0s autopkgtest [00:37:04]: starting date: 2024-03-19 0s autopkgtest [00:37:04]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [00:37:04]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z53i269n/out --timeout-copy=6000 --setup-commands 'sed -i "s/ports.ubuntu.com/ftpmaster.internal/; s/ubuntu-ports/ubuntu/" /etc/apt/sources.list `ls /etc/apt/sources.list.d/*.list 2>/dev/null || true`; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.44.124.162 lxd-armhf-10.44.124.162:autopkgtest/ubuntu/noble/armhf 55s autopkgtest [00:37:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 58s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 59s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 59s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3748 kB] 61s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 61s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 61s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [585 kB] 61s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 61s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 61s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 61s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3626 kB] 62s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 62s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [35.6 kB] 62s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 71s Fetched 8668 kB in 5s (1736 kB/s) 72s Reading package lists... 91s tee: /proc/self/fd/2: Permission denied 123s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 123s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 123s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 123s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease 123s Hit:5 http://ftpmaster.internal/ubuntu noble-security InRelease 123s Hit:6 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 123s Hit:7 http://ftpmaster.internal/ubuntu noble-proposed InRelease 123s Hit:8 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 129s Reading package lists... 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 132s Calculating upgrade... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s autopkgtest [00:39:23]: rebooting testbed after setup commands that affected boot 175s autopkgtest [00:39:59]: testbed running kernel: Linux 5.4.0-170-generic #188-Ubuntu SMP Wed Jan 10 09:51:10 UTC 2024 180s autopkgtest [00:40:04]: testbed dpkg architecture: armhf 196s autopkgtest [00:40:20]: @@@@@@@@@@@@@@@@@@@@ apt-source tree-puzzle 207s Get:1 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (dsc) [2231 B] 207s Get:2 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (tar) [591 kB] 207s Get:3 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (diff) [31.2 kB] 208s gpgv: Signature made Thu Feb 17 06:17:13 2022 UTC 208s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 208s gpgv: issuer "tille@debian.org" 208s gpgv: Can't check signature: No public key 208s dpkg-source: warning: cannot verify inline signature for ./tree-puzzle_5.3~rc16+dfsg-9.dsc: no acceptable signature found 209s autopkgtest [00:40:33]: testing package tree-puzzle version 5.3~rc16+dfsg-9 209s autopkgtest [00:40:33]: build not needed 216s autopkgtest [00:40:40]: test run-unit-test: preparing testbed 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 234s Correcting dependencies...Starting pkgProblemResolver with broken count: 1 235s Starting 2 pkgProblemResolver with broken count: 1 235s Investigating (0) tree-ppuzzle:armhf < none -> 5.3~rc16+dfsg-9 @un uN Ib > 235s Broken tree-ppuzzle:armhf Depends on libopenmpi3:armhf < none | 4.1.6-5ubuntu1 @un uH > (>= 4.1.2) 235s Considering libopenmpi3:armhf 0 as a solution to tree-ppuzzle:armhf 3 235s Holding Back tree-ppuzzle:armhf rather than change libopenmpi3:armhf 235s Investigating (0) autopkgtest-satdep:armhf < 0 @iU K Nb Ib > 235s Broken autopkgtest-satdep:armhf Depends on tree-ppuzzle:armhf < none | 5.3~rc16+dfsg-9 @un uH > 235s Considering tree-ppuzzle:armhf 3 as a solution to autopkgtest-satdep:armhf -2 235s Removing autopkgtest-satdep:armhf rather than change tree-ppuzzle:armhf 235s Done 236s Done 237s Starting pkgProblemResolver with broken count: 0 237s Starting 2 pkgProblemResolver with broken count: 0 237s Done 239s The following packages will be REMOVED: 239s autopkgtest-satdep 240s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 240s 1 not fully installed or removed. 240s After this operation, 0 B of additional disk space will be used. 241s (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 ... 58620 files and directories currently installed.) 241s Removing autopkgtest-satdep (0) ... 247s autopkgtest: WARNING: package tree-puzzle is not installed though it should be 251s autopkgtest: WARNING: package tree-ppuzzle is not installed though it should be 255s autopkgtest: WARNING: package tree-puzzle-doc is not installed though it should be 258s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 268s Reading package lists... 268s Building dependency tree... 268s Reading state information... 270s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 270s Starting 2 pkgProblemResolver with broken count: 0 270s Done 271s Done 272s Starting pkgProblemResolver with broken count: 0 272s Starting 2 pkgProblemResolver with broken count: 0 273s Done 274s The following additional packages will be installed: 274s libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libhwloc-plugins 274s libhwloc15 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 274s libsprng2 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common 274s tree-ppuzzle tree-puzzle tree-puzzle-doc 274s Suggested packages: 274s opencl-icd gfortran | fortran-compiler phylip treetool 275s The following NEW packages will be installed: 275s libevent-pthreads-2.1-7 libfabric1 libhwloc-plugins libhwloc15 libmunge2 275s libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 libsprng2 libxnvctrl0 275s ocl-icd-libopencl1 openmpi-bin openmpi-common tree-ppuzzle tree-puzzle 275s tree-puzzle-doc 275s The following packages will be upgraded: 275s libevent-core-2.1-7 275s 1 upgraded, 17 newly installed, 0 to remove and 226 not upgraded. 275s 1 not fully installed or removed. 275s Need to get 4535 kB of archives. 275s After this operation, 11.3 MB of additional disk space will be used. 275s Get:1 http://ftpmaster.internal/ubuntu noble/universe armhf libsprng2 armhf 2.0a-13 [76.0 kB] 275s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf tree-puzzle armhf 5.3~rc16+dfsg-9build1 [152 kB] 275s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 275s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-9build1 [7370 B] 275s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librdmacm1t64 armhf 50.0-2build1 [63.0 kB] 275s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfabric1 armhf 1.17.0-3build1 [419 kB] 275s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB] 275s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmunge2 armhf 0.5.15-4 [17.1 kB] 275s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libpciaccess0 armhf 0.17-3 [16.3 kB] 275s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu1 [10.4 kB] 275s Get:11 http://ftpmaster.internal/ubuntu noble/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1 [34.4 kB] 275s Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-plugins armhf 2.10.0-1 [13.7 kB] 275s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpmix2t64 armhf 5.0.1-4.1 [616 kB] 276s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu1 [2041 kB] 276s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-common all 4.1.6-7ubuntu1 [170 kB] 276s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-bin armhf 4.1.6-7ubuntu1 [83.2 kB] 276s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf tree-ppuzzle armhf 5.3~rc16+dfsg-9build1 [169 kB] 276s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf tree-puzzle-doc all 5.3~rc16+dfsg-9build1 [419 kB] 278s Fetched 4535 kB in 2s (3017 kB/s) 278s Selecting previously unselected package libsprng2. 278s (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 ... 58620 files and directories currently installed.) 278s Preparing to unpack .../00-libsprng2_2.0a-13_armhf.deb ... 278s Unpacking libsprng2 (2.0a-13) ... 278s Selecting previously unselected package tree-puzzle. 278s Preparing to unpack .../01-tree-puzzle_5.3~rc16+dfsg-9build1_armhf.deb ... 278s Unpacking tree-puzzle (5.3~rc16+dfsg-9build1) ... 278s Preparing to unpack .../02-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 278s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 278s Selecting previously unselected package libevent-pthreads-2.1-7:armhf. 278s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9build1_armhf.deb ... 278s Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 278s Selecting previously unselected package librdmacm1t64:armhf. 278s Preparing to unpack .../04-librdmacm1t64_50.0-2build1_armhf.deb ... 278s Unpacking librdmacm1t64:armhf (50.0-2build1) ... 279s Selecting previously unselected package libfabric1:armhf. 279s Preparing to unpack .../05-libfabric1_1.17.0-3build1_armhf.deb ... 279s Unpacking libfabric1:armhf (1.17.0-3build1) ... 279s Selecting previously unselected package libhwloc15:armhf. 279s Preparing to unpack .../06-libhwloc15_2.10.0-1_armhf.deb ... 279s Unpacking libhwloc15:armhf (2.10.0-1) ... 279s Selecting previously unselected package libmunge2:armhf. 279s Preparing to unpack .../07-libmunge2_0.5.15-4_armhf.deb ... 279s Unpacking libmunge2:armhf (0.5.15-4) ... 279s Selecting previously unselected package libpciaccess0:armhf. 279s Preparing to unpack .../08-libpciaccess0_0.17-3_armhf.deb ... 279s Unpacking libpciaccess0:armhf (0.17-3) ... 279s Selecting previously unselected package libxnvctrl0:armhf. 279s Preparing to unpack .../09-libxnvctrl0_510.47.03-0ubuntu1_armhf.deb ... 279s Unpacking libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 279s Selecting previously unselected package ocl-icd-libopencl1:armhf. 279s Preparing to unpack .../10-ocl-icd-libopencl1_2.3.2-1_armhf.deb ... 279s Unpacking ocl-icd-libopencl1:armhf (2.3.2-1) ... 279s Selecting previously unselected package libhwloc-plugins:armhf. 280s Preparing to unpack .../11-libhwloc-plugins_2.10.0-1_armhf.deb ... 280s Unpacking libhwloc-plugins:armhf (2.10.0-1) ... 280s Selecting previously unselected package libpmix2t64:armhf. 280s Preparing to unpack .../12-libpmix2t64_5.0.1-4.1_armhf.deb ... 280s Unpacking libpmix2t64:armhf (5.0.1-4.1) ... 280s Selecting previously unselected package libopenmpi3t64:armhf. 280s Preparing to unpack .../13-libopenmpi3t64_4.1.6-7ubuntu1_armhf.deb ... 280s Unpacking libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 280s Selecting previously unselected package openmpi-common. 280s Preparing to unpack .../14-openmpi-common_4.1.6-7ubuntu1_all.deb ... 280s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 280s Selecting previously unselected package openmpi-bin. 280s Preparing to unpack .../15-openmpi-bin_4.1.6-7ubuntu1_armhf.deb ... 280s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 280s Selecting previously unselected package tree-ppuzzle. 281s Preparing to unpack .../16-tree-ppuzzle_5.3~rc16+dfsg-9build1_armhf.deb ... 281s Unpacking tree-ppuzzle (5.3~rc16+dfsg-9build1) ... 281s Selecting previously unselected package tree-puzzle-doc. 281s Preparing to unpack .../17-tree-puzzle-doc_5.3~rc16+dfsg-9build1_all.deb ... 281s Unpacking tree-puzzle-doc (5.3~rc16+dfsg-9build1) ... 281s Setting up libpciaccess0:armhf (0.17-3) ... 281s Setting up libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 281s Setting up libmunge2:armhf (0.5.15-4) ... 281s Setting up libhwloc15:armhf (2.10.0-1) ... 281s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 281s Setting up tree-puzzle-doc (5.3~rc16+dfsg-9build1) ... 281s Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ... 281s Setting up openmpi-common (4.1.6-7ubuntu1) ... 281s Setting up librdmacm1t64:armhf (50.0-2build1) ... 281s Setting up libsprng2 (2.0a-13) ... 281s Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 281s Setting up libfabric1:armhf (1.17.0-3build1) ... 281s Setting up tree-puzzle (5.3~rc16+dfsg-9build1) ... 281s Setting up libhwloc-plugins:armhf (2.10.0-1) ... 281s Setting up libpmix2t64:armhf (5.0.1-4.1) ... 281s Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 281s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 281s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 281s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 281s Setting up tree-ppuzzle (5.3~rc16+dfsg-9build1) ... 281s Setting up autopkgtest-satdep (0) ... 281s Processing triggers for man-db (2.12.0-3) ... 283s Processing triggers for libc-bin (2.39-0ubuntu2) ... 309s (Reading database ... 59259 files and directories currently installed.) 309s Removing autopkgtest-satdep (0) ... 322s autopkgtest [00:42:26]: test run-unit-test: [----------------------- 325s .: 325s EF.3trees 325s EF.phy 325s atp6.a 325s globin.a 325s globin.ctrees 325s globin.trees 325s marswolf.ctrees 325s marswolf.n 325s marswolf.trees 325s primates.b 325s primates.ctrees 325s primates.trees 325s tests 325s 325s ./tests: 325s check-cons-pure-prot 325s check-lm-pure-prot 325s check-qp-clock 325s check-qp-hky-clock-nucl 325s check-qp-hky-rhet-clock-nucl 325s check-qp-hky-rhet-nucl 325s check-qp-jtt-prot 325s check-qp-jtt-rhet-clock-prot 325s check-qp-jtt-rhet-prot 325s check-qp-mtrev-prot 325s check-qp-pure-bin 325s check-qp-pure-nucl 325s check-qp-pure-prot 325s check-qp-tn-nucl 325s check-qp-vt-prot 325s check-qp-wag-prot 325s check-ut-pure-prot 325s cons-pure-prot.ctrees 325s cons-pure-prot.ctrees.clean 325s cons-pure-prot.ctrees.dist 325s cons-pure-prot.ctrees.puzzle 325s cons-pure-prot.ctrees.tree 325s cons-pure-prot.param 325s cons-pure-prot.prot 325s cons-pure-prot.prot.out 325s cons-pure-prot.test 325s generate-scripts.sh 325s lm-pure-prot.param 325s lm-pure-prot.prot 325s lm-pure-prot.prot.clean 325s lm-pure-prot.prot.dist 325s lm-pure-prot.prot.eps 325s lm-pure-prot.prot.out 325s lm-pure-prot.prot.puzzle 325s lm-pure-prot.prot.svg 325s lm-pure-prot.test 325s qp-clock.nucl 325s qp-clock.nucl.clean 325s qp-clock.nucl.dist 325s qp-clock.nucl.out 325s qp-clock.nucl.puzzle 325s qp-clock.nucl.tree 325s qp-clock.param 325s qp-clock.test 325s qp-hky-clock-nucl.nucl 325s qp-hky-clock-nucl.nucl.clean 325s qp-hky-clock-nucl.nucl.dist 325s qp-hky-clock-nucl.nucl.out 325s qp-hky-clock-nucl.nucl.puzzle 325s qp-hky-clock-nucl.nucl.tree 325s qp-hky-clock-nucl.param 325s qp-hky-clock-nucl.test 325s qp-hky-rhet-clock-nucl.nucl 325s qp-hky-rhet-clock-nucl.nucl.clean 325s qp-hky-rhet-clock-nucl.nucl.dist 325s qp-hky-rhet-clock-nucl.nucl.out 325s qp-hky-rhet-clock-nucl.nucl.puzzle 325s qp-hky-rhet-clock-nucl.nucl.tree 325s qp-hky-rhet-clock-nucl.param 325s qp-hky-rhet-clock-nucl.test 325s qp-hky-rhet-nucl.nucl 325s qp-hky-rhet-nucl.nucl.clean 325s qp-hky-rhet-nucl.nucl.dist 325s qp-hky-rhet-nucl.nucl.out 325s qp-hky-rhet-nucl.nucl.puzzle 325s qp-hky-rhet-nucl.nucl.tree 325s qp-hky-rhet-nucl.param 325s qp-hky-rhet-nucl.test 325s qp-jtt-prot.param 325s qp-jtt-prot.prot 325s qp-jtt-prot.prot.clean 325s qp-jtt-prot.prot.dist 325s qp-jtt-prot.prot.out 325s qp-jtt-prot.prot.puzzle 325s qp-jtt-prot.prot.tree 325s qp-jtt-prot.test 325s qp-jtt-rhet-clock-prot.param 325s qp-jtt-rhet-clock-prot.prot 325s qp-jtt-rhet-clock-prot.prot.clean 325s qp-jtt-rhet-clock-prot.prot.dist 325s qp-jtt-rhet-clock-prot.prot.out 325s qp-jtt-rhet-clock-prot.prot.puzzle 325s qp-jtt-rhet-clock-prot.prot.tree 325s qp-jtt-rhet-clock-prot.test 325s qp-jtt-rhet-prot.param 325s qp-jtt-rhet-prot.prot 325s qp-jtt-rhet-prot.prot.clean 325s qp-jtt-rhet-prot.prot.dist 325s qp-jtt-rhet-prot.prot.out 325s qp-jtt-rhet-prot.prot.puzzle 325s qp-jtt-rhet-prot.prot.tree 325s qp-jtt-rhet-prot.test 325s qp-mtrev-prot.param 325s qp-mtrev-prot.prot 325s qp-mtrev-prot.prot.clean 325s qp-mtrev-prot.prot.dist 325s qp-mtrev-prot.prot.out 325s qp-mtrev-prot.prot.puzzle 325s qp-mtrev-prot.prot.tree 325s qp-mtrev-prot.test 325s qp-pure-bin.bin 325s qp-pure-bin.bin.clean 325s qp-pure-bin.bin.dist 325s qp-pure-bin.bin.out 325s qp-pure-bin.bin.puzzle 325s qp-pure-bin.bin.tree 325s qp-pure-bin.param 325s qp-pure-bin.test 325s qp-pure-nucl.nucl 325s qp-pure-nucl.nucl.clean 325s qp-pure-nucl.nucl.dist 325s qp-pure-nucl.nucl.out 325s qp-pure-nucl.nucl.puzzle 325s qp-pure-nucl.nucl.tree 325s qp-pure-nucl.param 325s qp-pure-nucl.test 325s qp-pure-prot.param 325s qp-pure-prot.prot 325s qp-pure-prot.prot.clean 325s qp-pure-prot.prot.dist 325s qp-pure-prot.prot.out 325s qp-pure-prot.prot.puzzle 325s qp-pure-prot.prot.tree 325s qp-pure-prot.test 325s qp-tn-nucl.nucl 325s qp-tn-nucl.nucl.clean 325s qp-tn-nucl.nucl.dist 325s qp-tn-nucl.nucl.out 325s qp-tn-nucl.nucl.puzzle 325s qp-tn-nucl.nucl.tree 325s qp-tn-nucl.param 325s qp-tn-nucl.test 325s qp-vt-prot.param 325s qp-vt-prot.prot 325s qp-vt-prot.prot.clean 325s qp-vt-prot.prot.dist 325s qp-vt-prot.prot.out 325s qp-vt-prot.prot.puzzle 325s qp-vt-prot.prot.tree 325s qp-vt-prot.test 325s qp-wag-prot.param 325s qp-wag-prot.prot 325s qp-wag-prot.prot.clean 325s qp-wag-prot.prot.dist 325s qp-wag-prot.prot.out 325s qp-wag-prot.prot.puzzle 325s qp-wag-prot.prot.tree 325s qp-wag-prot.test 325s template-test 325s ut-pure-prot.param 325s ut-pure-prot.prot 325s ut-pure-prot.prot.out 325s ut-pure-prot.test 325s ut-pure-prot.trees 325s ut-pure-prot.trees.clean 325s ut-pure-prot.trees.dist 325s ut-pure-prot.trees.puzzle 325s ut-pure-prot.trees.tree 325s Test 1 325s 325s 325s 325s WELCOME TO TREE-PUZZLE 5.3.rc16! 325s 325s 325s 325s argv[1] = '-randseed1001' 325s argv[2] = 'tests/qp-pure-bin.bin' 325s Input file: tests/qp-pure-bin.bin 325s Using SPRNG -- Scalable Parallel Random Number Generator 325s RANDOM SEED: 1001 325s 325s Input data set (tests/qp-pure-bin.bin) contains 5 sequences of length 895 325s 1. Gibbon 325s 2. Human 325s 3. Chimpanzee 325s 4. Gorilla 325s 5. Orangutan 325s (consists very likely of binary state data) 325s 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Exact maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Gibbon (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Auto: Binary states 325s m Model of substitution? Two-state model (Felsenstein 1981) 325s f Binary state frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Exact maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Gibbon (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Exact maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Gibbon (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Amino acids 325s m Model of substitution? Def.: JTT (Jones et al. 1992) 325s f Amino acid frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 325s 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Exact maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Gibbon (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Binary states 325s m Model of substitution? Two-state model (Felsenstein 1981) 325s f Binary state frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s Writing parameters to file tests/qp-pure-bin.bin.puzzle 325s Writing parameters to file tests/qp-pure-bin.bin.puzzle 325s Writing pairwise distances to file tests/qp-pure-bin.bin.dist 325s Writing parameters to file tests/qp-pure-bin.bin.puzzle 325s Writing parameters to file tests/qp-pure-bin.bin.puzzle 325s Computing quartet maximum likelihood trees 325s Computing quartet puzzling trees 325s WARNING: random seed set to 1001 for debugging! 325s Computing maximum likelihood branch lengths (without clock) 325s 325s All results written to disk: 325s Puzzle report file: tests/qp-pure-bin.bin.puzzle 325s Likelihood distances: tests/qp-pure-bin.bin.dist 325s Phylip tree file: tests/qp-pure-bin.bin.tree 325s 325s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s Passed 325s 325s Test 2 325s 325s 325s 325s WELCOME TO TREE-PUZZLE 5.3.rc16! 325s 325s 325s 325s argv[1] = '-randseed1001' 325s argv[2] = 'tests/qp-pure-nucl.nucl' 325s Input file: tests/qp-pure-nucl.nucl 325s Using SPRNG -- Scalable Parallel Random Number Generator 325s RANDOM SEED: 1001 325s 325s Input data set (tests/qp-pure-nucl.nucl) contains 8 sequences of length 116 325s 1. Thylacinus 325s 2. Sarcophilu 325s 3. Dasyurus 325s 4. Echymipera 325s 5. Trichosuru 325s 6. Phalanger 325s 7. Philander 325s 8. Bos 325s (consists very likely of nucleotides) 325s 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Auto: Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s Optimizing missing substitution process parameters 325s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 325s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 325s Writing pairwise distances to file tests/qp-pure-nucl.nucl.dist 325s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 325s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 325s Computing quartet maximum likelihood trees 325s Computing quartet puzzling trees 325s Computing maximum likelihood branch lengths (without clock) 325s 325s All results written to disk: 325s Puzzle report file: tests/qp-pure-nucl.nucl.puzzle 325s Likelihood distances: tests/qp-pure-nucl.nucl.dist 325s Phylip tree file: tests/qp-pure-nucl.nucl.tree 325s 325s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s Passed 325s 325s Test 3 325s 325s 325s 325s WELCOME TO TREE-PUZZLE 5.3.rc16! 325s 325s 325s 325s argv[1] = '-randseed1001' 325s argv[2] = 'tests/qp-tn-nucl.nucl' 325s Input file: tests/qp-tn-nucl.nucl 325s Using SPRNG -- Scalable Parallel Random Number Generator 325s WARNING: random seed set to 1001 for debugging! 325s RANDOM SEED: 1001 325s 325s Input data set (tests/qp-tn-nucl.nucl) contains 8 sequences of length 116 325s 1. Thylacinus 325s 2. Sarcophilu 325s 3. Dasyurus 325s 4. Echymipera 325s 5. Trichosuru 325s 6. Phalanger 325s 7. Philander 325s 8. Bos 325s (consists very likely of nucleotides) 325s 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Auto: Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Nucleotides 325s m Model of substitution? TN (Tamura-Nei 1993) 325s p Constrain TN model to F84 model? No 325s t Transition/transversion parameter? Estimate from data set 325s r Y/R transition parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s Optimizing missing substitution process parameters 325s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 325s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 325s Writing pairwise distances to file tests/qp-tn-nucl.nucl.dist 325s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 325s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 325s Computing quartet maximum likelihood trees 325s Computing quartet puzzling trees 325s Computing maximum likelihood branch lengths (without clock) 325s 325s All results written to disk: 325s Puzzle report file: tests/qp-tn-nucl.nucl.puzzle 325s Likelihood distances: tests/qp-tn-nucl.nucl.dist 325s Phylip tree file: tests/qp-tn-nucl.nucl.tree 325s 325s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 325s Passed 325s 325s Test 4 325s 325s 325s 325s WELCOME TO TREE-PUZZLE 5.3.rc16! 325s 325s 325s 325s argv[1] = '-randseed1001' 325s argv[2] = 'tests/qp-hky-clock-nucl.nucl' 325s Input file: tests/qp-hky-clock-nucl.nucl 325s Using SPRNG -- Scalable Parallel Random Number Generator 325s RANDOM SEED: 1001 325s 325s Input data set (tests/qp-hky-clock-nucl.nucl) contains 8 sequences of length 116 325s 1. Thylacinus 325s 2. Sarcophilu 325s 3. Dasyurus 325s 4. Echymipera 325s 5. Trichosuru 325s 6. Phalanger 325s 7. Philander 325s 8. Bos 325s (consists very likely of nucleotides) 325s 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Auto: Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? No 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s 325s 325s GENERAL OPTIONS 325s b Type of analysis? Tree reconstruction 325s k Tree search procedure? Quartet puzzling 325s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 325s n Number of puzzling steps? 1000 325s o Display as outgroup? Thylacinus (1) 325s z Compute clocklike branch lengths? Yes 325s l Location of root? Best place (automatic search) 325s e Parameter estimates? Approximate (faster) 325s x Parameter estimation uses? Neighbor-joining tree 325s OUTPUT OPTIONS 325s 9 List puzzling trees/splits (NEXUS)? No 325s u List unresolved quartets? No 325s j List puzzling step trees? No 325s SUBSTITUTION PROCESS 325s d Type of sequence input data? Nucleotides 325s m Model of substitution? HKY (Hasegawa et al. 1985) 325s t Transition/transversion parameter? Estimate from data set 325s f Nucleotide frequencies? Estimate from data set 325s RATE HETEROGENEITY 325s w Model of rate heterogeneity? Uniform rate 325s 325s Quit [q], confirm [y], or change [menu] settings: 325s Optimizing missing substitution process parameters 325s WARNING: random seed set to 1001 for debugging! 325s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 325s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 325s Writing pairwise distances to file tests/qp-hky-clock-nucl.nucl.dist 325s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 325s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 325s Computing quartet maximum likelihood trees 325s Computing quartet puzzling trees 325s Computing maximum likelihood branch lengths (without clock) 325s Computing maximum likelihood branch lengths (with clock) 326s 326s All results written to disk: 326s Puzzle report file: tests/qp-hky-clock-nucl.nucl.puzzle 326s Likelihood distances: tests/qp-hky-clock-nucl.nucl.dist 326s Phylip tree file: tests/qp-hky-clock-nucl.nucl.tree 326s 326s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 326s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 326s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 326s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 326s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 326s Passed 326s 326s Test 5 326s 326s 326s 326s WELCOME TO TREE-PUZZLE 5.3.rc16! 326s 326s 326s 326s argv[1] = '-randseed1001' 326s argv[2] = 'tests/qp-hky-rhet-nucl.nucl' 326s Input file: tests/qp-hky-rhet-nucl.nucl 326s Using SPRNG -- Scalable Parallel Random Number Generator 326s WARNING: random seed set to 1001 for debugging! 326s RANDOM SEED: 1001 326s 326s Input data set (tests/qp-hky-rhet-nucl.nucl) contains 8 sequences of length 116 326s 1. Thylacinus 326s 2. Sarcophilu 326s 3. Dasyurus 326s 4. Echymipera 326s 5. Trichosuru 326s 6. Phalanger 326s 7. Philander 326s 8. Bos 326s (consists very likely of nucleotides) 326s 326s 326s 326s GENERAL OPTIONS 326s b Type of analysis? Tree reconstruction 326s k Tree search procedure? Quartet puzzling 326s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 326s n Number of puzzling steps? 1000 326s o Display as outgroup? Thylacinus (1) 326s z Compute clocklike branch lengths? No 326s e Parameter estimates? Approximate (faster) 326s x Parameter estimation uses? Neighbor-joining tree 326s OUTPUT OPTIONS 326s 9 List puzzling trees/splits (NEXUS)? No 326s u List unresolved quartets? No 326s j List puzzling step trees? No 326s SUBSTITUTION PROCESS 326s d Type of sequence input data? Auto: Nucleotides 326s m Model of substitution? HKY (Hasegawa et al. 1985) 326s t Transition/transversion parameter? Estimate from data set 326s f Nucleotide frequencies? Estimate from data set 326s RATE HETEROGENEITY 326s w Model of rate heterogeneity? Uniform rate 326s 326s Quit [q], confirm [y], or change [menu] settings: 326s 326s 326s GENERAL OPTIONS 326s b Type of analysis? Tree reconstruction 326s k Tree search procedure? Quartet puzzling 326s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 326s n Number of puzzling steps? 1000 326s o Display as outgroup? Thylacinus (1) 326s z Compute clocklike branch lengths? No 326s e Parameter estimates? Approximate (faster) 326s x Parameter estimation uses? Neighbor-joining tree 326s OUTPUT OPTIONS 326s 9 List puzzling trees/splits (NEXUS)? No 326s u List unresolved quartets? No 326s j List puzzling step trees? No 326s SUBSTITUTION PROCESS 326s d Type of sequence input data? Nucleotides 326s m Model of substitution? HKY (Hasegawa et al. 1985) 326s t Transition/transversion parameter? Estimate from data set 326s f Nucleotide frequencies? Estimate from data set 326s RATE HETEROGENEITY 326s w Model of rate heterogeneity? Uniform rate 326s 326s Quit [q], confirm [y], or change [menu] settings: 326s 326s 326s GENERAL OPTIONS 326s b Type of analysis? Tree reconstruction 326s k Tree search procedure? Quartet puzzling 326s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 326s n Number of puzzling steps? 1000 326s o Display as outgroup? Thylacinus (1) 326s z Compute clocklike branch lengths? No 326s e Parameter estimates? Approximate (faster) 326s x Parameter estimation uses? Neighbor-joining tree 326s OUTPUT OPTIONS 326s 9 List puzzling trees/splits (NEXUS)? No 326s u List unresolved quartets? No 326s j List puzzling step trees? No 326s SUBSTITUTION PROCESS 326s d Type of sequence input data? Nucleotides 326s m Model of substitution? HKY (Hasegawa et al. 1985) 326s t Transition/transversion parameter? Estimate from data set 326s f Nucleotide frequencies? Estimate from data set 326s RATE HETEROGENEITY 326s w Model of rate heterogeneity? Gamma distributed rates 326s a Gamma distribution parameter alpha? Estimate from data set 326s c Number of Gamma rate categories? 4 326s 326s Quit [q], confirm [y], or change [menu] settings: 326s Optimizing missing substitution process parameters 326s Optimizing missing rate heterogeneity parameters 326s Optimizing missing substitution process parameters 326s Optimizing missing rate heterogeneity parameters 326s Optimizing missing substitution process parameters 326s Optimizing missing rate heterogeneity parameters 326s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 326s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 326s Writing pairwise distances to file tests/qp-hky-rhet-nucl.nucl.dist 326s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 326s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 326s Computing quartet maximum likelihood trees 326s Computing quartet puzzling trees 326s WARNING: random seed set to 1001 for debugging! 326s Computing maximum likelihood branch lengths (without clock) 326s 326s All results written to disk: 326s Puzzle report file: tests/qp-hky-rhet-nucl.nucl.puzzle 326s Likelihood distances: tests/qp-hky-rhet-nucl.nucl.dist 326s Phylip tree file: tests/qp-hky-rhet-nucl.nucl.tree 326s 326s The parameter estimation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 326s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 326s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 326s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 326s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 326s Passed 326s 326s Test 6 326s 326s 326s 326s WELCOME TO TREE-PUZZLE 5.3.rc16! 326s 326s 326s 326s argv[1] = '-randseed1001' 326s argv[2] = 'tests/qp-hky-rhet-clock-nucl.nucl' 326s Input file: tests/qp-hky-rhet-clock-nucl.nucl 326s Using SPRNG -- Scalable Parallel Random Number Generator 326s RANDOM SEED: 1001 326s 326s Input data set (tests/qp-hky-rhet-clock-nucl.nucl) contains 8 sequences of length 116 326s 1. Thylacinus 326s 2. Sarcophilu 326s 3. Dasyurus 326s 4. Echymipera 326s 5. Trichosuru 326s 6. Phalanger 326s 7. Philander 326s 8. Bos 326s (consists very likely of nucleotides) 326s 326s 326s 326s GENERAL OPTIONS 326s b Type of analysis? Tree reconstruction 326s k Tree search procedure? Quartet puzzling 326s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 326s n Number of puzzling steps? 1000 326s o Display as outgroup? Thylacinus (1) 326s z Compute clocklike branch lengths? No 326s e Parameter estimates? Approximate (faster) 326s x Parameter estimation uses? Neighbor-joining tree 326s OUTPUT OPTIONS 326s 9 List puzzling trees/splits (NEXUS)? No 326s u List unresolved quartets? No 326s j List puzzling step trees? No 326s SUBSTITUTION PROCESS 326s d Type of sequence input data? Auto: Nucleotides 326s m Model of substitution? HKY (Hasegawa et al. 1985) 326s t Transition/transversion parameter? Estimate from data set 326s f Nucleotide frequencies? Estimate from data set 326s RATE HETEROGENEITY 326s w Model of rate heterogeneity? Uniform rate 326s 326s Quit [q], confirm [y], or change [menu] settings: 326s 326s 326s GENERAL OPTIONS 326s b Type of analysis? Tree reconstruction 326s k Tree search procedure? Quartet puzzling 326s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 326s n Number of puzzling steps? 1000 326s o Display as outgroup? Thylacinus (1) 326s z Compute clocklike branch lengths? No 326s e Parameter estimates? Approximate (faster) 326s x Parameter estimation uses? Neighbor-joining tree 326s OUTPUT OPTIONS 326s 9 List puzzling trees/splits (NEXUS)? No 326s u List unresolved quartets? No 326s j List puzzling step trees? No 326s SUBSTITUTION PROCESS 326s d Type of sequence input data? Nucleotides 326s m Model of substitution? HKY (Hasegawa et al. 1985) 326s t Transition/transversion parameter? Estimate from data set 326s f Nucleotide frequencies? Estimate from data set 326s RATE HETEROGENEITY 326s w Model of rate heterogeneity? Uniform rate 326s 326s Quit [q], confirm [y], or change [menu] settings: 326s 326s 326s GENERAL OPTIONS 326s b Type of analysis? Tree reconstruction 326s k Tree search procedure? Quartet puzzling 326s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 326s n Number of puzzling steps? 1000 326s o Display as outgroup? Thylacinus (1) 326s z Compute clocklike branch lengths? Yes 326s l Location of root? Best place (automatic search) 326s e Parameter estimates? Approximate (faster) 326s x Parameter estimation uses? Neighbor-joining tree 326s OUTPUT OPTIONS 326s 9 List puzzling trees/splits (NEXUS)? No 326s u List unresolved quartets? No 326s j List puzzling step trees? No 326s SUBSTITUTION PROCESS 326s d Type of sequence input data? Nucleotides 326s m Model of substitution? HKY (Hasegawa et al. 1985) 326s t Transition/transversion parameter? Estimate from data set 326s f Nucleotide frequencies? Estimate from data set 326s RATE HETEROGENEITY 326s w Model of rate heterogeneity? Uniform rate 326s 326s Quit [q], confirm [y], or change [menu] settings: 326s 326s 326s GENERAL OPTIONS 326s b Type of analysis? Tree reconstruction 326s k Tree search procedure? Quartet puzzling 326s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 326s n Number of puzzling steps? 1000 326s o Display as outgroup? Thylacinus (1) 326s z Compute clocklike branch lengths? Yes 326s l Location of root? Best place (automatic search) 326s e Parameter estimates? Approximate (faster) 326s x Parameter estimation uses? Neighbor-joining tree 326s OUTPUT OPTIONS 326s 9 List puzzling trees/splits (NEXUS)? No 326s u List unresolved quartets? No 326s j List puzzling step trees? No 326s SUBSTITUTION PROCESS 326s d Type of sequence input data? Nucleotides 326s m Model of substitution? HKY (Hasegawa et al. 1985) 326s t Transition/transversion parameter? Estimate from data set 326s f Nucleotide frequencies? Estimate from data set 326s RATE HETEROGENEITY 326s w Model of rate heterogeneity? Gamma distributed rates 326s a Gamma distribution parameter alpha? Estimate from data set 326s c Number of Gamma rate categories? 4 326s 326s Quit [q], confirm [y], or change [menu] settings: 326s Optimizing missing substitution process parameters 326s Optimizing missing rate heterogeneity parameters 326s Optimizing missing substitution process parameters 326s Optimizing missing rate heterogeneity parameters 326s Optimizing missing substitution process parameters 326s Optimizing missing rate heterogeneity parameters 326s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 326s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 326s Writing pairwise distances to file tests/qp-hky-rhet-clock-nucl.nucl.dist 326s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 326s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 326s Computing quartet maximum likelihood trees 326s Computing quartet puzzling trees 326s Computing maximum likelihood branch lengths (without clock) 326s Computing maximum likelihood branch lengths (with clock) 327s 327s All results written to disk: 327s Puzzle report file: tests/qp-hky-rhet-clock-nucl.nucl.puzzle 327s Likelihood distances: tests/qp-hky-rhet-clock-nucl.nucl.dist 327s Phylip tree file: tests/qp-hky-rhet-clock-nucl.nucl.tree 327s 327s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 327s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 327s Passed 327s 327s Test 7 327s 327s 327s 327s WELCOME TO TREE-PUZZLE 5.3.rc16! 327s 327s 327s 327s argv[1] = '-randseed1001' 327s argv[2] = 'tests/qp-pure-prot.prot' 327s Input file: tests/qp-pure-prot.prot 327s Using SPRNG -- Scalable Parallel Random Number Generator 327s RANDOM SEED: 1001 327s 327s Input data set (tests/qp-pure-prot.prot) contains 7 sequences of length 128 327s 1. HBB_HUMAN 327s 2. HBB_HORSE 327s 3. HBA_HUMAN 327s 4. HBA_HORSE 327s 5. MYG_PHYCA 327s 6. GLB5_PETMA 327s 7. LGB2_LUPLU 327s (consists very likely of amino acids encoded on nuclear DNA) 327s 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Auto: Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Nucleotides 327s m Model of substitution? HKY (Hasegawa et al. 1985) 327s t Transition/transversion parameter? Estimate from data set 327s f Nucleotide frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 327s 327s Writing parameters to file tests/qp-pure-prot.prot.puzzle 327s Writing parameters to file tests/qp-pure-prot.prot.puzzle 327s Writing pairwise distances to file tests/qp-pure-prot.prot.dist 327s Writing parameters to file tests/qp-pure-prot.prot.puzzle 327s Writing parameters to file tests/qp-pure-prot.prot.puzzle 327s Computing quartet maximum likelihood trees 327s Computing quartet puzzling trees 327s Computing maximum likelihood branch lengths (without clock) 327s 327s All results written to disk: 327s Puzzle report file: tests/qp-pure-prot.prot.puzzle 327s Likelihood distances: tests/qp-pure-prot.prot.dist 327s Phylip tree file: tests/qp-pure-prot.prot.tree 327s 327s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s WARNING: random seed set to 1001 for debugging! 327s Passed 327s 327s Test 8 327s 327s 327s 327s WELCOME TO TREE-PUZZLE 5.3.rc16! 327s 327s 327s 327s argv[1] = '-randseed1001' 327s argv[2] = 'tests/qp-mtrev-prot.prot' 327s Input file: tests/qp-mtrev-prot.prot 327s Using SPRNG -- Scalable Parallel Random Number Generator 327s RANDOM SEED: 1001 327s 327s Input data set (tests/qp-mtrev-prot.prot) contains 7 sequences of length 128 327s 1. HBB_HUMAN 327s 2. HBB_HORSE 327s 3. HBA_HUMAN 327s 4. HBA_HORSE 327s 5. MYG_PHYCA 327s 6. GLB5_PETMA 327s 7. LGB2_LUPLU 327s (consists very likely of amino acids encoded on nuclear DNA) 327s 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Auto: Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Nucleotides 327s m Model of substitution? HKY (Hasegawa et al. 1985) 327s t Transition/transversion parameter? Estimate from data set 327s f Nucleotide frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? JTT (Jones et al. 1992) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 327s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 327s Writing pairwise distances to file tests/qp-mtrev-prot.prot.dist 327s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 327s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 327s Computing quartet maximum likelihood trees 327s Computing quartet puzzling trees 327s Computing maximum likelihood branch lengths (without clock) 327s 327s All results written to disk: 327s Puzzle report file: tests/qp-mtrev-prot.prot.puzzle 327s Likelihood distances: tests/qp-mtrev-prot.prot.dist 327s Phylip tree file: tests/qp-mtrev-prot.prot.tree 327s 327s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s Passed 327s 327s Test 9 327s WARNING: random seed set to 1001 for debugging! 327s 327s 327s 327s WELCOME TO TREE-PUZZLE 5.3.rc16! 327s 327s 327s 327s argv[1] = '-randseed1001' 327s argv[2] = 'tests/qp-vt-prot.prot' 327s Input file: tests/qp-vt-prot.prot 327s Using SPRNG -- Scalable Parallel Random Number Generator 327s RANDOM SEED: 1001 327s 327s Input data set (tests/qp-vt-prot.prot) contains 7 sequences of length 128 327s 1. HBB_HUMAN 327s 2. HBB_HORSE 327s 3. HBA_HUMAN 327s 4. HBA_HORSE 327s 5. MYG_PHYCA 327s 6. GLB5_PETMA 327s 7. LGB2_LUPLU 327s (consists very likely of amino acids encoded on nuclear DNA) 327s 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Auto: Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Nucleotides 327s m Model of substitution? HKY (Hasegawa et al. 1985) 327s t Transition/transversion parameter? Estimate from data set 327s f Nucleotide frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? JTT (Jones et al. 1992) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? VT (Mueller-Vingron 2000) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s Writing parameters to file tests/qp-vt-prot.prot.puzzle 327s Writing parameters to file tests/qp-vt-prot.prot.puzzle 327s Writing pairwise distances to file tests/qp-vt-prot.prot.dist 327s Writing parameters to file tests/qp-vt-prot.prot.puzzle 327s Writing parameters to file tests/qp-vt-prot.prot.puzzle 327s Computing quartet maximum likelihood trees 327s Computing quartet puzzling trees 327s Computing maximum likelihood branch lengths (without clock) 327s 327s All results written to disk: 327s Puzzle report file: tests/qp-vt-prot.prot.puzzle 327s Likelihood distances: tests/qp-vt-prot.prot.dist 327s Phylip tree file: tests/qp-vt-prot.prot.tree 327s 327s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 327s Passed 327s 327s Test 10 327s 327s 327s 327s WELCOME TO TREE-PUZZLE 5.3.rc16! 327s 327s 327s 327s argv[1] = '-randseed1001' 327s argv[2] = 'tests/qp-wag-prot.prot' 327s Input file: tests/qp-wag-prot.prot 327s Using SPRNG -- Scalable Parallel Random Number Generator 327s WARNING: random seed set to 1001 for debugging! 327s RANDOM SEED: 1001 327s 327s Input data set (tests/qp-wag-prot.prot) contains 7 sequences of length 128 327s 1. HBB_HUMAN 327s 2. HBB_HORSE 327s 3. HBA_HUMAN 327s 4. HBA_HORSE 327s 5. MYG_PHYCA 327s 6. GLB5_PETMA 327s 7. LGB2_LUPLU 327s (consists very likely of amino acids encoded on nuclear DNA) 327s 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Auto: Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Nucleotides 327s m Model of substitution? HKY (Hasegawa et al. 1985) 327s t Transition/transversion parameter? Estimate from data set 327s f Nucleotide frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? JTT (Jones et al. 1992) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? VT (Mueller-Vingron 2000) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s 327s 327s GENERAL OPTIONS 327s b Type of analysis? Tree reconstruction 327s k Tree search procedure? Quartet puzzling 327s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 327s n Number of puzzling steps? 1000 327s o Display as outgroup? HBB_HUMAN (1) 327s z Compute clocklike branch lengths? No 327s e Parameter estimates? Approximate (faster) 327s x Parameter estimation uses? Neighbor-joining tree 327s OUTPUT OPTIONS 327s 9 List puzzling trees/splits (NEXUS)? No 327s u List unresolved quartets? No 327s j List puzzling step trees? No 327s SUBSTITUTION PROCESS 327s d Type of sequence input data? Amino acids 327s m Model of substitution? WAG (Whelan-Goldman 2000) 327s f Amino acid frequencies? Estimate from data set 327s RATE HETEROGENEITY 327s w Model of rate heterogeneity? Uniform rate 327s 327s Quit [q], confirm [y], or change [menu] settings: 327s Writing parameters to file tests/qp-wag-prot.prot.puzzle 327s Writing parameters to file tests/qp-wag-prot.prot.puzzle 327s Writing pairwise distances to file tests/qp-wag-prot.prot.dist 327s Writing parameters to file tests/qp-wag-prot.prot.puzzle 327s Writing parameters to file tests/qp-wag-prot.prot.puzzle 327s Computing quartet maximum likelihood trees 328s Computing quartet puzzling trees 328s Computing maximum likelihood branch lengths (without clock) 328s 328s All results written to disk: 328s Puzzle report file: tests/qp-wag-prot.prot.puzzle 328s Likelihood distances: tests/qp-wag-prot.prot.dist 328s Phylip tree file: tests/qp-wag-prot.prot.tree 328s 328s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The ML step took 1.00 seconds (= 0.02 minutes = 0.00 hours) 328s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 328s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 328s Passed 328s 328s Test 11 328s 328s 328s 328s WELCOME TO TREE-PUZZLE 5.3.rc16! 328s 328s 328s 328s argv[1] = '-randseed1001' 328s argv[2] = 'tests/qp-clock.nucl' 328s Input file: tests/qp-clock.nucl 328s Using SPRNG -- Scalable Parallel Random Number Generator 328s WARNING: random seed set to 1001 for debugging! 328s RANDOM SEED: 1001 328s 328s Input data set (tests/qp-clock.nucl) contains 8 sequences of length 116 328s 1. Thylacinus 328s 2. Sarcophilu 328s 3. Dasyurus 328s 4. Echymipera 328s 5. Trichosuru 328s 6. Phalanger 328s 7. Philander 328s 8. Bos 328s (consists very likely of nucleotides) 328s 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? Thylacinus (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Auto: Nucleotides 328s m Model of substitution? HKY (Hasegawa et al. 1985) 328s t Transition/transversion parameter? Estimate from data set 328s f Nucleotide frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? Thylacinus (1) 328s z Compute clocklike branch lengths? Yes 328s l Location of root? Best place (automatic search) 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Auto: Nucleotides 328s m Model of substitution? HKY (Hasegawa et al. 1985) 328s t Transition/transversion parameter? Estimate from data set 328s f Nucleotide frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s Optimizing missing substitution process parameters 328s Writing parameters to file tests/qp-clock.nucl.puzzle 328s Writing parameters to file tests/qp-clock.nucl.puzzle 328s Writing pairwise distances to file tests/qp-clock.nucl.dist 328s Writing parameters to file tests/qp-clock.nucl.puzzle 328s Writing parameters to file tests/qp-clock.nucl.puzzle 328s Computing quartet maximum likelihood trees 328s Computing quartet puzzling trees 328s Computing maximum likelihood branch lengths (without clock) 328s Computing maximum likelihood branch lengths (with clock) 328s 328s All results written to disk: 328s Puzzle report file: tests/qp-clock.nucl.puzzle 328s Likelihood distances: tests/qp-clock.nucl.dist 328s Phylip tree file: tests/qp-clock.nucl.tree 328s 328s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s Passed 328s 328s Test 12 328s 328s 328s 328s WELCOME TO TREE-PUZZLE 5.3.rc16! 328s 328s 328s 328s argv[1] = '-randseed1001' 328s argv[2] = 'tests/qp-jtt-prot.prot' 328s Input file: tests/qp-jtt-prot.prot 328s Using SPRNG -- Scalable Parallel Random Number Generator 328s RANDOM SEED: 1001 328s 328s Input data set (tests/qp-jtt-prot.prot) contains 7 sequences of length 128 328s 1. HBB_HUMAN 328s 2. HBB_HORSE 328s 3. HBA_HUMAN 328s 4. HBA_HORSE 328s 5. MYG_PHYCA 328s 6. GLB5_PETMA 328s 7. LGB2_LUPLU 328s (consists very likely of amino acids encoded on nuclear DNA) 328s 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Auto: Amino acids 328s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Nucleotides 328s m Model of substitution? HKY (Hasegawa et al. 1985) 328s t Transition/transversion parameter? Estimate from data set 328s f Nucleotide frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 328s 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Amino acids 328s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Amino acids 328s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Amino acids 328s m Model of substitution? JTT (Jones et al. 1992) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 328s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 328s Writing pairwise distances to file tests/qp-jtt-prot.prot.dist 328s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 328s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 328s Computing quartet maximum likelihood trees 328s Computing quartet puzzling trees 328s Computing maximum likelihood branch lengths (without clock) 328s 328s All results written to disk: 328s Puzzle report file: tests/qp-jtt-prot.prot.puzzle 328s Likelihood distances: tests/qp-jtt-prot.prot.dist 328s Phylip tree file: tests/qp-jtt-prot.prot.tree 328s 328s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 328s Passed 328s 328s Test 13 328s WARNING: random seed set to 1001 for debugging! 328s 328s 328s 328s WELCOME TO TREE-PUZZLE 5.3.rc16! 328s 328s 328s 328s argv[1] = '-randseed1001' 328s argv[2] = 'tests/qp-jtt-rhet-prot.prot' 328s Input file: tests/qp-jtt-rhet-prot.prot 328s Using SPRNG -- Scalable Parallel Random Number Generator 328s RANDOM SEED: 1001 328s 328s Input data set (tests/qp-jtt-rhet-prot.prot) contains 7 sequences of length 128 328s 1. HBB_HUMAN 328s 2. HBB_HORSE 328s 3. HBA_HUMAN 328s 4. HBA_HORSE 328s 5. MYG_PHYCA 328s 6. GLB5_PETMA 328s 7. LGB2_LUPLU 328s (consists very likely of amino acids encoded on nuclear DNA) 328s 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Auto: Amino acids 328s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Nucleotides 328s m Model of substitution? HKY (Hasegawa et al. 1985) 328s t Transition/transversion parameter? Estimate from data set 328s f Nucleotide frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Amino acids 328s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Amino acids 328s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Amino acids 328s m Model of substitution? JTT (Jones et al. 1992) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Uniform rate 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s 328s 328s GENERAL OPTIONS 328s b Type of analysis? Tree reconstruction 328s k Tree search procedure? Quartet puzzling 328s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 328s n Number of puzzling steps? 1000 328s o Display as outgroup? HBB_HUMAN (1) 328s z Compute clocklike branch lengths? No 328s e Parameter estimates? Approximate (faster) 328s x Parameter estimation uses? Neighbor-joining tree 328s OUTPUT OPTIONS 328s 9 List puzzling trees/splits (NEXUS)? No 328s u List unresolved quartets? No 328s j List puzzling step trees? No 328s SUBSTITUTION PROCESS 328s d Type of sequence input data? Amino acids 328s m Model of substitution? JTT (Jones et al. 1992) 328s f Amino acid frequencies? Estimate from data set 328s RATE HETEROGENEITY 328s w Model of rate heterogeneity? Gamma distributed rates 328s a Gamma distribution parameter alpha? Estimate from data set 328s c Number of Gamma rate categories? 4 328s 328s Quit [q], confirm [y], or change [menu] settings: 328s Optimizing missing rate heterogeneity parameters 329s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 329s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 329s Writing pairwise distances to file tests/qp-jtt-rhet-prot.prot.dist 329s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 329s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 329s Computing quartet maximum likelihood trees 329s Computing quartet puzzling trees 329s Computing maximum likelihood branch lengths (without clock) 329s 329s All results written to disk: 329s Puzzle report file: tests/qp-jtt-rhet-prot.prot.puzzle 329s Likelihood distances: tests/qp-jtt-rhet-prot.prot.dist 329s Phylip tree file: tests/qp-jtt-rhet-prot.prot.tree 329s 329s The parameter estimation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 329s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 329s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 329s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 329s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 329s Passed 329s 329s Test 14 329s WARNING: random seed set to 1001 for debugging! 329s 329s 329s 329s WELCOME TO TREE-PUZZLE 5.3.rc16! 329s 329s 329s 329s argv[1] = '-randseed1001' 329s argv[2] = 'tests/qp-jtt-rhet-clock-prot.prot' 329s Input file: tests/qp-jtt-rhet-clock-prot.prot 329s Using SPRNG -- Scalable Parallel Random Number Generator 329s RANDOM SEED: 1001 329s 329s Input data set (tests/qp-jtt-rhet-clock-prot.prot) contains 7 sequences of length 128 329s 1. HBB_HUMAN 329s 2. HBB_HORSE 329s 3. HBA_HUMAN 329s 4. HBA_HORSE 329s 5. MYG_PHYCA 329s 6. GLB5_PETMA 329s 7. LGB2_LUPLU 329s (consists very likely of amino acids encoded on nuclear DNA) 329s 329s 329s 329s GENERAL OPTIONS 329s b Type of analysis? Tree reconstruction 329s k Tree search procedure? Quartet puzzling 329s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 329s n Number of puzzling steps? 1000 329s o Display as outgroup? HBB_HUMAN (1) 329s z Compute clocklike branch lengths? No 329s e Parameter estimates? Approximate (faster) 329s x Parameter estimation uses? Neighbor-joining tree 329s OUTPUT OPTIONS 329s 9 List puzzling trees/splits (NEXUS)? No 329s u List unresolved quartets? No 329s j List puzzling step trees? No 329s SUBSTITUTION PROCESS 329s d Type of sequence input data? Auto: Amino acids 329s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 329s f Amino acid frequencies? Estimate from data set 329s RATE HETEROGENEITY 329s w Model of rate heterogeneity? Uniform rate 329s 329s Quit [q], confirm [y], or change [menu] settings: 329s 329s 329s GENERAL OPTIONS 329s b Type of analysis? Tree reconstruction 329s k Tree search procedure? Quartet puzzling 329s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 329s n Number of puzzling steps? 1000 329s o Display as outgroup? HBB_HUMAN (1) 329s z Compute clocklike branch lengths? No 329s e Parameter estimates? Approximate (faster) 329s x Parameter estimation uses? Neighbor-joining tree 329s OUTPUT OPTIONS 329s 9 List puzzling trees/splits (NEXUS)? No 329s u List unresolved quartets? No 329s j List puzzling step trees? No 329s SUBSTITUTION PROCESS 329s d Type of sequence input data? Nucleotides 329s m Model of substitution? HKY (Hasegawa et al. 1985) 329s t Transition/transversion parameter? Estimate from data set 329s f Nucleotide frequencies? Estimate from data set 329s RATE HETEROGENEITY 329s w Model of rate heterogeneity? Uniform rate 329s 329s Quit [q], confirm [y], or change [menu] settings: 329s 329s 329s GENERAL OPTIONS 329s b Type of analysis? Tree reconstruction 329s k Tree search procedure? Quartet puzzling 329s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 329s n Number of puzzling steps? 1000 329s o Display as outgroup? HBB_HUMAN (1) 329s z Compute clocklike branch lengths? No 329s e Parameter estimates? Approximate (faster) 329s x Parameter estimation uses? Neighbor-joining tree 329s OUTPUT OPTIONS 329s 9 List puzzling trees/splits (NEXUS)? No 329s u List unresolved quartets? No 329s j List puzzling step trees? No 329s SUBSTITUTION PROCESS 329s d Type of sequence input data? Amino acids 329s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 329s f Amino acid frequencies? Estimate from data set 329s RATE HETEROGENEITY 329s w Model of rate heterogeneity? Uniform rate 329s 329s Quit [q], confirm [y], or change [menu] settings: 329s 329s 329s GENERAL OPTIONS 329s b Type of analysis? Tree reconstruction 329s k Tree search procedure? Quartet puzzling 329s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 329s n Number of puzzling steps? 1000 329s o Display as outgroup? HBB_HUMAN (1) 329s z Compute clocklike branch lengths? No 329s e Parameter estimates? Approximate (faster) 329s x Parameter estimation uses? Neighbor-joining tree 329s OUTPUT OPTIONS 329s 9 List puzzling trees/splits (NEXUS)? No 329s u List unresolved quartets? No 329s j List puzzling step trees? No 329s SUBSTITUTION PROCESS 329s d Type of sequence input data? Amino acids 329s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 329s f Amino acid frequencies? Estimate from data set 329s RATE HETEROGENEITY 329s w Model of rate heterogeneity? Uniform rate 329s 329s Quit [q], confirm [y], or change [menu] settings: 329s 329s 329s GENERAL OPTIONS 329s b Type of analysis? Tree reconstruction 329s k Tree search procedure? Quartet puzzling 329s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 329s n Number of puzzling steps? 1000 329s o Display as outgroup? HBB_HUMAN (1) 329s z Compute clocklike branch lengths? No 329s e Parameter estimates? Approximate (faster) 329s x Parameter estimation uses? Neighbor-joining tree 329s OUTPUT OPTIONS 329s 9 List puzzling trees/splits (NEXUS)? No 329s u List unresolved quartets? No 329s j List puzzling step trees? No 329s SUBSTITUTION PROCESS 329s d Type of sequence input data? Amino acids 329s m Model of substitution? JTT (Jones et al. 1992) 329s f Amino acid frequencies? Estimate from data set 329s RATE HETEROGENEITY 329s w Model of rate heterogeneity? Uniform rate 329s 329s Quit [q], confirm [y], or change [menu] settings: 329s 329s 329s GENERAL OPTIONS 329s b Type of analysis? Tree reconstruction 329s k Tree search procedure? Quartet puzzling 329s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 329s n Number of puzzling steps? 1000 329s o Display as outgroup? HBB_HUMAN (1) 329s z Compute clocklike branch lengths? Yes 329s l Location of root? Best place (automatic search) 329s e Parameter estimates? Approximate (faster) 329s x Parameter estimation uses? Neighbor-joining tree 329s OUTPUT OPTIONS 329s 9 List puzzling trees/splits (NEXUS)? No 329s u List unresolved quartets? No 329s j List puzzling step trees? No 329s SUBSTITUTION PROCESS 329s d Type of sequence input data? Amino acids 329s m Model of substitution? JTT (Jones et al. 1992) 329s f Amino acid frequencies? Estimate from data set 329s RATE HETEROGENEITY 329s w Model of rate heterogeneity? Uniform rate 329s 329s Quit [q], confirm [y], or change [menu] settings: 329s 329s 329s GENERAL OPTIONS 329s b Type of analysis? Tree reconstruction 329s k Tree search procedure? Quartet puzzling 329s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 329s n Number of puzzling steps? 1000 329s o Display as outgroup? HBB_HUMAN (1) 329s z Compute clocklike branch lengths? Yes 329s l Location of root? Best place (automatic search) 329s e Parameter estimates? Approximate (faster) 329s x Parameter estimation uses? Neighbor-joining tree 329s OUTPUT OPTIONS 329s 9 List puzzling trees/splits (NEXUS)? No 329s u List unresolved quartets? No 329s j List puzzling step trees? No 329s SUBSTITUTION PROCESS 329s d Type of sequence input data? Amino acids 329s m Model of substitution? JTT (Jones et al. 1992) 329s f Amino acid frequencies? Estimate from data set 329s RATE HETEROGENEITY 329s w Model of rate heterogeneity? Gamma distributed rates 329s a Gamma distribution parameter alpha? Estimate from data set 329s c Number of Gamma rate categories? 4 329s 329s Quit [q], confirm [y], or change [menu] settings: 329s Optimizing missing rate heterogeneity parameters 330s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 330s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 330s Writing pairwise distances to file tests/qp-jtt-rhet-clock-prot.prot.dist 330s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 330s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 330s Computing quartet maximum likelihood trees 330s Computing quartet puzzling trees 330s Computing maximum likelihood branch lengths (without clock) 330s Computing maximum likelihood branch lengths (with clock) 332s WARNING: random seed set to 1001 for debugging! 332s 332s All results written to disk: 332s Puzzle report file: tests/qp-jtt-rhet-clock-prot.prot.puzzle 332s Likelihood distances: tests/qp-jtt-rhet-clock-prot.prot.dist 332s Phylip tree file: tests/qp-jtt-rhet-clock-prot.prot.tree 332s 332s The parameter estimation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 332s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 332s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 332s The computation took 3.00 seconds (= 0.05 minutes = 0.00 hours) 332s including input 3.00 seconds (= 0.05 minutes = 0.00 hours) 332s Passed 332s 332s Test 15 332s 332s 332s 332s WELCOME TO TREE-PUZZLE 5.3.rc16! 332s 332s 332s 332s argv[1] = '-randseed1001' 332s argv[2] = 'tests/lm-pure-prot.prot' 332s Input file: tests/lm-pure-prot.prot 332s Using SPRNG -- Scalable Parallel Random Number Generator 332s RANDOM SEED: 1001 332s 332s Input data set (tests/lm-pure-prot.prot) contains 7 sequences of length 128 332s 1. HBB_HUMAN 332s 2. HBB_HORSE 332s 3. HBA_HUMAN 332s 4. HBA_HORSE 332s 5. MYG_PHYCA 332s 6. GLB5_PETMA 332s 7. LGB2_LUPLU 332s (consists very likely of amino acids encoded on nuclear DNA) 332s 332s 332s 332s GENERAL OPTIONS 332s b Type of analysis? Tree reconstruction 332s k Tree search procedure? Quartet puzzling 332s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 332s n Number of puzzling steps? 1000 332s o Display as outgroup? HBB_HUMAN (1) 332s z Compute clocklike branch lengths? No 332s e Parameter estimates? Approximate (faster) 332s x Parameter estimation uses? Neighbor-joining tree 332s OUTPUT OPTIONS 332s 9 List puzzling trees/splits (NEXUS)? No 332s u List unresolved quartets? No 332s j List puzzling step trees? No 332s SUBSTITUTION PROCESS 332s d Type of sequence input data? Auto: Amino acids 332s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 332s f Amino acid frequencies? Estimate from data set 332s RATE HETEROGENEITY 332s w Model of rate heterogeneity? Uniform rate 332s 332s Quit [q], confirm [y], or change [menu] settings: 332s 332s 332s GENERAL OPTIONS 332s b Type of analysis? Tree reconstruction 332s k Tree search procedure? Quartet puzzling 332s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 332s n Number of puzzling steps? 1000 332s o Display as outgroup? HBB_HUMAN (1) 332s z Compute clocklike branch lengths? No 332s e Parameter estimates? Approximate (faster) 332s x Parameter estimation uses? Neighbor-joining tree 332s OUTPUT OPTIONS 332s 9 List puzzling trees/splits (NEXUS)? No 332s u List unresolved quartets? No 332s j List puzzling step trees? No 332s SUBSTITUTION PROCESS 332s d Type of sequence input data? Nucleotides 332s m Model of substitution? HKY (Hasegawa et al. 1985) 332s t Transition/transversion parameter? Estimate from data set 332s f Nucleotide frequencies? Estimate from data set 332s RATE HETEROGENEITY 332s w Model of rate heterogeneity? Uniform rate 332s 332s Quit [q], confirm [y], or change [menu] settings: 332s 332s 332s GENERAL OPTIONS 332s b Type of analysis? Tree reconstruction 332s k Tree search procedure? Quartet puzzling 332s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 332s n Number of puzzling steps? 1000 332s o Display as outgroup? HBB_HUMAN (1) 332s z Compute clocklike branch lengths? No 332s e Parameter estimates? Approximate (faster) 332s x Parameter estimation uses? Neighbor-joining tree 332s OUTPUT OPTIONS 332s 9 List puzzling trees/splits (NEXUS)? No 332s u List unresolved quartets? No 332s j List puzzling step trees? No 332s SUBSTITUTION PROCESS 332s d Type of sequence input data? Amino acids 332s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 332s f Amino acid frequencies? Estimate from data set 332s RATE HETEROGENEITY 332s w Model of rate heterogeneity? Uniform rate 332s 332s Quit [q], confirm [y], or change [menu] settings: 332s 332s 332s GENERAL OPTIONS 332s b Type of analysis? Likelihood mapping 332s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 332s g Group sequences in clusters? No 332s n Number of quartets? 35 (all possible) 332s e Parameter estimates? Approximate (faster) 332s x Parameter estimation uses? Neighbor-joining tree 332s SUBSTITUTION PROCESS 332s d Type of sequence input data? Amino acids 332s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 332s f Amino acid frequencies? Estimate from data set 332s RATE HETEROGENEITY 332s w Model of rate heterogeneity? Uniform rate 332s 332s Quit [q], confirm [y], or change [menu] settings: PPP1: 0 (./puzzle1.c:8696) 332s 332s Writing parameters to file tests/lm-pure-prot.prot.puzzle 332s Writing parameters to file tests/lm-pure-prot.prot.puzzle 332s Writing pairwise distances to file tests/lm-pure-prot.prot.dist 332s Writing parameters to file tests/lm-pure-prot.prot.puzzle 332s Writing parameters to file tests/lm-pure-prot.prot.puzzle 332s Performing likelihood mapping analysis 332s PPP1: 1 (./puzzle1.c:8702) 332s 332s All results written to disk: 332s Puzzle report file: tests/lm-pure-prot.prot.puzzle 332s Likelihood distances: tests/lm-pure-prot.prot.dist 332s Likelihood mapping diagram (EPS): tests/lm-pure-prot.prot.eps 332s Likelihood mapping diagram (SVG): tests/lm-pure-prot.prot.svg 332s 332s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 332s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 332s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 332s Passed 332s 332s autopkgtest [00:42:36]: test run-unit-test: -----------------------] 338s autopkgtest [00:42:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 338s run-unit-test PASS 343s autopkgtest [00:42:47]: @@@@@@@@@@@@@@@@@@@@ summary 343s run-unit-test PASS