0s autopkgtest [01:18:18]: starting date and time: 2024-03-19 01:18:18+0000 0s autopkgtest [01:18:18]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [01:18:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.upermw0s/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade tree-puzzle --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-20.secgroup --name adt-noble-ppc64el-tree-puzzle-20240319-011818-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 271s autopkgtest [01:22:49]: testbed dpkg architecture: ppc64el 271s autopkgtest [01:22:49]: testbed apt version: 2.7.12 271s autopkgtest [01:22:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 272s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 272s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3748 kB] 273s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 273s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 273s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 273s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [645 kB] 274s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 274s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 274s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 274s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4015 kB] 274s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 274s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.3 kB] 274s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 278s Fetched 9129 kB in 3s (2763 kB/s) 278s Reading package lists... 280s Reading package lists... 281s Building dependency tree... 281s Reading state information... 281s Calculating upgrade... 281s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 282s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 282s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 282s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 282s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 282s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 284s Reading package lists... 284s Reading package lists... 284s Building dependency tree... 284s Reading state information... 284s Calculating upgrade... 284s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 284s Reading package lists... 285s Building dependency tree... 285s Reading state information... 285s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 288s autopkgtest [01:23:06]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 288s autopkgtest [01:23:06]: @@@@@@@@@@@@@@@@@@@@ apt-source tree-puzzle 292s Get:1 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (dsc) [2231 B] 292s Get:2 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (tar) [591 kB] 292s Get:3 http://ftpmaster.internal/ubuntu noble/universe tree-puzzle 5.3~rc16+dfsg-9 (diff) [31.2 kB] 292s gpgv: Signature made Thu Feb 17 06:17:13 2022 UTC 292s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 292s gpgv: issuer "tille@debian.org" 292s gpgv: Can't check signature: No public key 292s dpkg-source: warning: cannot verify inline signature for ./tree-puzzle_5.3~rc16+dfsg-9.dsc: no acceptable signature found 292s autopkgtest [01:23:10]: testing package tree-puzzle version 5.3~rc16+dfsg-9 292s autopkgtest [01:23:10]: build not needed 294s autopkgtest [01:23:12]: test run-unit-test: preparing testbed 298s Reading package lists... 298s Building dependency tree... 298s Reading state information... 298s Starting pkgProblemResolver with broken count: 0 298s Starting 2 pkgProblemResolver with broken count: 0 298s Done 298s The following additional packages will be installed: 298s libamd-comgr2 libamdhip64-5 libdrm-amdgpu1 libevent-pthreads-2.1-7 298s libfabric1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 298s libllvm17 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 298s libsprng2 libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common 298s tree-ppuzzle tree-puzzle tree-puzzle-doc 298s Suggested packages: 298s opencl-icd gfortran | fortran-compiler phylip treetool 298s The following NEW packages will be installed: 298s autopkgtest-satdep libamd-comgr2 libamdhip64-5 libdrm-amdgpu1 298s libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 libhsakmt1 298s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libopenmpi3t64 libpciaccess0 299s libpmix2t64 librdmacm1t64 libsprng2 libucx0 libxnvctrl0 ocl-icd-libopencl1 299s openmpi-bin openmpi-common tree-ppuzzle tree-puzzle tree-puzzle-doc 299s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 299s Need to get 54.9 MB/55.0 MB of archives. 299s After this operation, 256 MB of additional disk space will be used. 299s Get:1 /tmp/autopkgtest.mkCyF4/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 299s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libllvm17 ppc64el 1:17.0.6-5build1 [27.3 MB] 301s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3 [15.3 MB] 302s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] 302s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsakmt1 ppc64el 5.7.0-1 [76.5 kB] 302s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-1 [330 kB] 302s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamdhip64-5 ppc64el 5.2.3-12 [5004 kB] 302s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-9 [7844 B] 302s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el librdmacm1t64 ppc64el 50.0-2 [80.9 kB] 302s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfabric1 ppc64el 1.17.0-3 [677 kB] 302s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] 302s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmunge2 ppc64el 0.5.15-3ubuntu1 [17.6 kB] 302s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] 302s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] 302s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] 302s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] 302s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix2t64 ppc64el 5.0.1-4.1 [765 kB] 302s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el libucx0 ppc64el 1.16.0+ds-4 [1203 kB] 302s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-7ubuntu1 [2721 kB] 302s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsprng2 ppc64el 2.0a-13 [79.6 kB] 302s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-common all 4.1.6-7ubuntu1 [170 kB] 302s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-bin ppc64el 4.1.6-7ubuntu1 [118 kB] 302s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el tree-ppuzzle ppc64el 5.3~rc16+dfsg-9 [209 kB] 302s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el tree-puzzle ppc64el 5.3~rc16+dfsg-9 [185 kB] 302s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el tree-puzzle-doc all 5.3~rc16+dfsg-9 [421 kB] 302s Fetched 54.9 MB in 4s (15.1 MB/s) 302s Selecting previously unselected package libllvm17:ppc64el. 303s (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 ... 70095 files and directories currently installed.) 303s Preparing to unpack .../00-libllvm17_1%3a17.0.6-5build1_ppc64el.deb ... 303s Unpacking libllvm17:ppc64el (1:17.0.6-5build1) ... 304s Selecting previously unselected package libamd-comgr2:ppc64el. 304s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_ppc64el.deb ... 304s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 304s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 304s Preparing to unpack .../02-libdrm-amdgpu1_2.4.120-2_ppc64el.deb ... 304s Unpacking libdrm-amdgpu1:ppc64el (2.4.120-2) ... 304s Selecting previously unselected package libhsakmt1:ppc64el. 304s Preparing to unpack .../03-libhsakmt1_5.7.0-1_ppc64el.deb ... 304s Unpacking libhsakmt1:ppc64el (5.7.0-1) ... 304s Selecting previously unselected package libhsa-runtime64-1. 304s Preparing to unpack .../04-libhsa-runtime64-1_5.7.1-1_ppc64el.deb ... 304s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 304s Selecting previously unselected package libamdhip64-5. 304s Preparing to unpack .../05-libamdhip64-5_5.2.3-12_ppc64el.deb ... 304s Unpacking libamdhip64-5 (5.2.3-12) ... 304s Selecting previously unselected package libevent-pthreads-2.1-7:ppc64el. 304s Preparing to unpack .../06-libevent-pthreads-2.1-7_2.1.12-stable-9_ppc64el.deb ... 304s Unpacking libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 304s Selecting previously unselected package librdmacm1t64:ppc64el. 304s Preparing to unpack .../07-librdmacm1t64_50.0-2_ppc64el.deb ... 304s Unpacking librdmacm1t64:ppc64el (50.0-2) ... 304s Selecting previously unselected package libfabric1:ppc64el. 304s Preparing to unpack .../08-libfabric1_1.17.0-3_ppc64el.deb ... 304s Unpacking libfabric1:ppc64el (1.17.0-3) ... 304s Selecting previously unselected package libhwloc15:ppc64el. 304s Preparing to unpack .../09-libhwloc15_2.10.0-1_ppc64el.deb ... 304s Unpacking libhwloc15:ppc64el (2.10.0-1) ... 304s Selecting previously unselected package libmunge2:ppc64el. 304s Preparing to unpack .../10-libmunge2_0.5.15-3ubuntu1_ppc64el.deb ... 304s Unpacking libmunge2:ppc64el (0.5.15-3ubuntu1) ... 304s Selecting previously unselected package libpciaccess0:ppc64el. 304s Preparing to unpack .../11-libpciaccess0_0.17-3_ppc64el.deb ... 304s Unpacking libpciaccess0:ppc64el (0.17-3) ... 304s Selecting previously unselected package libxnvctrl0:ppc64el. 304s Preparing to unpack .../12-libxnvctrl0_510.47.03-0ubuntu1_ppc64el.deb ... 304s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 304s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 304s Preparing to unpack .../13-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... 304s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 304s Selecting previously unselected package libhwloc-plugins:ppc64el. 304s Preparing to unpack .../14-libhwloc-plugins_2.10.0-1_ppc64el.deb ... 304s Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... 304s Selecting previously unselected package libpmix2t64:ppc64el. 304s Preparing to unpack .../15-libpmix2t64_5.0.1-4.1_ppc64el.deb ... 304s Unpacking libpmix2t64:ppc64el (5.0.1-4.1) ... 304s Selecting previously unselected package libucx0:ppc64el. 305s Preparing to unpack .../16-libucx0_1.16.0+ds-4_ppc64el.deb ... 305s Unpacking libucx0:ppc64el (1.16.0+ds-4) ... 305s Selecting previously unselected package libopenmpi3t64:ppc64el. 305s Preparing to unpack .../17-libopenmpi3t64_4.1.6-7ubuntu1_ppc64el.deb ... 305s Unpacking libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 305s Selecting previously unselected package libsprng2. 305s Preparing to unpack .../18-libsprng2_2.0a-13_ppc64el.deb ... 305s Unpacking libsprng2 (2.0a-13) ... 305s Selecting previously unselected package openmpi-common. 305s Preparing to unpack .../19-openmpi-common_4.1.6-7ubuntu1_all.deb ... 305s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 305s Selecting previously unselected package openmpi-bin. 305s Preparing to unpack .../20-openmpi-bin_4.1.6-7ubuntu1_ppc64el.deb ... 305s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 305s Selecting previously unselected package tree-ppuzzle. 305s Preparing to unpack .../21-tree-ppuzzle_5.3~rc16+dfsg-9_ppc64el.deb ... 305s Unpacking tree-ppuzzle (5.3~rc16+dfsg-9) ... 305s Selecting previously unselected package tree-puzzle. 305s Preparing to unpack .../22-tree-puzzle_5.3~rc16+dfsg-9_ppc64el.deb ... 305s Unpacking tree-puzzle (5.3~rc16+dfsg-9) ... 305s Selecting previously unselected package tree-puzzle-doc. 305s Preparing to unpack .../23-tree-puzzle-doc_5.3~rc16+dfsg-9_all.deb ... 305s Unpacking tree-puzzle-doc (5.3~rc16+dfsg-9) ... 305s Selecting previously unselected package autopkgtest-satdep. 305s Preparing to unpack .../24-1-autopkgtest-satdep.deb ... 305s Unpacking autopkgtest-satdep (0) ... 305s Setting up libpciaccess0:ppc64el (0.17-3) ... 305s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 305s Setting up libmunge2:ppc64el (0.5.15-3ubuntu1) ... 305s Setting up libhwloc15:ppc64el (2.10.0-1) ... 305s Setting up tree-puzzle-doc (5.3~rc16+dfsg-9) ... 305s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 305s Setting up openmpi-common (4.1.6-7ubuntu1) ... 305s Setting up librdmacm1t64:ppc64el (50.0-2) ... 305s Setting up libllvm17:ppc64el (1:17.0.6-5build1) ... 305s Setting up libsprng2 (2.0a-13) ... 305s Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 305s Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... 305s Setting up libfabric1:ppc64el (1.17.0-3) ... 305s Setting up tree-puzzle (5.3~rc16+dfsg-9) ... 305s Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... 305s Setting up libpmix2t64:ppc64el (5.0.1-4.1) ... 305s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 305s Setting up libhsakmt1:ppc64el (5.7.0-1) ... 305s Setting up libhsa-runtime64-1 (5.7.1-1) ... 305s Setting up libamdhip64-5 (5.2.3-12) ... 305s Setting up libucx0:ppc64el (1.16.0+ds-4) ... 305s Setting up libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 305s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 305s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 305s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 305s Setting up tree-ppuzzle (5.3~rc16+dfsg-9) ... 305s Setting up autopkgtest-satdep (0) ... 305s Processing triggers for man-db (2.12.0-3) ... 306s Processing triggers for libc-bin (2.39-0ubuntu2) ... 310s (Reading database ... 70834 files and directories currently installed.) 310s Removing autopkgtest-satdep (0) ... 310s autopkgtest [01:23:28]: test run-unit-test: [----------------------- 310s .: 310s EF.3trees 310s EF.phy 310s atp6.a 310s globin.a 310s globin.ctrees 310s globin.trees 310s marswolf.ctrees 310s marswolf.n 310s marswolf.trees 310s primates.b 310s primates.ctrees 310s primates.trees 310s tests 310s 310s ./tests: 310s check-cons-pure-prot 310s check-lm-pure-prot 310s check-qp-clock 310s check-qp-hky-clock-nucl 310s check-qp-hky-rhet-clock-nucl 310s check-qp-hky-rhet-nucl 310s check-qp-jtt-prot 310s check-qp-jtt-rhet-clock-prot 310s check-qp-jtt-rhet-prot 310s check-qp-mtrev-prot 310s check-qp-pure-bin 310s check-qp-pure-nucl 310s check-qp-pure-prot 310s check-qp-tn-nucl 310s check-qp-vt-prot 310s check-qp-wag-prot 310s check-ut-pure-prot 310s cons-pure-prot.ctrees 310s cons-pure-prot.ctrees.clean 310s cons-pure-prot.ctrees.dist 310s cons-pure-prot.ctrees.puzzle 310s cons-pure-prot.ctrees.tree 310s cons-pure-prot.param 310s cons-pure-prot.prot 310s cons-pure-prot.prot.out 310s cons-pure-prot.test 310s generate-scripts.sh 310s lm-pure-prot.param 310s lm-pure-prot.prot 310s lm-pure-prot.prot.clean 310s lm-pure-prot.prot.dist 310s lm-pure-prot.prot.eps 310s lm-pure-prot.prot.out 310s lm-pure-prot.prot.puzzle 310s lm-pure-prot.prot.svg 310s lm-pure-prot.test 310s qp-clock.nucl 310s qp-clock.nucl.clean 310s qp-clock.nucl.dist 310s qp-clock.nucl.out 310s qp-clock.nucl.puzzle 310s qp-clock.nucl.tree 310s qp-clock.param 310s qp-clock.test 310s qp-hky-clock-nucl.nucl 310s qp-hky-clock-nucl.nucl.clean 310s qp-hky-clock-nucl.nucl.dist 310s qp-hky-clock-nucl.nucl.out 310s qp-hky-clock-nucl.nucl.puzzle 310s qp-hky-clock-nucl.nucl.tree 310s qp-hky-clock-nucl.param 310s qp-hky-clock-nucl.test 310s qp-hky-rhet-clock-nucl.nucl 310s qp-hky-rhet-clock-nucl.nucl.clean 310s qp-hky-rhet-clock-nucl.nucl.dist 310s qp-hky-rhet-clock-nucl.nucl.out 310s qp-hky-rhet-clock-nucl.nucl.puzzle 310s qp-hky-rhet-clock-nucl.nucl.tree 310s qp-hky-rhet-clock-nucl.param 310s qp-hky-rhet-clock-nucl.test 310s qp-hky-rhet-nucl.nucl 310s qp-hky-rhet-nucl.nucl.clean 310s qp-hky-rhet-nucl.nucl.dist 310s qp-hky-rhet-nucl.nucl.out 310s qp-hky-rhet-nucl.nucl.puzzle 310s qp-hky-rhet-nucl.nucl.tree 310s qp-hky-rhet-nucl.param 310s qp-hky-rhet-nucl.test 310s qp-jtt-prot.param 310s qp-jtt-prot.prot 310s qp-jtt-prot.prot.clean 310s qp-jtt-prot.prot.dist 310s qp-jtt-prot.prot.out 310s qp-jtt-prot.prot.puzzle 310s qp-jtt-prot.prot.tree 310s qp-jtt-prot.test 310s qp-jtt-rhet-clock-prot.param 310s qp-jtt-rhet-clock-prot.prot 310s qp-jtt-rhet-clock-prot.prot.clean 310s qp-jtt-rhet-clock-prot.prot.dist 310s qp-jtt-rhet-clock-prot.prot.out 310s qp-jtt-rhet-clock-prot.prot.puzzle 310s qp-jtt-rhet-clock-prot.prot.tree 310s qp-jtt-rhet-clock-prot.test 310s qp-jtt-rhet-prot.param 310s qp-jtt-rhet-prot.prot 310s qp-jtt-rhet-prot.prot.clean 310s qp-jtt-rhet-prot.prot.dist 310s qp-jtt-rhet-prot.prot.out 310s qp-jtt-rhet-prot.prot.puzzle 310s qp-jtt-rhet-prot.prot.tree 310s qp-jtt-rhet-prot.test 310s qp-mtrev-prot.param 310s qp-mtrev-prot.prot 310s qp-mtrev-prot.prot.clean 310s qp-mtrev-prot.prot.dist 310s qp-mtrev-prot.prot.out 310s qp-mtrev-prot.prot.puzzle 310s qp-mtrev-prot.prot.tree 310s qp-mtrev-prot.test 310s qp-pure-bin.bin 310s qp-pure-bin.bin.clean 310s qp-pure-bin.bin.dist 310s qp-pure-bin.bin.out 310s qp-pure-bin.bin.puzzle 310s qp-pure-bin.bin.tree 310s qp-pure-bin.param 310s qp-pure-bin.test 310s qp-pure-nucl.nucl 310s qp-pure-nucl.nucl.clean 310s qp-pure-nucl.nucl.dist 310s qp-pure-nucl.nucl.out 310s qp-pure-nucl.nucl.puzzle 310s qp-pure-nucl.nucl.tree 310s qp-pure-nucl.param 310s qp-pure-nucl.test 310s qp-pure-prot.param 310s qp-pure-prot.prot 310s qp-pure-prot.prot.clean 310s qp-pure-prot.prot.dist 310s qp-pure-prot.prot.out 310s qp-pure-prot.prot.puzzle 310s qp-pure-prot.prot.tree 310s qp-pure-prot.test 310s qp-tn-nucl.nucl 310s qp-tn-nucl.nucl.clean 310s qp-tn-nucl.nucl.dist 310s qp-tn-nucl.nucl.out 310s qp-tn-nucl.nucl.puzzle 310s qp-tn-nucl.nucl.tree 310s qp-tn-nucl.param 310s qp-tn-nucl.test 310s qp-vt-prot.param 310s qp-vt-prot.prot 310s qp-vt-prot.prot.clean 310s qp-vt-prot.prot.dist 310s qp-vt-prot.prot.out 310s qp-vt-prot.prot.puzzle 310s qp-vt-prot.prot.tree 310s qp-vt-prot.test 310s qp-wag-prot.param 310s qp-wag-prot.prot 310s qp-wag-prot.prot.clean 310s qp-wag-prot.prot.dist 310s qp-wag-prot.prot.out 310s qp-wag-prot.prot.puzzle 310s qp-wag-prot.prot.tree 310s qp-wag-prot.test 310s template-test 310s ut-pure-prot.param 310s ut-pure-prot.prot 310s ut-pure-prot.prot.out 310s ut-pure-prot.test 310s ut-pure-prot.trees 310s ut-pure-prot.trees.clean 310s ut-pure-prot.trees.dist 310s ut-pure-prot.trees.puzzle 310s ut-pure-prot.trees.tree 310s Test 1 310s WARNING: random seed set to 1001 for debugging! 310s 310s 310s 310s WELCOME TO TREE-PUZZLE 5.3.rc16! 310s 310s 310s 310s argv[1] = '-randseed1001' 310s argv[2] = 'tests/qp-pure-bin.bin' 310s Input file: tests/qp-pure-bin.bin 310s Using SPRNG -- Scalable Parallel Random Number Generator 310s RANDOM SEED: 1001 310s 310s Input data set (tests/qp-pure-bin.bin) contains 5 sequences of length 895 310s 1. Gibbon 310s 2. Human 310s 3. Chimpanzee 310s 4. Gorilla 310s 5. Orangutan 310s (consists very likely of binary state data) 310s 310s 310s 310s GENERAL OPTIONS 310s b Type of analysis? Tree reconstruction 310s k Tree search procedure? Quartet puzzling 310s v Quartet evaluation criterion? Exact maximum likelihood (ML) 310s n Number of puzzling steps? 1000 310s o Display as outgroup? Gibbon (1) 310s z Compute clocklike branch lengths? No 310s e Parameter estimates? Approximate (faster) 310s x Parameter estimation uses? Neighbor-joining tree 310s OUTPUT OPTIONS 310s 9 List puzzling trees/splits (NEXUS)? No 310s u List unresolved quartets? No 310s j List puzzling step trees? No 310s SUBSTITUTION PROCESS 310s d Type of sequence input data? Auto: Binary states 310s m Model of substitution? Two-state model (Felsenstein 1981) 310s f Binary state frequencies? Estimate from data set 310s RATE HETEROGENEITY 310s w Model of rate heterogeneity? Uniform rate 310s 310s Quit [q], confirm [y], or change [menu] settings: 310s 310s 310s GENERAL OPTIONS 310s b Type of analysis? Tree reconstruction 310s k Tree search procedure? Quartet puzzling 310s v Quartet evaluation criterion? Exact maximum likelihood (ML) 310s n Number of puzzling steps? 1000 310s o Display as outgroup? Gibbon (1) 310s z Compute clocklike branch lengths? No 310s e Parameter estimates? Approximate (faster) 310s x Parameter estimation uses? Neighbor-joining tree 310s OUTPUT OPTIONS 310s 9 List puzzling trees/splits (NEXUS)? No 310s u List unresolved quartets? No 310s j List puzzling step trees? No 310s SUBSTITUTION PROCESS 310s d Type of sequence input data? Nucleotides 310s m Model of substitution? HKY (Hasegawa et al. 1985) 310s t Transition/transversion parameter? Estimate from data set 310s f Nucleotide frequencies? Estimate from data set 310s RATE HETEROGENEITY 310s w Model of rate heterogeneity? Uniform rate 310s 310s Quit [q], confirm [y], or change [menu] settings: 310s 310s 310s GENERAL OPTIONS 310s b Type of analysis? Tree reconstruction 310s k Tree search procedure? Quartet puzzling 310s v Quartet evaluation criterion? Exact maximum likelihood (ML) 310s n Number of puzzling steps? 1000 310s o Display as outgroup? Gibbon (1) 310s z Compute clocklike branch lengths? No 310s e Parameter estimates? Approximate (faster) 310s x Parameter estimation uses? Neighbor-joining tree 310s OUTPUT OPTIONS 310s 9 List puzzling trees/splits (NEXUS)? No 310s u List unresolved quartets? No 310s j List puzzling step trees? No 310s SUBSTITUTION PROCESS 310s d Type of sequence input data? Amino acids 310s m Model of substitution? Def.: JTT (Jones et al. 1992) 310s f Amino acid frequencies? Estimate from data set 310s RATE HETEROGENEITY 310s w Model of rate heterogeneity? Uniform rate 310s 310s Quit [q], confirm [y], or change [menu] settings: 310s 310s 310s GENERAL OPTIONS 310s b Type of analysis? Tree reconstruction 310s k Tree search procedure? Quartet puzzling 310s v Quartet evaluation criterion? Exact maximum likelihood (ML) 310s n Number of puzzling steps? 1000 310s o Display as outgroup? Gibbon (1) 310s z Compute clocklike branch lengths? No 310s e Parameter estimates? Approximate (faster) 310s x Parameter estimation uses? Neighbor-joining tree 310s OUTPUT OPTIONS 310s 9 List puzzling trees/splits (NEXUS)? No 310s u List unresolved quartets? No 310s j List puzzling step trees? No 310s SUBSTITUTION PROCESS 310s d Type of sequence input data? Binary states 310s m Model of substitution? Two-state model (Felsenstein 1981) 310s f Binary state frequencies? Estimate from data set 310s RATE HETEROGENEITY 310s w Model of rate heterogeneity? Uniform rate 310s 310s Quit [q], confirm [y], or change [menu] settings: 310s Writing parameters to file tests/qp-pure-bin.bin.puzzle 310s Writing parameters to file tests/qp-pure-bin.bin.puzzle 310s Writing pairwise distances to file tests/qp-pure-bin.bin.dist 310s Writing parameters to file tests/qp-pure-bin.bin.puzzle 310s Writing parameters to file tests/qp-pure-bin.bin.puzzle 310s Computing quartet maximum likelihood trees 310s Computing quartet puzzling trees 310s Computing maximum likelihood branch lengths (without clock) 310s 310s All results written to disk: 310s Puzzle report file: tests/qp-pure-bin.bin.puzzle 310s Likelihood distances: tests/qp-pure-bin.bin.dist 310s Phylip tree file: tests/qp-pure-bin.bin.tree 310s 310s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 310s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 310s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 310s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 310s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 310s Passed 310s 311s Test 2 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-pure-nucl.nucl' 311s Input file: tests/qp-pure-nucl.nucl 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s WARNING: random seed set to 1001 for debugging! 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-pure-nucl.nucl) contains 8 sequences of length 116 311s 1. Thylacinus 311s 2. Sarcophilu 311s 3. Dasyurus 311s 4. Echymipera 311s 5. Trichosuru 311s 6. Phalanger 311s 7. Philander 311s 8. Bos 311s (consists very likely of nucleotides) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Optimizing missing substitution process parameters 311s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 311s Writing pairwise distances to file tests/qp-pure-nucl.nucl.dist 311s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-pure-nucl.nucl.puzzle 311s Likelihood distances: tests/qp-pure-nucl.nucl.dist 311s Phylip tree file: tests/qp-pure-nucl.nucl.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 3 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-tn-nucl.nucl' 311s Input file: tests/qp-tn-nucl.nucl 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-tn-nucl.nucl) contains 8 sequences of length 116 311s 1. Thylacinus 311s 2. Sarcophilu 311s 3. Dasyurus 311s 4. Echymipera 311s 5. Trichosuru 311s 6. Phalanger 311s 7. Philander 311s 8. Bos 311s (consists very likely of nucleotides) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? TN (Tamura-Nei 1993) 311s p Constrain TN model to F84 model? No 311s t Transition/transversion parameter? Estimate from data set 311s r Y/R transition parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Optimizing missing substitution process parameters 311s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 311s Writing pairwise distances to file tests/qp-tn-nucl.nucl.dist 311s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-tn-nucl.nucl.puzzle 311s Likelihood distances: tests/qp-tn-nucl.nucl.dist 311s Phylip tree file: tests/qp-tn-nucl.nucl.tree 311s 311s The parameter estimation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 311s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 311s Passed 311s 311s Test 4 311s WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-hky-clock-nucl.nucl' 311s Input file: tests/qp-hky-clock-nucl.nucl 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-hky-clock-nucl.nucl) contains 8 sequences of length 116 311s 1. Thylacinus 311s 2. Sarcophilu 311s 3. Dasyurus 311s 4. Echymipera 311s 5. Trichosuru 311s 6. Phalanger 311s 7. Philander 311s 8. Bos 311s (consists very likely of nucleotides) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? Yes 311s l Location of root? Best place (automatic search) 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Optimizing missing substitution process parameters 311s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 311s Writing pairwise distances to file tests/qp-hky-clock-nucl.nucl.dist 311s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s Computing maximum likelihood branch lengths (with clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-hky-clock-nucl.nucl.puzzle 311s Likelihood distances: tests/qp-hky-clock-nucl.nucl.dist 311s Phylip tree file: tests/qp-hky-clock-nucl.nucl.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 5 311s WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-hky-rhet-nucl.nucl' 311s Input file: tests/qp-hky-rhet-nucl.nucl 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-hky-rhet-nucl.nucl) contains 8 sequences of length 116 311s 1. Thylacinus 311s 2. Sarcophilu 311s 3. Dasyurus 311s 4. Echymipera 311s 5. Trichosuru 311s 6. Phalanger 311s 7. Philander 311s 8. Bos 311s (consists very likely of nucleotides) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Gamma distributed rates 311s a Gamma distribution parameter alpha? Estimate from data set 311s c Number of Gamma rate categories? 4 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Optimizing missing substitution process parameters 311s Optimizing missing rate heterogeneity parameters 311s Optimizing missing substitution process parameters 311s Optimizing missing rate heterogeneity parameters 311s Optimizing missing substitution process parameters 311s Optimizing missing rate heterogeneity parameters 311s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 311s Writing pairwise distances to file tests/qp-hky-rhet-nucl.nucl.dist 311s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-hky-rhet-nucl.nucl.puzzle 311s Likelihood distances: tests/qp-hky-rhet-nucl.nucl.dist 311s Phylip tree file: tests/qp-hky-rhet-nucl.nucl.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 6 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-hky-rhet-clock-nucl.nucl' 311s Input file: tests/qp-hky-rhet-clock-nucl.nucl 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s WARNING: random seed set to 1001 for debugging! 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-hky-rhet-clock-nucl.nucl) contains 8 sequences of length 116 311s 1. Thylacinus 311s 2. Sarcophilu 311s 3. Dasyurus 311s 4. Echymipera 311s 5. Trichosuru 311s 6. Phalanger 311s 7. Philander 311s 8. Bos 311s (consists very likely of nucleotides) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? Yes 311s l Location of root? Best place (automatic search) 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? Yes 311s l Location of root? Best place (automatic search) 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Gamma distributed rates 311s a Gamma distribution parameter alpha? Estimate from data set 311s c Number of Gamma rate categories? 4 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Optimizing missing substitution process parameters 311s Optimizing missing rate heterogeneity parameters 311s Optimizing missing substitution process parameters 311s Optimizing missing rate heterogeneity parameters 311s Optimizing missing substitution process parameters 311s Optimizing missing rate heterogeneity parameters 311s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 311s Writing pairwise distances to file tests/qp-hky-rhet-clock-nucl.nucl.dist 311s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 311s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s Computing maximum likelihood branch lengths (with clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-hky-rhet-clock-nucl.nucl.puzzle 311s Likelihood distances: tests/qp-hky-rhet-clock-nucl.nucl.dist 311s Phylip tree file: tests/qp-hky-rhet-clock-nucl.nucl.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 7 311s WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-pure-prot.prot' 311s Input file: tests/qp-pure-prot.prot 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-pure-prot.prot) contains 7 sequences of length 128 311s 1. HBB_HUMAN 311s 2. HBB_HORSE 311s 3. HBA_HUMAN 311s 4. HBA_HORSE 311s 5. MYG_PHYCA 311s 6. GLB5_PETMA 311s 7. LGB2_LUPLU 311s (consists very likely of amino acids encoded on nuclear DNA) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Writing parameters to file tests/qp-pure-prot.prot.puzzle 311s Writing parameters to file tests/qp-pure-prot.prot.puzzle 311s Writing pairwise distances to file tests/qp-pure-prot.prot.dist 311s Writing parameters to file tests/qp-pure-prot.prot.puzzle 311s Writing parameters to file tests/qp-pure-prot.prot.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-pure-prot.prot.puzzle 311s Likelihood distances: tests/qp-pure-prot.prot.dist 311s Phylip tree file: tests/qp-pure-prot.prot.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 8 311s WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-mtrev-prot.prot' 311s Input file: tests/qp-mtrev-prot.prot 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-mtrev-prot.prot) contains 7 sequences of length 128 311s 1. HBB_HUMAN 311s 2. HBB_HORSE 311s 3. HBA_HUMAN 311s 4. HBA_HORSE 311s 5. MYG_PHYCA 311s 6. GLB5_PETMA 311s 7. LGB2_LUPLU 311s (consists very likely of amino acids encoded on nuclear DNA) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? JTT (Jones et al. 1992) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 311s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 311s Writing pairwise distances to file tests/qp-mtrev-prot.prot.dist 311s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 311s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-mtrev-prot.prot.puzzle 311s Likelihood distances: tests/qp-mtrev-prot.prot.dist 311s Phylip tree file: tests/qp-mtrev-prot.prot.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 9 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-vt-prot.prot' 311s Input file: tests/qp-vt-prot.prot 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-vt-prot.prot) contains 7 sequences of length 128 311s 1. HBB_HUMAN 311s 2. HBB_HORSE 311s 3. HBA_HUMAN 311s 4. HBA_HORSE 311s 5. MYG_PHYCA 311s 6. GLB5_PETMA 311s 7. LGB2_LUPLU 311s (consists very likely of amino acids encoded on nuclear DNA) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? JTT (Jones et al. 1992) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? VT (Mueller-Vingron 2000) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Writing parameters to file tests/qp-vt-prot.prot.puzzle 311s Writing parameters to file tests/qp-vt-prot.prot.puzzle 311s Writing pairwise distances to file tests/qp-vt-prot.prot.dist 311s Writing parameters to file tests/qp-vt-prot.prot.puzzle 311s Writing parameters to file tests/qp-vt-prot.prot.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-vt-prot.prot.puzzle 311s Likelihood distances: tests/qp-vt-prot.prot.dist 311s Phylip tree file: tests/qp-vt-prot.prot.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 10 311s WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-wag-prot.prot' 311s Input file: tests/qp-wag-prot.prot 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-wag-prot.prot) contains 7 sequences of length 128 311s 1. HBB_HUMAN 311s 2. HBB_HORSE 311s 3. HBA_HUMAN 311s 4. HBA_HORSE 311s 5. MYG_PHYCA 311s 6. GLB5_PETMA 311s 7. LGB2_LUPLU 311s (consists very likely of amino acids encoded on nuclear DNA) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? JTT (Jones et al. 1992) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? VT (Mueller-Vingron 2000) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? WAG (Whelan-Goldman 2000) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Writing parameters to file tests/qp-wag-prot.prot.puzzle 311s Writing parameters to file tests/qp-wag-prot.prot.puzzle 311s Writing pairwise distances to file tests/qp-wag-prot.prot.dist 311s Writing parameters to file tests/qp-wag-prot.prot.puzzle 311s Writing parameters to file tests/qp-wag-prot.prot.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-wag-prot.prot.puzzle 311s Likelihood distances: tests/qp-wag-prot.prot.dist 311s Phylip tree file: tests/qp-wag-prot.prot.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 11 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-clock.nucl' 311s Input file: tests/qp-clock.nucl 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-clock.nucl) contains 8 sequences of length 116 311s 1. Thylacinus 311s 2. Sarcophilu 311s 3. Dasyurus 311s 4. Echymipera 311s 5. Trichosuru 311s 6. Phalanger 311s 7. Philander 311s 8. Bos 311s (consists very likely of nucleotides) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? Thylacinus (1) 311s z Compute clocklike branch lengths? Yes 311s l Location of root? Best place (automatic search) 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 311s 311s Optimizing missing substitution process parameters 311s Writing parameters to file tests/qp-clock.nucl.puzzle 311s Writing parameters to file tests/qp-clock.nucl.puzzle 311s Writing pairwise distances to file tests/qp-clock.nucl.dist 311s Writing parameters to file tests/qp-clock.nucl.puzzle 311s Writing parameters to file tests/qp-clock.nucl.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s Computing maximum likelihood branch lengths (with clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-clock.nucl.puzzle 311s Likelihood distances: tests/qp-clock.nucl.dist 311s Phylip tree file: tests/qp-clock.nucl.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 12 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-jtt-prot.prot' 311s Input file: tests/qp-jtt-prot.prot 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-jtt-prot.prot) contains 7 sequences of length 128 311s 1. HBB_HUMAN 311s 2. HBB_HORSE 311s 3. HBA_HUMAN 311s 4. HBA_HORSE 311s 5. MYG_PHYCA 311s 6. GLB5_PETMA 311s 7. LGB2_LUPLU 311s (consists very likely of amino acids encoded on nuclear DNA) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? JTT (Jones et al. 1992) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 311s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 311s Writing pairwise distances to file tests/qp-jtt-prot.prot.dist 311s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 311s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 311s Computing quartet maximum likelihood trees 311s Computing quartet puzzling trees 311s Computing maximum likelihood branch lengths (without clock) 311s 311s All results written to disk: 311s Puzzle report file: tests/qp-jtt-prot.prot.puzzle 311s Likelihood distances: tests/qp-jtt-prot.prot.dist 311s Phylip tree file: tests/qp-jtt-prot.prot.tree 311s 311s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 311s Passed 311s 311s Test 13 311s WARNING: random seed set to 1001 for debugging! 311s 311s 311s 311s WELCOME TO TREE-PUZZLE 5.3.rc16! 311s 311s 311s 311s argv[1] = '-randseed1001' 311s argv[2] = 'tests/qp-jtt-rhet-prot.prot' 311s Input file: tests/qp-jtt-rhet-prot.prot 311s Using SPRNG -- Scalable Parallel Random Number Generator 311s RANDOM SEED: 1001 311s 311s Input data set (tests/qp-jtt-rhet-prot.prot) contains 7 sequences of length 128 311s 1. HBB_HUMAN 311s 2. HBB_HORSE 311s 3. HBA_HUMAN 311s 4. HBA_HORSE 311s 5. MYG_PHYCA 311s 6. GLB5_PETMA 311s 7. LGB2_LUPLU 311s (consists very likely of amino acids encoded on nuclear DNA) 311s 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Auto: Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Nucleotides 311s m Model of substitution? HKY (Hasegawa et al. 1985) 311s t Transition/transversion parameter? Estimate from data set 311s f Nucleotide frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? JTT (Jones et al. 1992) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Uniform rate 311s 311s Quit [q], confirm [y], or change [menu] settings: 311s 311s 311s GENERAL OPTIONS 311s b Type of analysis? Tree reconstruction 311s k Tree search procedure? Quartet puzzling 311s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 311s n Number of puzzling steps? 1000 311s o Display as outgroup? HBB_HUMAN (1) 311s z Compute clocklike branch lengths? No 311s e Parameter estimates? Approximate (faster) 311s x Parameter estimation uses? Neighbor-joining tree 311s OUTPUT OPTIONS 311s 9 List puzzling trees/splits (NEXUS)? No 311s u List unresolved quartets? No 311s j List puzzling step trees? No 311s SUBSTITUTION PROCESS 311s d Type of sequence input data? Amino acids 311s m Model of substitution? JTT (Jones et al. 1992) 311s f Amino acid frequencies? Estimate from data set 311s RATE HETEROGENEITY 311s w Model of rate heterogeneity? Gamma distributed rates 311s a Gamma distribution parameter alpha? Estimate from data set 311s c Number of Gamma rate categories? 4 311s 312s Quit [q], confirm [y], or change [menu] settings: 312s Optimizing missing rate heterogeneity parameters 312s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 312s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 312s Writing pairwise distances to file tests/qp-jtt-rhet-prot.prot.dist 312s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 312s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 312s Computing quartet maximum likelihood trees 312s Computing quartet puzzling trees 312s Computing maximum likelihood branch lengths (without clock) 312s 312s All results written to disk: 312s Puzzle report file: tests/qp-jtt-rhet-prot.prot.puzzle 312s Likelihood distances: tests/qp-jtt-rhet-prot.prot.dist 312s Phylip tree file: tests/qp-jtt-rhet-prot.prot.tree 312s 312s The parameter estimation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 312s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 312s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 312s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 312s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 312s Passed 312s 312s Test 14 312s 312s 312s 312s WELCOME TO TREE-PUZZLE 5.3.rc16! 312s 312s 312s 312s argv[1] = '-randseed1001' 312s argv[2] = 'tests/qp-jtt-rhet-clock-prot.prot' 312s Input file: tests/qp-jtt-rhet-clock-prot.prot 312s Using SPRNG -- Scalable Parallel Random Number Generator 312s WARNING: random seed set to 1001 for debugging! 312s RANDOM SEED: 1001 312s 312s Input data set (tests/qp-jtt-rhet-clock-prot.prot) contains 7 sequences of length 128 312s 1. HBB_HUMAN 312s 2. HBB_HORSE 312s 3. HBA_HUMAN 312s 4. HBA_HORSE 312s 5. MYG_PHYCA 312s 6. GLB5_PETMA 312s 7. LGB2_LUPLU 312s (consists very likely of amino acids encoded on nuclear DNA) 312s 312s 312s 312s GENERAL OPTIONS 312s b Type of analysis? Tree reconstruction 312s k Tree search procedure? Quartet puzzling 312s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 312s n Number of puzzling steps? 1000 312s o Display as outgroup? HBB_HUMAN (1) 312s z Compute clocklike branch lengths? No 312s e Parameter estimates? Approximate (faster) 312s x Parameter estimation uses? Neighbor-joining tree 312s OUTPUT OPTIONS 312s 9 List puzzling trees/splits (NEXUS)? No 312s u List unresolved quartets? No 312s j List puzzling step trees? No 312s SUBSTITUTION PROCESS 312s d Type of sequence input data? Auto: Amino acids 312s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 312s f Amino acid frequencies? Estimate from data set 312s RATE HETEROGENEITY 312s w Model of rate heterogeneity? Uniform rate 312s 312s Quit [q], confirm [y], or change [menu] settings: 312s 312s 312s GENERAL OPTIONS 312s b Type of analysis? Tree reconstruction 312s k Tree search procedure? Quartet puzzling 312s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 312s n Number of puzzling steps? 1000 312s o Display as outgroup? HBB_HUMAN (1) 312s z Compute clocklike branch lengths? No 312s e Parameter estimates? Approximate (faster) 312s x Parameter estimation uses? Neighbor-joining tree 312s OUTPUT OPTIONS 312s 9 List puzzling trees/splits (NEXUS)? No 312s u List unresolved quartets? No 312s j List puzzling step trees? No 312s SUBSTITUTION PROCESS 312s d Type of sequence input data? Nucleotides 312s m Model of substitution? HKY (Hasegawa et al. 1985) 312s t Transition/transversion parameter? Estimate from data set 312s f Nucleotide frequencies? Estimate from data set 312s RATE HETEROGENEITY 312s w Model of rate heterogeneity? Uniform rate 312s 312s Quit [q], confirm [y], or change [menu] settings: 312s 312s 312s GENERAL OPTIONS 312s b Type of analysis? Tree reconstruction 312s k Tree search procedure? Quartet puzzling 312s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 312s n Number of puzzling steps? 1000 312s o Display as outgroup? HBB_HUMAN (1) 312s z Compute clocklike branch lengths? No 312s e Parameter estimates? Approximate (faster) 312s x Parameter estimation uses? Neighbor-joining tree 312s OUTPUT OPTIONS 312s 9 List puzzling trees/splits (NEXUS)? No 312s u List unresolved quartets? No 312s j List puzzling step trees? No 312s SUBSTITUTION PROCESS 312s d Type of sequence input data? Amino acids 312s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 312s f Amino acid frequencies? Estimate from data set 312s RATE HETEROGENEITY 312s w Model of rate heterogeneity? Uniform rate 312s 312s Quit [q], confirm [y], or change [menu] settings: 312s 312s 312s GENERAL OPTIONS 312s b Type of analysis? Tree reconstruction 312s k Tree search procedure? Quartet puzzling 312s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 312s n Number of puzzling steps? 1000 312s o Display as outgroup? HBB_HUMAN (1) 312s z Compute clocklike branch lengths? No 312s e Parameter estimates? Approximate (faster) 312s x Parameter estimation uses? Neighbor-joining tree 312s OUTPUT OPTIONS 312s 9 List puzzling trees/splits (NEXUS)? No 312s u List unresolved quartets? No 312s j List puzzling step trees? No 312s SUBSTITUTION PROCESS 312s d Type of sequence input data? Amino acids 312s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 312s f Amino acid frequencies? Estimate from data set 312s RATE HETEROGENEITY 312s w Model of rate heterogeneity? Uniform rate 312s 312s Quit [q], confirm [y], or change [menu] settings: 312s 312s 312s GENERAL OPTIONS 312s b Type of analysis? Tree reconstruction 312s k Tree search procedure? Quartet puzzling 312s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 312s n Number of puzzling steps? 1000 312s o Display as outgroup? HBB_HUMAN (1) 312s z Compute clocklike branch lengths? No 312s e Parameter estimates? Approximate (faster) 312s x Parameter estimation uses? Neighbor-joining tree 312s OUTPUT OPTIONS 312s 9 List puzzling trees/splits (NEXUS)? No 312s u List unresolved quartets? No 312s j List puzzling step trees? No 312s SUBSTITUTION PROCESS 312s d Type of sequence input data? Amino acids 312s m Model of substitution? JTT (Jones et al. 1992) 312s f Amino acid frequencies? Estimate from data set 312s RATE HETEROGENEITY 312s w Model of rate heterogeneity? Uniform rate 312s 312s Quit [q], confirm [y], or change [menu] settings: 312s 312s 312s GENERAL OPTIONS 312s b Type of analysis? Tree reconstruction 312s k Tree search procedure? Quartet puzzling 312s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 312s n Number of puzzling steps? 1000 312s o Display as outgroup? HBB_HUMAN (1) 312s z Compute clocklike branch lengths? Yes 312s l Location of root? Best place (automatic search) 312s e Parameter estimates? Approximate (faster) 312s x Parameter estimation uses? Neighbor-joining tree 312s OUTPUT OPTIONS 312s 9 List puzzling trees/splits (NEXUS)? No 312s u List unresolved quartets? No 312s j List puzzling step trees? No 312s SUBSTITUTION PROCESS 312s d Type of sequence input data? Amino acids 312s m Model of substitution? JTT (Jones et al. 1992) 312s f Amino acid frequencies? Estimate from data set 312s RATE HETEROGENEITY 312s w Model of rate heterogeneity? Uniform rate 312s 312s Quit [q], confirm [y], or change [menu] settings: 312s 312s 312s GENERAL OPTIONS 312s b Type of analysis? Tree reconstruction 312s k Tree search procedure? Quartet puzzling 312s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 312s n Number of puzzling steps? 1000 312s o Display as outgroup? HBB_HUMAN (1) 312s z Compute clocklike branch lengths? Yes 312s l Location of root? Best place (automatic search) 312s e Parameter estimates? Approximate (faster) 312s x Parameter estimation uses? Neighbor-joining tree 312s OUTPUT OPTIONS 312s 9 List puzzling trees/splits (NEXUS)? No 312s u List unresolved quartets? No 312s j List puzzling step trees? No 312s SUBSTITUTION PROCESS 312s d Type of sequence input data? Amino acids 312s m Model of substitution? JTT (Jones et al. 1992) 312s f Amino acid frequencies? Estimate from data set 312s RATE HETEROGENEITY 312s w Model of rate heterogeneity? Gamma distributed rates 312s a Gamma distribution parameter alpha? Estimate from data set 312s c Number of Gamma rate categories? 4 312s 312s Quit [q], confirm [y], or change [menu] settings: 312s Optimizing missing rate heterogeneity parameters 312s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 312s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 312s Writing pairwise distances to file tests/qp-jtt-rhet-clock-prot.prot.dist 312s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 312s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 312s Computing quartet maximum likelihood trees 313s Computing quartet puzzling trees 313s Computing maximum likelihood branch lengths (without clock) 313s Computing maximum likelihood branch lengths (with clock) 313s 313s All results written to disk: 313s Puzzle report file: tests/qp-jtt-rhet-clock-prot.prot.puzzle 313s Likelihood distances: tests/qp-jtt-rhet-clock-prot.prot.dist 313s Phylip tree file: tests/qp-jtt-rhet-clock-prot.prot.tree 313s 313s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 313s The ML step took 1.00 seconds (= 0.02 minutes = 0.00 hours) 313s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 313s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 313s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 313s Passed 313s 313s Test 15 313s 313s 313s 313s WELCOME TO TREE-PUZZLE 5.3.rc16! 313s 313s 313s 313s argv[1] = '-randseed1001' 313s argv[2] = 'tests/lm-pure-prot.prot' 313s Input file: tests/lm-pure-prot.prot 313s Using SPRNG -- Scalable Parallel Random Number Generator 313s RANDOM SEED: 1001 313s 313s Input data set (tests/lm-pure-prot.prot) contains 7 sequences of length 128 313s 1. HBB_HUMAN 313s 2. HBB_HORSE 313s 3. HBA_HUMAN 313s 4. HBA_HORSE 313s 5. MYG_PHYCA 313s 6. GLB5_PETMA 313s 7. LGB2_LUPLU 313s (consists very likely of amino acids encoded on nuclear DNA) 313s 313s 313s 313s GENERAL OPTIONS 313s b Type of analysis? Tree reconstruction 313s k Tree search procedure? Quartet puzzling 313s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 313s n Number of puzzling steps? 1000 313s o Display as outgroup? HBB_HUMAN (1) 313s z Compute clocklike branch lengths? No 313s e Parameter estimates? Approximate (faster) 313s x Parameter estimation uses? Neighbor-joining tree 313s OUTPUT OPTIONS 313s 9 List puzzling trees/splits (NEXUS)? No 313s u List unresolved quartets? No 313s j List puzzling step trees? No 313s SUBSTITUTION PROCESS 313s d Type of sequence input data? Auto: Amino acids 313s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 313s f Amino acid frequencies? Estimate from data set 313s RATE HETEROGENEITY 313s w Model of rate heterogeneity? Uniform rate 313s 313s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 313s 313s 313s 313s GENERAL OPTIONS 313s b Type of analysis? Tree reconstruction 313s k Tree search procedure? Quartet puzzling 313s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 313s n Number of puzzling steps? 1000 313s o Display as outgroup? HBB_HUMAN (1) 313s z Compute clocklike branch lengths? No 313s e Parameter estimates? Approximate (faster) 313s x Parameter estimation uses? Neighbor-joining tree 313s OUTPUT OPTIONS 313s 9 List puzzling trees/splits (NEXUS)? No 313s u List unresolved quartets? No 313s j List puzzling step trees? No 313s SUBSTITUTION PROCESS 313s d Type of sequence input data? Nucleotides 313s m Model of substitution? HKY (Hasegawa et al. 1985) 313s t Transition/transversion parameter? Estimate from data set 313s f Nucleotide frequencies? Estimate from data set 313s RATE HETEROGENEITY 313s w Model of rate heterogeneity? Uniform rate 313s 313s Quit [q], confirm [y], or change [menu] settings: 313s 313s 313s GENERAL OPTIONS 313s b Type of analysis? Tree reconstruction 313s k Tree search procedure? Quartet puzzling 313s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 313s n Number of puzzling steps? 1000 313s o Display as outgroup? HBB_HUMAN (1) 313s z Compute clocklike branch lengths? No 313s e Parameter estimates? Approximate (faster) 313s x Parameter estimation uses? Neighbor-joining tree 313s OUTPUT OPTIONS 313s 9 List puzzling trees/splits (NEXUS)? No 313s u List unresolved quartets? No 313s j List puzzling step trees? No 313s SUBSTITUTION PROCESS 313s d Type of sequence input data? Amino acids 313s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 313s f Amino acid frequencies? Estimate from data set 313s RATE HETEROGENEITY 313s w Model of rate heterogeneity? Uniform rate 313s 313s Quit [q], confirm [y], or change [menu] settings: 313s 313s 313s GENERAL OPTIONS 313s b Type of analysis? Likelihood mapping 313s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 313s g Group sequences in clusters? No 313s n Number of quartets? 35 (all possible) 313s e Parameter estimates? Approximate (faster) 313s x Parameter estimation uses? Neighbor-joining tree 313s SUBSTITUTION PROCESS 313s d Type of sequence input data? Amino acids 313s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 313s f Amino acid frequencies? Estimate from data set 313s RATE HETEROGENEITY 313s w Model of rate heterogeneity? Uniform rate 313s 313s Quit [q], confirm [y], or change [menu] settings: PPP1: 0 (./puzzle1.c:8696) 313s 313s Writing parameters to file tests/lm-pure-prot.prot.puzzle 313s Writing parameters to file tests/lm-pure-prot.prot.puzzle 313s Writing pairwise distances to file tests/lm-pure-prot.prot.dist 313s Writing parameters to file tests/lm-pure-prot.prot.puzzle 313s Writing parameters to file tests/lm-pure-prot.prot.puzzle 313s Performing likelihood mapping analysis 314s PPP1: 1 (./puzzle1.c:8702) 314s 314s All results written to disk: 314s Puzzle report file: tests/lm-pure-prot.prot.puzzle 314s Likelihood distances: tests/lm-pure-prot.prot.dist 314s Likelihood mapping diagram (EPS): tests/lm-pure-prot.prot.eps 314s Likelihood mapping diagram (SVG): tests/lm-pure-prot.prot.svg 314s 314s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 314s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 314s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 314s Passed 314s 314s autopkgtest [01:23:32]: test run-unit-test: -----------------------] 314s autopkgtest [01:23:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 314s run-unit-test PASS 315s autopkgtest [01:23:33]: @@@@@@@@@@@@@@@@@@@@ summary 315s run-unit-test PASS 333s Creating nova instance adt-noble-ppc64el-tree-puzzle-20240319-011818-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240318.img (UUID 290ce4c5-ca44-4691-9a55-79589f8700e4)...