.ctrees.clean 272s cons-pure-prot.ctrees.dist 272s cons-pure-prot.ctrees.puzzle 272s cons-pure-prot.ctrees.tree 272s cons-pure-prot.param 272s cons-pure-prot.prot 272s cons-pure-prot.prot.out 272s cons-pure-prot.test 272s generate-scripts.sh 272s lm-pure-prot.param 272s lm-pure-prot.prot 272s lm-pure-prot.prot.clean 272s lm-pure-prot.prot.dist 272s lm-pure-prot.prot.eps 272s lm-pure-prot.prot.out 272s lm-pure-prot.prot.puzzle 272s lm-pure-prot.prot.svg 272s lm-pure-prot.test 272s qp-clock.nucl 272s qp-clock.nucl.clean 272s qp-clock.nucl.dist 272s qp-clock.nucl.out 272s qp-clock.nucl.puzzle 272s qp-clock.nucl.tree 272s qp-clock.param 272s qp-clock.test 272s qp-hky-clock-nucl.nucl 272s qp-hky-clock-nucl.nucl.clean 272s qp-hky-clock-nucl.nucl.dist 272s qp-hky-clock-nucl.nucl.out 272s qp-hky-clock-nucl.nucl.puzzle 272s qp-hky-clock-nucl.nucl.tree 272s qp-hky-clock-nucl.param 272s qp-hky-clock-nucl.test 272s qp-hky-rhet-clock-nucl.nucl 272s qp-hky-rhet-clock-nucl.nucl.clean 272s qp-hky-rhet-clock-nucl.nucl.dist 272s qp-hky-rhet-clock-nucl.nucl.out 272s qp-hky-rhet-clock-nucl.nucl.puzzle 272s qp-hky-rhet-clock-nucl.nucl.tree 272s qp-hky-rhet-clock-nucl.param 272s qp-hky-rhet-clock-nucl.test 272s qp-hky-rhet-nucl.nucl 272s qp-hky-rhet-nucl.nucl.clean 272s qp-hky-rhet-nucl.nucl.dist 272s qp-hky-rhet-nucl.nucl.out 272s qp-hky-rhet-nucl.nucl.puzzle 272s qp-hky-rhet-nucl.nucl.tree 272s qp-hky-rhet-nucl.param 272s qp-hky-rhet-nucl.test 272s qp-jtt-prot.param 272s qp-jtt-prot.prot 272s qp-jtt-prot.prot.clean 272s qp-jtt-prot.prot.dist 272s qp-jtt-prot.prot.out 272s qp-jtt-prot.prot.puzzle 272s qp-jtt-prot.prot.tree 272s qp-jtt-prot.test 272s qp-jtt-rhet-clock-prot.param 272s qp-jtt-rhet-clock-prot.prot 272s qp-jtt-rhet-clock-prot.prot.clean 272s qp-jtt-rhet-clock-prot.prot.dist 272s qp-jtt-rhet-clock-prot.prot.out 272s qp-jtt-rhet-clock-prot.prot.puzzle 272s qp-jtt-rhet-clock-prot.prot.tree 272s qp-jtt-rhet-clock-prot.test 272s qp-jtt-rhet-prot.param 272s qp-jtt-rhet-prot.prot 272s qp-jtt-rhet-prot.prot.clean 272s qp-jtt-rhet-prot.prot.dist 272s qp-jtt-rhet-prot.prot.out 272s qp-jtt-rhet-prot.prot.puzzle 272s qp-jtt-rhet-prot.prot.tree 272s qp-jtt-rhet-prot.test 272s qp-mtrev-prot.param 272s qp-mtrev-prot.prot 272s qp-mtrev-prot.prot.clean 272s qp-mtrev-prot.prot.dist 272s qp-mtrev-prot.prot.out 272s qp-mtrev-prot.prot.puzzle 272s qp-mtrev-prot.prot.tree 272s qp-mtrev-prot.test 272s qp-pure-bin.bin 272s qp-pure-bin.bin.clean 272s qp-pure-bin.bin.dist 272s qp-pure-bin.bin.out 272s qp-pure-bin.bin.puzzle 272s qp-pure-bin.bin.tree 272s qp-pure-bin.param 272s qp-pure-bin.test 272s qp-pure-nucl.nucl 272s qp-pure-nucl.nucl.clean 272s qp-pure-nucl.nucl.dist 272s qp-pure-nucl.nucl.out 272s qp-pure-nucl.nucl.puzzle 272s qp-pure-nucl.nucl.tree 272s qp-pure-nucl.param 272s qp-pure-nucl.test 272s qp-pure-prot.param 272s qp-pure-prot.prot 272s qp-pure-prot.prot.clean 272s qp-pure-prot.prot.dist 272s qp-pure-prot.prot.out 272s qp-pure-prot.prot.puzzle 272s qp-pure-prot.prot.tree 272s qp-pure-prot.test 272s qp-tn-nucl.nucl 272s qp-tn-nucl.nucl.clean 272s qp-tn-nucl.nucl.dist 272s qp-tn-nucl.nucl.out 272s qp-tn-nucl.nucl.puzzle 272s qp-tn-nucl.nucl.tree 272s qp-tn-nucl.param 272s qp-tn-nucl.test 272s qp-vt-prot.param 272s qp-vt-prot.prot 272s qp-vt-prot.prot.clean 272s qp-vt-prot.prot.dist 272s qp-vt-prot.prot.out 272s qp-vt-prot.prot.puzzle 272s qp-vt-prot.prot.tree 272s qp-vt-prot.test 272s qp-wag-prot.param 272s qp-wag-prot.prot 272s qp-wag-prot.prot.clean 272s qp-wag-prot.prot.dist 272s qp-wag-prot.prot.out 272s qp-wag-prot.prot.puzzle 272s qp-wag-prot.prot.tree 272s qp-wag-prot.test 272s template-test 272s ut-pure-prot.param 272s ut-pure-prot.prot 272s ut-pure-prot.prot.out 272s ut-pure-prot.test 272s ut-pure-prot.trees 272s ut-pure-prot.trees.clean 272s ut-pure-prot.trees.dist 272s ut-pure-prot.trees.puzzle 272s ut-pure-prot.trees.tree 272s Test 1 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-pure-bin.bin' 272s Input file: tests/qp-pure-bin.bin 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-pure-bin.bin) contains 5 sequences of length 895 272s 1. Gibbon 272s 2. Human 272s 3. Chimpanzee 272s 4. Gorilla 272s 5. Orangutan 272s (consists very likely of binary state data) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Exact maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Gibbon (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Binary states 272s m Model of substitution? Two-state model (Felsenstein 1981) 272s f Binary state frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Exact maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Gibbon (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Exact maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Gibbon (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Def.: JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Exact maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Gibbon (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Binary states 272s m Model of substitution? Two-state model (Felsenstein 1981) 272s f Binary state frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Writing parameters to file tests/qp-pure-bin.bin.puzzle 272s Writing parameters to file tests/qp-pure-bin.bin.puzzle 272s Writing pairwise distances to file tests/qp-pure-bin.bin.dist 272s Writing parameters to file tests/qp-pure-bin.bin.puzzle 272s Writing parameters to file tests/qp-pure-bin.bin.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-pure-bin.bin.puzzle 272s Likelihood distances: tests/qp-pure-bin.bin.dist 272s Phylip tree file: tests/qp-pure-bin.bin.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 2 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-pure-nucl.nucl' 272s Input file: tests/qp-pure-nucl.nucl 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s WARNING: random seed set to 1001 for debugging! 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-pure-nucl.nucl) contains 8 sequences of length 116 272s 1. Thylacinus 272s 2. Sarcophilu 272s 3. Dasyurus 272s 4. Echymipera 272s 5. Trichosuru 272s 6. Phalanger 272s 7. Philander 272s 8. Bos 272s (consists very likely of nucleotides) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing substitution process parameters 272s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 272s Writing pairwise distances to file tests/qp-pure-nucl.nucl.dist 272s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s WARNING: random seed set to 1001 for debugging! 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-pure-nucl.nucl.puzzle 272s Likelihood distances: tests/qp-pure-nucl.nucl.dist 272s Phylip tree file: tests/qp-pure-nucl.nucl.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 3 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-tn-nucl.nucl' 272s Input file: tests/qp-tn-nucl.nucl 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-tn-nucl.nucl) contains 8 sequences of length 116 272s 1. Thylacinus 272s 2. Sarcophilu 272s 3. Dasyurus 272s 4. Echymipera 272s 5. Trichosuru 272s 6. Phalanger 272s 7. Philander 272s 8. Bos 272s (consists very likely of nucleotides) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? TN (Tamura-Nei 1993) 272s p Constrain TN model to F84 model? No 272s t Transition/transversion parameter? Estimate from data set 272s r Y/R transition parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing substitution process parameters 272s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 272s Writing pairwise distances to file tests/qp-tn-nucl.nucl.dist 272s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-tn-nucl.nucl.puzzle 272s Likelihood distances: tests/qp-tn-nucl.nucl.dist 272s Phylip tree file: tests/qp-tn-nucl.nucl.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s WARNING: random seed set to 1001 for debugging! 272s Passed 272s 272s Test 4 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-hky-clock-nucl.nucl' 272s Input file: tests/qp-hky-clock-nucl.nucl 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-hky-clock-nucl.nucl) contains 8 sequences of length 116 272s 1. Thylacinus 272s 2. Sarcophilu 272s 3. Dasyurus 272s 4. Echymipera 272s 5. Trichosuru 272s 6. Phalanger 272s 7. Philander 272s 8. Bos 272s (consists very likely of nucleotides) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? Yes 272s l Location of root? Best place (automatic search) 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing substitution process parameters 272s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 272s Writing pairwise distances to file tests/qp-hky-clock-nucl.nucl.dist 272s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s Computing maximum likelihood branch lengths (with clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-hky-clock-nucl.nucl.puzzle 272s Likelihood distances: tests/qp-hky-clock-nucl.nucl.dist 272s Phylip tree file: tests/qp-hky-clock-nucl.nucl.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 5 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-hky-rhet-nucl.nucl' 272s Input file: tests/qp-hky-rhet-nucl.nucl 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-hky-rhet-nucl.nucl) contains 8 sequences of length 116 272s 1. Thylacinus 272s 2. Sarcophilu 272s 3. Dasyurus 272s 4. Echymipera 272s 5. Trichosuru 272s 6. Phalanger 272s 7. Philander 272s 8. Bos 272s (consists very likely of nucleotides) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Gamma distributed rates 272s a Gamma distribution parameter alpha? Estimate from data set 272s c Number of Gamma rate categories? 4 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing substitution process parameters 272s Optimizing missing rate heterogeneity parameters 272s Optimizing missing substitution process parameters 272s Optimizing missing rate heterogeneity parameters 272s Optimizing missing substitution process parameters 272s Optimizing missing rate heterogeneity parameters 272s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 272s Writing pairwise distances to file tests/qp-hky-rhet-nucl.nucl.dist 272s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-hky-rhet-nucl.nucl.puzzle 272s Likelihood distances: tests/qp-hky-rhet-nucl.nucl.dist 272s Phylip tree file: tests/qp-hky-rhet-nucl.nucl.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 6 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-hky-rhet-clock-nucl.nucl' 272s Input file: tests/qp-hky-rhet-clock-nucl.nucl 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-hky-rhet-clock-nucl.nucl) contains 8 sequences of length 116 272s 1. Thylacinus 272s 2. Sarcophilu 272s 3. Dasyurus 272s 4. Echymipera 272s 5. Trichosuru 272s 6. Phalanger 272s 7. Philander 272s 8. Bos 272s (consists very likely of nucleotides) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? Yes 272s l Location of root? Best place (automatic search) 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? Yes 272s l Location of root? Best place (automatic search) 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Gamma distributed rates 272s a Gamma distribution parameter alpha? Estimate from data set 272s c Number of Gamma rate categories? 4 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing substitution process parameters 272s Optimizing missing rate heterogeneity parameters 272s Optimizing missing substitution process parameters 272s Optimizing missing rate heterogeneity parameters 272s Optimizing missing substitution process parameters 272s Optimizing missing rate heterogeneity parameters 272s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 272s Writing pairwise distances to file tests/qp-hky-rhet-clock-nucl.nucl.dist 272s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 272s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s Computing maximum likelihood branch lengths (with clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-hky-rhet-clock-nucl.nucl.puzzle 272s Likelihood distances: tests/qp-hky-rhet-clock-nucl.nucl.dist 272s Phylip tree file: tests/qp-hky-rhet-clock-nucl.nucl.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 7 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-pure-prot.prot' 272s Input file: tests/qp-pure-prot.prot 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-pure-prot.prot) contains 7 sequences of length 128 272s 1. HBB_HUMAN 272s 2. HBB_HORSE 272s 3. HBA_HUMAN 272s 4. HBA_HORSE 272s 5. MYG_PHYCA 272s 6. GLB5_PETMA 272s 7. LGB2_LUPLU 272s (consists very likely of amino acids encoded on nuclear DNA) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Writing parameters to file tests/qp-pure-prot.prot.puzzle 272s Writing parameters to file tests/qp-pure-prot.prot.puzzle 272s Writing pairwise distances to file tests/qp-pure-prot.prot.dist 272s Writing parameters to file tests/qp-pure-prot.prot.puzzle 272s Writing parameters to file tests/qp-pure-prot.prot.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-pure-prot.prot.puzzle 272s Likelihood distances: tests/qp-pure-prot.prot.dist 272s Phylip tree file: tests/qp-pure-prot.prot.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 8 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-mtrev-prot.prot' 272s Input file: tests/qp-mtrev-prot.prot 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-mtrev-prot.prot) contains 7 sequences of length 128 272s 1. HBB_HUMAN 272s 2. HBB_HORSE 272s 3. HBA_HUMAN 272s 4. HBA_HORSE 272s 5. MYG_PHYCA 272s 6. GLB5_PETMA 272s 7. LGB2_LUPLU 272s (consists very likely of amino acids encoded on nuclear DNA) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 272s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 272s Writing pairwise distances to file tests/qp-mtrev-prot.prot.dist 272s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 272s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-mtrev-prot.prot.puzzle 272s Likelihood distances: tests/qp-mtrev-prot.prot.dist 272s Phylip tree file: tests/qp-mtrev-prot.prot.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 9 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-vt-prot.prot' 272s Input file: tests/qp-vt-prot.prot 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-vt-prot.prot) contains 7 sequences of length 128 272s 1. HBB_HUMAN 272s 2. HBB_HORSE 272s 3. HBA_HUMAN 272s 4. HBA_HORSE 272s 5. MYG_PHYCA 272s 6. GLB5_PETMA 272s 7. LGB2_LUPLU 272s (consists very likely of amino acids encoded on nuclear DNA) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? VT (Mueller-Vingron 2000) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Writing parameters to file tests/qp-vt-prot.prot.puzzle 272s Writing parameters to file tests/qp-vt-prot.prot.puzzle 272s Writing pairwise distances to file tests/qp-vt-prot.prot.dist 272s Writing parameters to file tests/qp-vt-prot.prot.puzzle 272s Writing parameters to file tests/qp-vt-prot.prot.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-vt-prot.prot.puzzle 272s Likelihood distances: tests/qp-vt-prot.prot.dist 272s Phylip tree file: tests/qp-vt-prot.prot.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 10 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-wag-prot.prot' 272s Input file: tests/qp-wag-prot.prot 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s WARNING: random seed set to 1001 for debugging! 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-wag-prot.prot) contains 7 sequences of length 128 272s 1. HBB_HUMAN 272s 2. HBB_HORSE 272s 3. HBA_HUMAN 272s 4. HBA_HORSE 272s 5. MYG_PHYCA 272s 6. GLB5_PETMA 272s 7. LGB2_LUPLU 272s (consists very likely of amino acids encoded on nuclear DNA) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? VT (Mueller-Vingron 2000) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? WAG (Whelan-Goldman 2000) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Writing parameters to file tests/qp-wag-prot.prot.puzzle 272s Writing parameters to file tests/qp-wag-prot.prot.puzzle 272s Writing pairwise distances to file tests/qp-wag-prot.prot.dist 272s Writing parameters to file tests/qp-wag-prot.prot.puzzle 272s Writing parameters to file tests/qp-wag-prot.prot.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-wag-prot.prot.puzzle 272s Likelihood distances: tests/qp-wag-prot.prot.dist 272s Phylip tree file: tests/qp-wag-prot.prot.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 11 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-clock.nucl' 272s Input file: tests/qp-clock.nucl 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s WARNING: random seed set to 1001 for debugging! 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-clock.nucl) contains 8 sequences of length 116 272s 1. Thylacinus 272s 2. Sarcophilu 272s 3. Dasyurus 272s 4. Echymipera 272s 5. Trichosuru 272s 6. Phalanger 272s 7. Philander 272s 8. Bos 272s (consists very likely of nucleotides) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? Thylacinus (1) 272s z Compute clocklike branch lengths? Yes 272s l Location of root? Best place (automatic search) 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing substitution process parameters 272s Writing parameters to file tests/qp-clock.nucl.puzzle 272s Writing parameters to file tests/qp-clock.nucl.puzzle 272s Writing pairwise distances to file tests/qp-clock.nucl.dist 272s Writing parameters to file tests/qp-clock.nucl.puzzle 272s Writing parameters to file tests/qp-clock.nucl.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s Computing maximum likelihood branch lengths (with clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-clock.nucl.puzzle 272s Likelihood distances: tests/qp-clock.nucl.dist 272s Phylip tree file: tests/qp-clock.nucl.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s WARNING: random seed set to 1001 for debugging! 272s 272s Test 12 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-jtt-prot.prot' 272s Input file: tests/qp-jtt-prot.prot 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-jtt-prot.prot) contains 7 sequences of length 128 272s 1. HBB_HUMAN 272s 2. HBB_HORSE 272s 3. HBA_HUMAN 272s 4. HBA_HORSE 272s 5. MYG_PHYCA 272s 6. GLB5_PETMA 272s 7. LGB2_LUPLU 272s (consists very likely of amino acids encoded on nuclear DNA) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 272s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 272s Writing pairwise distances to file tests/qp-jtt-prot.prot.dist 272s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 272s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-jtt-prot.prot.puzzle 272s Likelihood distances: tests/qp-jtt-prot.prot.dist 272s Phylip tree file: tests/qp-jtt-prot.prot.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 13 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-jtt-rhet-prot.prot' 272s Input file: tests/qp-jtt-rhet-prot.prot 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-jtt-rhet-prot.prot) contains 7 sequences of length 128 272s 1. HBB_HUMAN 272s 2. HBB_HORSE 272s 3. HBA_HUMAN 272s 4. HBA_HORSE 272s 5. MYG_PHYCA 272s 6. GLB5_PETMA 272s 7. LGB2_LUPLU 272s (consists very likely of amino acids encoded on nuclear DNA) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Gamma distributed rates 272s a Gamma distribution parameter alpha? Estimate from data set 272s c Number of Gamma rate categories? 4 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing rate heterogeneity parameters 272s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 272s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 272s Writing pairwise distances to file tests/qp-jtt-rhet-prot.prot.dist 272s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 272s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 272s Computing quartet maximum likelihood trees 272s Computing quartet puzzling trees 272s Computing maximum likelihood branch lengths (without clock) 272s 272s All results written to disk: 272s Puzzle report file: tests/qp-jtt-rhet-prot.prot.puzzle 272s Likelihood distances: tests/qp-jtt-rhet-prot.prot.dist 272s Phylip tree file: tests/qp-jtt-rhet-prot.prot.tree 272s 272s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 272s Passed 272s 272s Test 14 272s WARNING: random seed set to 1001 for debugging! 272s 272s 272s 272s WELCOME TO TREE-PUZZLE 5.3.rc16! 272s 272s 272s 272s argv[1] = '-randseed1001' 272s argv[2] = 'tests/qp-jtt-rhet-clock-prot.prot' 272s Input file: tests/qp-jtt-rhet-clock-prot.prot 272s Using SPRNG -- Scalable Parallel Random Number Generator 272s RANDOM SEED: 1001 272s 272s Input data set (tests/qp-jtt-rhet-clock-prot.prot) contains 7 sequences of length 128 272s 1. HBB_HUMAN 272s 2. HBB_HORSE 272s 3. HBA_HUMAN 272s 4. HBA_HORSE 272s 5. MYG_PHYCA 272s 6. GLB5_PETMA 272s 7. LGB2_LUPLU 272s (consists very likely of amino acids encoded on nuclear DNA) 272s 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Auto: Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Nucleotides 272s m Model of substitution? HKY (Hasegawa et al. 1985) 272s t Transition/transversion parameter? Estimate from data set 272s f Nucleotide frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? No 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? Yes 272s l Location of root? Best place (automatic search) 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Uniform rate 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s 272s 272s GENERAL OPTIONS 272s b Type of analysis? Tree reconstruction 272s k Tree search procedure? Quartet puzzling 272s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 272s n Number of puzzling steps? 1000 272s o Display as outgroup? HBB_HUMAN (1) 272s z Compute clocklike branch lengths? Yes 272s l Location of root? Best place (automatic search) 272s e Parameter estimates? Approximate (faster) 272s x Parameter estimation uses? Neighbor-joining tree 272s OUTPUT OPTIONS 272s 9 List puzzling trees/splits (NEXUS)? No 272s u List unresolved quartets? No 272s j List puzzling step trees? No 272s SUBSTITUTION PROCESS 272s d Type of sequence input data? Amino acids 272s m Model of substitution? JTT (Jones et al. 1992) 272s f Amino acid frequencies? Estimate from data set 272s RATE HETEROGENEITY 272s w Model of rate heterogeneity? Gamma distributed rates 272s a Gamma distribution parameter alpha? Estimate from data set 272s c Number of Gamma rate categories? 4 272s 272s Quit [q], confirm [y], or change [menu] settings: 272s Optimizing missing rate heterogeneity parameters 273s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 273s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 273s Writing pairwise distances to file tests/qp-jtt-rhet-clock-prot.prot.dist 273s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 273s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 273s Computing quartet maximum likelihood trees 273s Computing quartet puzzling trees 273s Computing maximum likelihood branch lengths (without clock) 273s Computing maximum likelihood branch lengths (with clock) 273s 273s All results written to disk: 273s Puzzle report file: tests/qp-jtt-rhet-clock-prot.prot.puzzle 273s Likelihood distances: tests/qp-jtt-rhet-clock-prot.prot.dist 273s Phylip tree file: tests/qp-jtt-rhet-clock-prot.prot.tree 273s 273s The parameter estimation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 273s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 273s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 273s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 273s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 273s Passed 273s 273s Test 15 273s WARNING: random seed set to 1001 for debugging! 273s 273s 273s 273s WELCOME TO TREE-PUZZLE 5.3.rc16! 273s 273s 273s 273s argv[1] = '-randseed1001' 273s argv[2] = 'tests/lm-pure-prot.prot' 273s Input file: tests/lm-pure-prot.prot 273s Using SPRNG -- Scalable Parallel Random Number Generator 273s RANDOM SEED: 1001 273s 273s Input data set (tests/lm-pure-prot.prot) contains 7 sequences of length 128 273s 1. HBB_HUMAN 273s 2. HBB_HORSE 273s 3. HBA_HUMAN 273s 4. HBA_HORSE 273s 5. MYG_PHYCA 273s 6. GLB5_PETMA 273s 7. LGB2_LUPLU 273s (consists very likely of amino acids encoded on nuclear DNA) 273s 273s 273s 273s GENERAL OPTIONS 273s b Type of analysis? Tree reconstruction 273s k Tree search procedure? Quartet puzzling 273s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 273s n Number of puzzling steps? 1000 273s o Display as outgroup? HBB_HUMAN (1) 273s z Compute clocklike branch lengths? No 273s e Parameter estimates? Approximate (faster) 273s x Parameter estimation uses? Neighbor-joining tree 273s OUTPUT OPTIONS 273s 9 List puzzling trees/splits (NEXUS)? No 273s u List unresolved quartets? No 273s j List puzzling step trees? No 273s SUBSTITUTION PROCESS 273s d Type of sequence input data? Auto: Amino acids 273s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 273s f Amino acid frequencies? Estimate from data set 273s RATE HETEROGENEITY 273s w Model of rate heterogeneity? Uniform rate 273s 273s Quit [q], confirm [y], or change [menu] settings: 273s 273s 273s GENERAL OPTIONS 273s b Type of analysis? Tree reconstruction 273s k Tree search procedure? Quartet puzzling 273s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 273s n Number of puzzling steps? 1000 273s o Display as outgroup? HBB_HUMAN (1) 273s z Compute clocklike branch lengths? No 273s e Parameter estimates? Approximate (faster) 273s x Parameter estimation uses? Neighbor-joining tree 273s OUTPUT OPTIONS 273s 9 List puzzling trees/splits (NEXUS)? No 273s u List unresolved quartets? No 273s j List puzzling step trees? No 273s SUBSTITUTION PROCESS 273s d Type of sequence input data? Nucleotides 273s m Model of substitution? HKY (Hasegawa et al. 1985) 273s t Transition/transversion parameter? Estimate from data set 273s f Nucleotide frequencies? Estimate from data set 273s RATE HETEROGENEITY 273s w Model of rate heterogeneity? Uniform rate 273s 273s Quit [q], confirm [y], or change [menu] settings: 273s 273s 273s GENERAL OPTIONS 273s b Type of analysis? Tree reconstruction 273s k Tree search procedure? Quartet puzzling 273s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 273s n Number of puzzling steps? 1000 273s o Display as outgroup? HBB_HUMAN (1) 273s z Compute clocklike branch lengths? No 273s e Parameter estimates? Approximate (faster) 273s x Parameter estimation uses? Neighbor-joining tree 273s OUTPUT OPTIONS 273s 9 List puzzling trees/splits (NEXUS)? No 273s u List unresolved quartets? No 273s j List puzzling step trees? No 273s SUBSTITUTION PROCESS 273s d Type of sequence input data? Amino acids 273s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 273s f Amino acid frequencies? Estimate from data set 273s RATE HETEROGENEITY 273s w Model of rate heterogeneity? Uniform rate 273s 273s Quit [q], confirm [y], or change [menu] settings: 273s 273s 273s GENERAL OPTIONS 273s b Type of analysis? Likelihood mapping 273s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 273s g Group sequences in clusters? No 273s n Number of quartets? 35 (all possible) 273s e Parameter estimates? Approximate (faster) 273s x Parameter estimation uses? Neighbor-joining tree 273s SUBSTITUTION PROCESS 273s d Type of sequence input data? Amino acids 273s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 273s f Amino acid frequencies? Estimate from data set 273s RATE HETEROGENEITY 273s w Model of rate heterogeneity? Uniform rate 273s 273s Quit [q], confirm [y], or change [menu] settings: PPP1: 0 (./puzzle1.c:8696) 273s 273s Writing parameters to file tests/lm-pure-prot.prot.puzzle 273s Writing parameters to file tests/lm-pure-prot.prot.puzzle 273s Writing pairwise distances to file tests/lm-pure-prot.prot.dist 273s Writing parameters to file tests/lm-pure-prot.prot.puzzle 273s Writing parameters to file tests/lm-pure-prot.prot.puzzle 273s Performing likelihood mapping analysis 273s PPP1: 1 (./puzzle1.c:8702) 273s 273s All results written to disk: 273s Puzzle report file: tests/lm-pure-prot.prot.puzzle 273s Likelihood distances: tests/lm-pure-prot.prot.dist 273s Likelihood mapping diagram (EPS): tests/lm-pure-prot.prot.eps 273s Likelihood mapping diagram (SVG): tests/lm-pure-prot.prot.svg 273s 273s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 273s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 273s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 273s Passed 273s 273s autopkgtest [12:41:56]: test run-unit-test: -----------------------] 274s autopkgtest [12:41:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 274s run-unit-test PASS 274s autopkgtest [12:41:57]: @@@@@@@@@@@@@@@@@@@@ summary 274s run-unit-test PASS 292s Creating nova instance adt-noble-arm64-tree-puzzle-20240318-123723-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240317.img (UUID 7a23b7f2-4731-4803-bcc6-08355044298e)...