0s autopkgtest [10:37:18]: starting date and time: 2025-05-02 10:37:18+0000 0s autopkgtest [10:37:18]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [10:37:18]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u2eeeqhm/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:mpich --apt-upgrade hyphy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=mpich/4.3.0-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-5.secgroup --name adt-questing-arm64-hyphy-20250502-103717-juju-7f2275-prod-proposed-migration-environment-15-ac1c359d-5339-4d55-9706-19ac779a6f46 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 77s autopkgtest [10:38:35]: testbed dpkg architecture: arm64 77s autopkgtest [10:38:35]: testbed apt version: 3.0.0 77s autopkgtest [10:38:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 77s autopkgtest [10:38:35]: testbed release detected to be: None 78s autopkgtest [10:38:36]: updating testbed package index (apt update) 78s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 78s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 78s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2076 kB] 78s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [175 kB] 78s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [44.4 kB] 78s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [219 kB] 78s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1509 kB] 78s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [15.4 kB] 79s Fetched 4149 kB in 1s (6811 kB/s) 79s Reading package lists... 80s autopkgtest [10:38:38]: upgrading testbed (apt dist-upgrade and autopurge) 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 81s Starting 2 pkgProblemResolver with broken count: 0 81s Done 82s Entering ResolveByKeep 82s 82s Calculating upgrade... 82s The following packages will be upgraded: 82s htop libperl5.40 mtd-utils nano perl perl-base perl-modules-5.40 82s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 11.0 MB of archives. 82s After this operation, 727 kB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libperl5.40 arm64 5.40.1-3 [4780 kB] 83s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl arm64 5.40.1-3 [262 kB] 83s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-base arm64 5.40.1-3 [1786 kB] 83s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 83s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 nano arm64 8.4-1 [290 kB] 83s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 htop arm64 3.4.1-4 [177 kB] 83s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 mtd-utils arm64 1:2.3.0-1ubuntu1 [469 kB] 83s Fetched 11.0 MB in 0s (22.4 MB/s) 83s (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 ... 85224 files and directories currently installed.) 83s Preparing to unpack .../libperl5.40_5.40.1-3_arm64.deb ... 83s Unpacking libperl5.40:arm64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Preparing to unpack .../perl_5.40.1-3_arm64.deb ... 84s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Preparing to unpack .../perl-base_5.40.1-3_arm64.deb ... 84s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Setting up perl-base (5.40.1-3) ... 84s (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 ... 85224 files and directories currently installed.) 84s Preparing to unpack .../perl-modules-5.40_5.40.1-3_all.deb ... 84s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Preparing to unpack .../archives/nano_8.4-1_arm64.deb ... 84s Unpacking nano (8.4-1) over (8.3-1) ... 84s Preparing to unpack .../htop_3.4.1-4_arm64.deb ... 84s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 84s Preparing to unpack .../mtd-utils_1%3a2.3.0-1ubuntu1_arm64.deb ... 84s Unpacking mtd-utils (1:2.3.0-1ubuntu1) over (1:2.2.0-2ubuntu2) ... 84s Setting up htop (3.4.1-4) ... 84s Setting up mtd-utils (1:2.3.0-1ubuntu1) ... 84s Setting up nano (8.4-1) ... 84s Installing new version of config file /etc/nanorc ... 84s Setting up perl-modules-5.40 (5.40.1-3) ... 84s Setting up libperl5.40:arm64 (5.40.1-3) ... 84s Setting up perl (5.40.1-3) ... 84s Processing triggers for libc-bin (2.41-6ubuntu1) ... 84s Processing triggers for man-db (2.13.0-1) ... 86s Processing triggers for install-info (7.1.1-1) ... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 87s Solving dependencies... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [10:38:48]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 90s autopkgtest [10:38:48]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 92s Get:1 http://ftpmaster.internal/ubuntu questing/universe hyphy 2.5.68+dfsg-1 (dsc) [2420 B] 92s Get:2 http://ftpmaster.internal/ubuntu questing/universe hyphy 2.5.68+dfsg-1 (tar) [2633 kB] 92s Get:3 http://ftpmaster.internal/ubuntu questing/universe hyphy 2.5.68+dfsg-1 (diff) [17.3 kB] 92s gpgv: Signature made Sat Feb 15 21:16:28 2025 UTC 92s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 92s gpgv: issuer "emollier@debian.org" 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.68+dfsg-1.dsc: no acceptable signature found 92s autopkgtest [10:38:50]: testing package hyphy version 2.5.68+dfsg-1 93s autopkgtest [10:38:51]: build not needed 94s autopkgtest [10:38:52]: test run-unit-tests: preparing testbed 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 95s The following NEW packages will be installed: 95s hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 95s libevent-pthreads-2.1-7t64 libfabric1 libgomp1 libhsa-runtime64-1 libhsakmt1 95s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libllvm17t64 libmunge2 95s libopenmpi40 libpciaccess0 libpmix2t64 librdmacm1t64 libucx0 libxnvctrl0 95s ocl-icd-libopencl1 95s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 57.2 MB of archives. 95s After this operation, 239 MB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu questing/universe arm64 hyphy-common all 2.5.68+dfsg-1 [633 kB] 96s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 96s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 96s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 librdmacm1t64 arm64 56.0-4ubuntu1 [71.4 kB] 96s Get:5 http://ftpmaster.internal/ubuntu questing/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB] 96s Get:6 http://ftpmaster.internal/ubuntu questing/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB] 96s Get:7 http://ftpmaster.internal/ubuntu questing/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 96s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 96s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 96s Get:10 http://ftpmaster.internal/ubuntu questing/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 96s Get:11 http://ftpmaster.internal/ubuntu questing/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB] 96s Get:12 http://ftpmaster.internal/ubuntu questing/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB] 96s Get:13 http://ftpmaster.internal/ubuntu questing/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB] 96s Get:14 http://ftpmaster.internal/ubuntu questing/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 97s Get:15 http://ftpmaster.internal/ubuntu questing/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 97s Get:16 http://ftpmaster.internal/ubuntu questing/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 97s Get:17 http://ftpmaster.internal/ubuntu questing/universe arm64 libamdhip64-5 arm64 5.7.1-5build1 [9707 kB] 97s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libibumad3 arm64 56.0-4ubuntu1 [31.3 kB] 97s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libibmad5 arm64 56.0-4ubuntu1 [44.1 kB] 97s Get:20 http://ftpmaster.internal/ubuntu questing/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB] 97s Get:21 http://ftpmaster.internal/ubuntu questing/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB] 97s Get:22 http://ftpmaster.internal/ubuntu questing/universe arm64 hyphy-mpi arm64 2.5.68+dfsg-1 [1113 kB] 97s Get:23 http://ftpmaster.internal/ubuntu questing/universe arm64 hyphy-pt arm64 2.5.68+dfsg-1 [1086 kB] 98s Fetched 57.2 MB in 2s (32.6 MB/s) 98s Selecting previously unselected package hyphy-common. 98s (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 ... 85225 files and directories currently installed.) 98s Preparing to unpack .../00-hyphy-common_2.5.68+dfsg-1_all.deb ... 98s Unpacking hyphy-common (2.5.68+dfsg-1) ... 98s Selecting previously unselected package libgomp1:arm64. 98s Preparing to unpack .../01-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 98s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 98s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 98s Preparing to unpack .../02-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 98s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 98s Selecting previously unselected package librdmacm1t64:arm64. 98s Preparing to unpack .../03-librdmacm1t64_56.0-4ubuntu1_arm64.deb ... 98s Unpacking librdmacm1t64:arm64 (56.0-4ubuntu1) ... 98s Selecting previously unselected package libfabric1:arm64. 98s Preparing to unpack .../04-libfabric1_1.17.0-3.1_arm64.deb ... 98s Unpacking libfabric1:arm64 (1.17.0-3.1) ... 98s Selecting previously unselected package libhwloc15:arm64. 98s Preparing to unpack .../05-libhwloc15_2.12.0-1_arm64.deb ... 98s Unpacking libhwloc15:arm64 (2.12.0-1) ... 98s Selecting previously unselected package libmunge2:arm64. 98s Preparing to unpack .../06-libmunge2_0.5.16-1_arm64.deb ... 98s Unpacking libmunge2:arm64 (0.5.16-1) ... 98s Selecting previously unselected package libpciaccess0:arm64. 98s Preparing to unpack .../07-libpciaccess0_0.17-3build1_arm64.deb ... 98s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 98s Selecting previously unselected package libxnvctrl0:arm64. 98s Preparing to unpack .../08-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 98s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 98s Selecting previously unselected package ocl-icd-libopencl1:arm64. 98s Preparing to unpack .../09-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 98s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 98s Selecting previously unselected package libhwloc-plugins:arm64. 98s Preparing to unpack .../10-libhwloc-plugins_2.12.0-1_arm64.deb ... 98s Unpacking libhwloc-plugins:arm64 (2.12.0-1) ... 98s Selecting previously unselected package libpmix2t64:arm64. 98s Preparing to unpack .../11-libpmix2t64_5.0.6-5_arm64.deb ... 98s Unpacking libpmix2t64:arm64 (5.0.6-5) ... 98s Selecting previously unselected package libllvm17t64:arm64. 98s Preparing to unpack .../12-libllvm17t64_1%3a17.0.6-21_arm64.deb ... 98s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... 99s Selecting previously unselected package libamd-comgr2:arm64. 99s Preparing to unpack .../13-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 99s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 99s Selecting previously unselected package libhsakmt1:arm64. 99s Preparing to unpack .../14-libhsakmt1_5.7.0-1build1_arm64.deb ... 99s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 99s Selecting previously unselected package libhsa-runtime64-1. 99s Preparing to unpack .../15-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 99s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 99s Selecting previously unselected package libamdhip64-5. 99s Preparing to unpack .../16-libamdhip64-5_5.7.1-5build1_arm64.deb ... 99s Unpacking libamdhip64-5 (5.7.1-5build1) ... 99s Selecting previously unselected package libibumad3:arm64. 99s Preparing to unpack .../17-libibumad3_56.0-4ubuntu1_arm64.deb ... 99s Unpacking libibumad3:arm64 (56.0-4ubuntu1) ... 99s Selecting previously unselected package libibmad5:arm64. 99s Preparing to unpack .../18-libibmad5_56.0-4ubuntu1_arm64.deb ... 99s Unpacking libibmad5:arm64 (56.0-4ubuntu1) ... 99s Selecting previously unselected package libucx0:arm64. 99s Preparing to unpack .../19-libucx0_1.18.1+ds-2_arm64.deb ... 99s Unpacking libucx0:arm64 (1.18.1+ds-2) ... 99s Selecting previously unselected package libopenmpi40:arm64. 99s Preparing to unpack .../20-libopenmpi40_5.0.7-1_arm64.deb ... 99s Unpacking libopenmpi40:arm64 (5.0.7-1) ... 99s Selecting previously unselected package hyphy-mpi. 99s Preparing to unpack .../21-hyphy-mpi_2.5.68+dfsg-1_arm64.deb ... 99s Unpacking hyphy-mpi (2.5.68+dfsg-1) ... 99s Selecting previously unselected package hyphy-pt. 99s Preparing to unpack .../22-hyphy-pt_2.5.68+dfsg-1_arm64.deb ... 99s Unpacking hyphy-pt (2.5.68+dfsg-1) ... 99s Setting up libpciaccess0:arm64 (0.17-3build1) ... 99s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 99s Setting up libibumad3:arm64 (56.0-4ubuntu1) ... 99s Setting up libibmad5:arm64 (56.0-4ubuntu1) ... 99s Setting up hyphy-common (2.5.68+dfsg-1) ... 99s Setting up libgomp1:arm64 (15-20250404-0ubuntu1) ... 99s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 99s Setting up libmunge2:arm64 (0.5.16-1) ... 99s Setting up libllvm17t64:arm64 (1:17.0.6-21) ... 99s Setting up libhwloc15:arm64 (2.12.0-1) ... 99s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 99s Setting up librdmacm1t64:arm64 (56.0-4ubuntu1) ... 99s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 99s Setting up libhsakmt1:arm64 (5.7.0-1build1) ... 99s Setting up libfabric1:arm64 (1.17.0-3.1) ... 99s Setting up hyphy-pt (2.5.68+dfsg-1) ... 99s Setting up libhwloc-plugins:arm64 (2.12.0-1) ... 99s Setting up libpmix2t64:arm64 (5.0.6-5) ... 99s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 99s Setting up libamdhip64-5 (5.7.1-5build1) ... 99s Setting up libucx0:arm64 (1.18.1+ds-2) ... 99s Setting up libopenmpi40:arm64 (5.0.7-1) ... 99s Setting up hyphy-mpi (2.5.68+dfsg-1) ... 99s Processing triggers for libc-bin (2.41-6ubuntu1) ... 99s Processing triggers for man-db (2.13.0-1) ... 101s autopkgtest [10:38:59]: test run-unit-tests: [----------------------- 101s + for i in *.bf 101s + '[' -f ExonIntron.bf ']' 101s + hyphy ExonIntron.bf 102s Log Likelihood = -1113.34521787068; 102s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04135183085920264,(ZMUBIS27F:0,(ZMU29160:0.05439916153581031,ZMU29161:0.03971476615086916)Node8:0.01201900680705795)Node6:0)Node4:0.02459453967209719,BLYMUB1:0.0118616932053593); 102s Tree exon2Tree=(BLYMUB2:0.03542650072799974,(RICRMA630:0.02936152040963665,(ZMUBIS27F:0.0754804832053237,(ZMU29160:0.09106755210696099,ZMU29161:0.02590433222726088)Node8:0.01160289900113295)Node6:0.04930238309639432)Node4:0.02931466908914161,BLYMUB1:0.02204839981684653); 102s Tree intronTree=(BLYMUB2:0.03120554762248988,(RICRMA630:0.04156298777153747,(ZMUBIS27F:0.02044281560866124,(ZMU29160:0.02068874963897275,ZMU29161:0.01019740861952591)Node8:0.02069020549812875)Node6:0)Node4:0,BLYMUB1:0.01036532979958632); 102s + for i in *.bf 102s + '[' -f F81.bf ']' 102s + hyphy F81.bf 102s Log Likelihood = -1187.54703200711; 102s Tree givenTree=(256:0.01194157029282157,(822:0.0294535129530677,159:0.004470257088560238)Node2:0.003650055643926021,((113:0.02245388893339007,9939:0.07632630074490825)Node6:0.005078256026041796,(6760:0.06905819398735637,((317:0.03753835926185371,6767:0.07080218303646955)Node12:0.01229495343907191,((135:0.02047826937583377,(529:0.03338945320587338,105r:0.01321509437910577)Node18:0.02585928039409023)Node16:0.005410805240813846,(719:0.02967303154671798,136:0.008233024490714645)Node21:0.0488425321589614)Node15:0.01526772770290489)Node11:0.01379471890416059)Node9:0.02422003803814451)Node5:0.02149671376935503); 102s + for i in *.bf 102s + '[' -f F81relrate.bf ']' 102s + hyphy F81relrate.bf 102s 102s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.00100432925; 102s Tree threeTaxaTree=(a:0.08503862548226503,b:0.07334966611435387,c:0.1653229739494681); 102s 102s 102s 1). With the outgroup at taxon #1, the P-value is:0.002155111413028155 102s Log Likelihood = -948.707254543121; 102s Tree threeTaxaTree=(a:0.08232758522307435,b:0.1194341760905557,c:0.1194341760905557); 102s 102s 102s 2). With the outgroup at taxon #2, the P-value is:0.008353507893403056 102s Log Likelihood = -947.479041953643; 102s Tree threeTaxaTree=(a:0.1251764628080267,b:0.07126598668696901,c:0.1251764628080267); 102s 102s 102s 3). With the outgroup at taxon #3, the P-value is:0.6669136542305252 102s Log Likelihood = -944.093621107699; 102s Tree threeTaxaTree=(a:0.07918239880943308,b:0.07918239880943308,c:0.1653649517155191); 102s + for i in *.bf 102s + '[' -f F81relratio.bf ']' 102s + hyphy F81relratio.bf 102s 102s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059588138; 102s Tree fourTaxaTree1=((1:0.1129136787070425,2:0.1073284341681706)Node1:0.09981582481894515,3:0.3469184600765389,4:0.3218847023395098); 102s Tree fourTaxaTree2=((1:0.08585401408054617,2:0.09337672170473514)Node1:0.07363354745490575,3:0.3933488434280245,4:0.380193911034473); 102s 102s 102s 1). Relative ratio constraint; the P-value is:0.6932596818791188 102s Log Likelihood = -2575.74636482147; 102s Global Parameters: 102s R=1.005331648092245; 102s 102s Tree fourTaxaTree1=((1:0.09950107525140325,2:0.09952545024307487)Node1:0.08689424973463246,3:0.3693259754981048,4:0.3496333467621813); 102s Tree fourTaxaTree2=((1:0.09989658869399061,2:0.09992106057543797)Node1:0.08723965146789771,3:0.3707940338847817,4:0.3510231276089898); 102s + for i in *.bf 102s + '[' -f HKY85.bf ']' 102s + hyphy HKY85.bf 102s + for i in *.bf 102s + '[' -f HKY852blocks.bf ']' 102s + hyphy HKY852blocks.bf 102s Log Likelihood = -1152.88077834192; 102s Tree givenTree=(256:0.01162422800940009,(822:0.0298064959168288,159:0.004016578082570039)Node2:0.003751040185758832,((113:0.02130156459738439,9939:0.07786164689466689)Node6:0.004320097464722544,(6760:0.07314675150289161,((317:0.03809749579941498,6767:0.07103934249876631)Node12:0.006276017377168555,((135:0.01788765699286442,(529:0.03258473801190466,105r:0.01513842854201236)Node18:0.02833445653444989)Node16:0.007922004309421369,(719:0.02987921490116244,136:0.008041800694511542)Node21:0.04861604620008795)Node15:0.01598577297521521)Node11:0.01658539907131414)Node9:0.02665217597063236)Node5:0.02296628600172863); 102s 102s ----- RESULTS ----- 102s Log Likelihood = -6801.91479154369; 102s Tree actinTree1=(ZMU60513:0,ZMU60514:0.0105022936163165,((((((ZMU60511:0.01039879501362062,ZMU60510:0.02379617014902878)Node8:0.0834671118349504,OSRAC2:0.1885132265473414)Node7:0.05842006387014208,(OSRAC1:0.01535844847628616,SVSOAC1:0.07342930649614356)Node12:0.07290684101699392)Node6:0,((OSRAC3:0.07326182718305675,ZMU60507:0.06502635709866447)Node16:0.07976126239603164,ZMU60509:0.1289303908338587)Node15:0.001266015419780168)Node5:0.08267782651968814,(MZEACT1G:0.1142644834006327,OSRAC7:0.03422182170061312)Node20:0)Node4:0.105902948244735,ZMU60508:0.01700989088607593)Node3:0.05973117337625355); 102s Tree actinTree2=(ZMU60513:0.01013762204452443,ZMU60514:0.02362644626344624,((((((ZMU60511:0.03959555442464854,ZMU60510:0.02871061867306718)Node8:0.04600206706588217,OSRAC2:0.1281449897540325)Node7:0.02274125352059881,(OSRAC1:0.04040030091964288,SVSOAC1:0.05533587402374272)Node12:0.09056069319186402)Node6:0.02100608136178184,((OSRAC3:0.1082347722817344,ZMU60507:0.07346477449960043)Node16:0.05601726909550347,ZMU60509:0.1117727379571227)Node15:0.02915964228007881)Node5:0.04982863230401366,(MZEACT1G:0.1070058877603888,OSRAC7:0.09561860832543509)Node20:0.02268275899614722)Node4:0.04830935831128602,ZMU60508:0.02346427964480509)Node3:0.05653279292861778); 102s + for i in *.bf 102s + '[' -f HKY852blocks2models.bf ']' 102s + hyphy HKY852blocks2models.bf 102s 102s ----- RESULTS ----- 102s Log Likelihood = -6049.33430814106; 102s Tree actinTree1=(ZMU60513:0.01367587021403297,ZMU60514:0.06665920100449091,((((((ZMU60511:0.1014640954485428,ZMU60510:0.08944656076199245)Node8:0.2110888775123181,OSRAC2:0.3685049117741519)Node7:0.06394907628990368,(OSRAC1:0.04344899455321651,SVSOAC1:0.2449014676843651)Node12:0.4077786239468916)Node6:0.1003520215525063,((OSRAC3:0.1861497832773748,ZMU60507:0.3290590106537706)Node16:0.1591658865946541,ZMU60509:0.4443739252398894)Node15:0.04672955052519808)Node5:0.1894652217069437,(MZEACT1G:0.3244015584644229,OSRAC7:0.2477178070747944)Node20:0.009397304202882954)Node4:0.2662699930631933,ZMU60508:0.01033505098341177)Node3:0.2231171691705898); 102s Tree actinTree2=(ZMU60513:0.004498122558609297,ZMU60514:0.004483617402188215,((((((ZMU60511:0.00448258310880263,ZMU60510:0.005994558104449228)Node8:0.004874237165218833,OSRAC2:0.04746946928184934)Node7:0.003177874854621349,(OSRAC1:0.01209800098589918,SVSOAC1:0.007445359455393925)Node12:0.02730480434508033)Node6:0,((OSRAC3:0.04645235420348161,ZMU60507:0.009176465423083695)Node16:0.01045616828935878,ZMU60509:0.02448213439990488)Node15:0)Node5:0.01928018551227443,(MZEACT1G:0.03381565368666793,OSRAC7:0.03063271899567869)Node20:0.006213231678008959)Node4:0.007802704632045594,ZMU60508:0.004488393458859802)Node3:0.01512041561936696); 102s + for i in *.bf 102s + '[' -f HKY85relrate.bf ']' 102s + hyphy HKY85relrate.bf 102s 102s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371749483469; 102s Tree threeTaxaTree=(a:0.08472934038033358,b:0.07472890300982593,c:0.1740758557870929); 102s 102s 102s 1). Outgroup at taxon #1 102s a). Transition rate test. P-Value = 0.02098223878918115 102s Log Likelihood = -924.035882967928; 102s Tree threeTaxaTree=(a:0.08098747101852473,b:0.1064791186102118,c:0.1431094353080285); 102s 102s b). Transversion rate test. P-Value = 0.03655151929304512 102s Log Likelihood = -923.5573430455; 102s Tree threeTaxaTree=(a:0.08440222761985641,b:0.09108469950044172,c:0.1578859973747284); 102s 102s c). Both rates test. P-Value = 0.00632398552562452 102s Log Likelihood = -926.43515513196; 102s Tree threeTaxaTree=(a:0.08053673509578729,b:0.1248013468424451,c:0.1248013468424451); 102s 102s 102s 2). Outgroup at taxon #2 102s a). Transition rate test. P-Value = 0.02758027431599952 102s Log Likelihood = -923.79880651846; 102s Tree threeTaxaTree=(a:0.1158226503923256,b:0.07099209475261896,c:0.1443144818772613); 102s 102s b). Transversion rate test. P-Value = 0.1106459022191807 102s Log Likelihood = -922.644235271599; 102s Tree threeTaxaTree=(a:0.0976153100890622,b:0.07460630242365376,c:0.1609740142295277); 102s 102s c). Both rates test. P-Value = 0.02199510305637498 102s Log Likelihood = -925.188684922268; 102s Tree threeTaxaTree=(a:0.129915554411235,b:0.07082227006071581,c:0.129915554411235); 102s 102s 102s 3). Outgroup at taxon #3 102s a). Transition rate test. P-Value = 0.929141241087608 102s Log Likelihood = -921.375703341946; 102s Tree threeTaxaTree=(a:0.08355046076788929,b:0.07588581166790749,c:0.1740233672195783); 102s 102s b). Transversion rate test. P-Value = 0.5919912460093371 102s Log Likelihood = -921.515372127867; 102s Tree threeTaxaTree=(a:0.08113263883022565,b:0.07836683153370519,c:0.1741501079879088); 102s 102s c). Both rates test. P-Value = 0.8615417730720499 102s Log Likelihood = -921.520781218885; 102s Tree threeTaxaTree=(a:0.07975961348011378,b:0.07975961348011378,c:0.1741085573531514); 102s + for i in *.bf 102s + '[' -f HKY85relratio.bf ']' 102s + hyphy HKY85relratio.bf 102s 102s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.7844843755; 102s Tree fourTaxaTree1=((1:0.113747118745326,2:0.1109458249410974)Node1:0.1040858994385215,3:0.3524244723962854,4:0.3313458952678868); 102s Tree fourTaxaTree2=((1:0.08600483225827231,2:0.09359049729591006)Node1:0.08009543568058149,3:0.3858472367032365,4:0.3893811357657444); 102s 102s 102s 1). Relative ratio constraint on transitions; the P-value is:0.5738793600613836 102s Log Likelihood = -2541.23688980524; 102s Global Parameters: 102s R=0.8580636535067874; 102s 102s Tree fourTaxaTree1=((1:0.1087236130713008,2:0.09418261984146842)Node1:0.1115257374894883,3:0.3554308458607288,4:0.355232115177667); 102s Tree fourTaxaTree2=((1:0.09042940258132161,2:0.1091728098911587)Node1:0.07297293899937203,3:0.3839422993994727,4:0.3657415474100672); 102s 102s 102s 2). Relative ratio constraint on transversions; the P-value is:0.5738082324062876 102s Log Likelihood = -2541.23709908944; 102s Global Parameters: 102s R=0.8594124037576297; 102s 102s Tree fourTaxaTree1=((1:0.1087000694778133,2:0.09418985346020967)Node1:0.1117932119392115,3:0.3553746262439924,4:0.354771281236924); 102s Tree fourTaxaTree2=((1:0.09045801827248318,2:0.1092779809051462)Node1:0.07330035294529942,3:0.3842167417701483,4:0.3653957424492018); 102s 102s 102s 3). Relative ratio constraint on both rates; the P-value is:0.6566040383574479 102s Log Likelihood = -2543.19087645005; 102s Global Parameters: 102s R=0.9965230507486695; 102s 102s Tree fourTaxaTree1=((1:0.1004920690695875,2:0.1006762597910992)Node1:0.09259566697792666,3:0.3715109983982421,4:0.3581727450823879); 102s Tree fourTaxaTree2=((1:0.1003260530987093,2:0.1006688819883479)Node1:0.09288905947879754,3:0.3699541785547111,4:0.3576403474196995); 102s + for i in *.bf 102s + '[' -f HKY85shared.bf ']' 102s + hyphy HKY85shared.bf 102s Log Likelihood = -1165.70263636904; 102s Global Parameters: 102s R=2.979768058888189; 102s 102s Tree givenTree=(256:0.01208746823040377,(822:0.02961549886079614,159:0.004650946685559539)Node2:0.003522500915745789,((113:0.02179055771217426,9939:0.07946684158204975)Node6:0.00490738878035854,(6760:0.07150894960976234,((317:0.03799709410841506,6767:0.07150374338737829)Node12:0.01178540053109108,((135:0.02023004728614681,(529:0.0340563405430892,105r:0.01304907597682716)Node18:0.0263037216654483)Node16:0.005817634047290761,(719:0.02974526921171435,136:0.0081274539431533)Node21:0.04878635909505885)Node15:0.01555561535424805)Node11:0.01396339163281847)Node9:0.02325795966617287)Node5:0.02146718776910613); 102s + for i in *.bf 102s + '[' -f JC69.bf ']' 102s + hyphy JC69.bf 102s Log Likelihood = -1227.45123365416; 102s Tree givenTree=(256:0.01208696699306479,(822:0.02897007114976642,159:0.004657405757303415)Node2:0.003647035496735427,((113:0.02417514457362857,9939:0.07266454132609425)Node6:0.005833876367913781,(6760:0.06389376252119899,((317:0.04027897723569238,6767:0.06820677033153537)Node12:0.0144229774036915,((135:0.02428976199147378,(529:0.03327882357577603,105r:0.01296768393213606)Node18:0.01987279688327634)Node16:0.003610886705075024,(719:0.02785585494023452,136:0.009989733700737668)Node21:0.05116660036817344)Node15:0.01669646870630283)Node11:0.008467916018555529)Node9:0.02635252624649967)Node5:0.02073905481887288); 102s + for i in *.bf 102s + '[' -f K2P.bf ']' 102s + hyphy K2P.bf 102s Log Likelihood = -1198.26195968392; 102s Tree givenTree=(256:0.01176775193373103,(822:0.02927198630323601,159:0.004289897859515186)Node2:0.00366679887604105,((113:0.0236492969691756,9939:0.07263496230122923)Node6:0.003385248318772331,(6760:0.06222507593736217,((317:0.04073403728338189,6767:0.06828641356406272)Node12:0.01246127292330918,((135:0.02262882049775222,(529:0.03393140552960146,105r:0.01240146666937718)Node18:0.02140651774331342)Node16:0.004487018454802943,(719:0.02880164757314709,136:0.008846375392006754)Node21:0.05081174045118453)Node15:0.01733237213870967)Node11:0.0110591382645945)Node9:0.02821203006953314)Node5:0.02370773244465459); 102s + for i in *.bf 102s + '[' -f K2Pshared.bf ']' 102s + hyphy K2Pshared.bf 102s Log Likelihood = -1210.49410568055; 102s Global Parameters: 102s R=2.61937093433396; 102s 102s Tree givenTree=(256:0.01221904570324982,(822:0.02897582197814318,159:0.004777339139653893)Node2:0.003545957411603266,((113:0.02375587063508624,9939:0.07495471320197752)Node6:0.005887353385372873,(6760:0.06492979336274539,((317:0.03970085525313312,6767:0.06948858885421863)Node12:0.01422959937526332,((135:0.0238954251497315,(529:0.03395941029747046,105r:0.0126280960245586)Node18:0.0207200523750398)Node16:0.003966885627478393,(719:0.02813867645070166,136:0.009501536723275755)Node21:0.05080332007439338)Node15:0.01659015744021779)Node11:0.008799343836035058)Node9:0.02626539813698893)Node5:0.02011348712923801); 102s + for i in *.bf 102s + '[' -f MatrixIndexing.bf ']' 102s + hyphy MatrixIndexing.bf 102s 102s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 102s { 102s {0.2009806216696698, 0.4329595068546384, 0.3136500628464041, 0.5233550315078709, 0.0615716227473625, 0.4718661891463832} 102s {0.2097056604013093, 0.000496820779632968, 0.5872768153406859, 0.5393260520741637, 0.6762634838643166, 0.8693022345819749} 102s {0.4390131292024192, 0.9049526820669306, 0.5948747151053685, 0.3469571018002362, 0.8990904162402941, 0.2424444016633659} 102s {0.6369517621670272, 0.8614093684268671, 0.2452551255107986, 0.1582448922931787, 0.1769870145192805, 0.2911706981927088} 102s {0.9545574355764681, 0.6486512875763353, 0.8888784455808062, 0.3598908482491716, 0.01830399758608639, 0.9804181416939055} 102s } 102s 102s 2). Accessing a second-row third-column element and a random element. 102s 102s matrix[1][2]=0.5872768153406859 102s matrix[4][0]=0.9545574355764681 102s 102s 3). Accessing the fourth row. 102s 102s matrix[3][-1]= 102s { 102s {0.6369517621670272, 0.8614093684268671, 0.2452551255107986, 0.1582448922931787, 0.1769870145192805, 0.2911706981927088} 102s } 102s 102s 4). Accessing the first column. 102s 102s matrix[-1][0]= 102s { 102s {0.2009806216696698} 102s {0.2097056604013093} 102s {0.4390131292024192} 102s {0.6369517621670272} 102s {0.9545574355764681} 102s } 102s 102s 5). Populating a matrix template (below the diagonal). 102s 102s { 102s {0, 0, 0, 0, 0, 0} 102s {1, 0, 0, 0, 0, 0} 102s {1, 1, 0, 0, 0, 0} 102s {1, 1, 1, 0, 0, 0} 102s {1, 1, 1, 1, 0, 0} 102s } 102s 102s 6). Extracting (by row) matrix elements using the template. 102s 102s { 102s {0.2097056604013093, 0.4390131292024192, 0.9049526820669306, 0.6369517621670272, 0.8614093684268671, 0.2452551255107986, 0.9545574355764681, 0.6486512875763353, 0.8888784455808062, 0.3598908482491716} 102s } 102s 102s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 102s 102s matrix[{{1,1}}][{{3,2}}]= 102s { 102s {0.000496820779632968, 0.5872768153406859} 102s {0.9049526820669306, 0.5948747151053685} 102s {0.8614093684268671, 0.2452551255107986} 102s } 102s 102s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 102s 102s 102s { 102s {0.04039321028672694, 1.187453934575812, 1.098376361923553, 1.273900489004605, 1.003791064727743, 1.22265770045953} 102s {0.04397646400434926, 2.468308870751102e-07, 1.344894057836698, 1.290872590445904, 1.457332299608303, 1.755686375049215} 102s {0.1927325276121001, 0.8189393567801312, 0.3538759266716933, 1.120379230489619, 1.808363576575145, 1.058779287897907} 102s {0.4057075473276812, 0.7420261000135741, 0.06015007658931756, 0.02504144593687972, 1.031324403308448, 1.084780375486029} 102s {0.9111798978143231, 0.4207484928744376, 0.7901048910181503, 0.1295214226535083, 0.0003350363276314564, 1.961219732562531} 102s } 102s + for i in *.bf 102s + '[' -f MolecularClockF81.bf ']' 102s + hyphy MolecularClockF81.bf 102s 102s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124484594; 102s Tree theTree=(HVRNASS:0.02574919648607212,(RICRSS3:0.05627816138226531,((ZMSUCS1:0.07162024950106163,(OSRSS1A:0.06060618455025174,(TASUCSYN1:0.027881215970532,HVSSYNMR:0.02036946398772769)Internal1:0.05183456821889493)Node9:0.02014947575448358)Node7:0.158157289963955,(MZESUS1:0.07665747345170898,ORRSS2:0.05437772138326097)Internal2:0.02505248150682185)Node6:0.03255835314153621)Node4:0.05900617333429104,TAAJ153:0.01372210943158847); 102s 102s 102s 1). Global Molecular Clock; the P-value is:0 102s Log Likelihood = -11927.6152872483; 102s Tree theTree=(HVRNASS:0.02158166537353416,(RICRSS3:0.1233407363293412,((ZMSUCS1:0.05658071389824054,(OSRSS1A:0.0475112127520667,(TASUCSYN1:0.01824268051258092,HVSSYNMR:0.01824268051258092)Internal1:0.02926853223948578)Node9:0.009069501146173827)Node7:0.05763375083170364,(MZESUS1:0.07014762063876324,ORRSS2:0.07014762063876324)Internal2:0.04406684409118095)Node6:0.009126271599397006)Node4:0.02714857900690002,TAAJ153:0.1504893153362412); 103s 103s 103s 2). Molecular Clock starting at Internal1; the P-value is:0.160383605481566 103s Log Likelihood = -11476.6977512132; 103s Tree theTree=(HVRNASS:0.02574923709386281,(RICRSS3:0.05631403470116046,((ZMSUCS1:0.07170242086589627,(OSRSS1A:0.06051952696113196,(TASUCSYN1:0.02412397321145326,HVSSYNMR:0.02412397321145326)Internal1:0.05181347762551923)Node9:0.02018328958798754)Node7:0.1580767323832735,(MZESUS1:0.0766292019073662,ORRSS2:0.05441997799520763)Internal2:0.02508919186761595)Node6:0.03253193166955858)Node4:0.05897663116459115,TAAJ153:0.01372512844178986); 103s 103s 103s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610220638412008 103s Log Likelihood = -11479.8412474333; 103s Tree theTree=(HVRNASS:0.02577440764445427,(RICRSS3:0.05652985135275369,((ZMSUCS1:0.07147569225397804,(OSRSS1A:0.06061741282007693,(TASUCSYN1:0.02412260586497607,HVSSYNMR:0.02412260586497607)Internal1:0.05167997155761957)Node9:0.02036525018658264)Node7:0.158048818558748,(MZESUS1:0.0655345032290231,ORRSS2:0.0655345032290231)Internal2:0.02502717192031903)Node6:0.03236307024441316)Node4:0.0587445626600898,TAAJ153:0.01369828183438261); 103s + for i in *.bf 103s + '[' -f MolecularClockHKY85.bf ']' 103s + hyphy MolecularClockHKY85.bf 103s 103s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013168625; 103s Tree theTree=(HVRNASS:0.02587788288251212,(RICRSS3:0.05729259232813572,((ZMSUCS1:0.07271757470520503,(OSRSS1A:0.0609603088820527,(TASUCSYN1:0.02742675765933433,HVSSYNMR:0.02082543203892538)Node11:0.05283733261135826)Node9:0.02051371573021432)Node7:0.1590158574773157,(MZESUS1:0.07762572611879924,ORRSS2:0.05414486743885145)Node14:0.02601392415348987)Node6:0.03166985009668821)Node4:0.06041495117958786,TAAJ153:0.01384537552860272); 103s 103s 103s 1). Global Molecular Clock on transition rates; the P-value is:0 103s Log Likelihood = -11434.7016277317; 103s Tree theTree=(HVRNASS:0.02319852159761046,(RICRSS3:0.08333770536289575,((ZMSUCS1:0.06367115532975487,(OSRSS1A:0.05486245484878419,(TASUCSYN1:0.02325250841749454,HVSSYNMR:0.01890428713313991)Node11:0.04017750329132259)Node9:0.01327920201331256)Node7:0.1274462001743527,(MZESUS1:0.07239740737469204,ORRSS2:0.06226852904302001)Node14:0.03461587981067927)Node6:0.02067728954662343)Node4:0.03899762275745917,TAAJ153:0.08891418442074604); 103s 103s 103s 2). Global Molecular Clock on transversion rates; the P-value is:0 103s Log Likelihood = -11497.3782424388; 103s Tree theTree=(HVRNASS:0.02484414911780173,(RICRSS3:0.09398480834078647,((ZMSUCS1:0.069013958801922,(OSRSS1A:0.05468852330565803,(TASUCSYN1:0.02277004089759159,HVSSYNMR:0.02034704213766093)Node11:0.04373152337244427)Node9:0.01673398203735326)Node7:0.09973503047413095,(MZESUS1:0.07447325611514773,ORRSS2:0.06134761725046766)Node14:0.0338713427740145)Node6:0.02079759999415707)Node4:0.05008306464669197,TAAJ153:0.07305937714293841); 103s 103s 103s 3). Global Molecular Clock on both rates; the P-value is:0 103s Log Likelihood = -11703.626215866; 103s Tree theTree=(HVRNASS:0.02210036210473236,(RICRSS3:0.1239726140322025,((ZMSUCS1:0.05800841498003178,(OSRSS1A:0.04855580570414324,(TASUCSYN1:0.01834859550830333,HVSSYNMR:0.01834859550830333)Node11:0.03020721019583991)Node9:0.009452609275888528)Node7:0.0573053370982733,(MZESUS1:0.07024259700058169,ORRSS2:0.07024259700058169)Node14:0.04507115507772341)Node6:0.008658861953897404)Node4:0.02800775016213151,TAAJ153:0.151980364194334); 103s + for i in *.bf 103s + '[' -f Non-Rev.bf ']' 103s + hyphy Non-Rev.bf 103s Log Likelihood = -1152.80136563237; 103s Global Parameters: 103s GC=0.262883427236119; 103s CG=0.1862817610820183; 103s GA=1.878232008606248; 103s CT=1.253788798920075; 103s GT=0.08612587785147405; 103s CA=0.9071695538490665; 103s AT=0.4206536771544395; 103s AG=1.554495534323564; 103s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2554048918651579; 103s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.014057174331081; 103s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7858051461143387; 103s 103s Tree givenTree=(256:0.01341924426084246,(822:0.02845871642271768,159:0.006100543963924717)Node2:0.003450006798028214,((113:0.02186883739817506,9939:0.07936272233834009)Node6:0.005002045816627709,(6760:0.07330951280120193,((317:0.04007593030789284,6767:0.06984969697089105)Node12:0.01160994480421898,((135:0.02155402303174485,(529:0.03497234659405505,105r:0.01426031143786104)Node18:0.02374995110506308)Node16:0.005225805383438134,(719:0.02860511411827493,136:0.009603216330747691)Node21:0.04929017401603077)Node15:0.01634326719298295)Node11:0.01268863276395244)Node9:0.02194623522399064)Node5:0.02029439770799657); 103s + for i in *.bf 103s + '[' -f PBootstrapHetRates.bf ']' 103s + hyphy PBootstrapHetRates.bf 103s 103s ----ORIGINAL DATA---- 103s Log Likelihood = -1127.31556165166; 103s Global Parameters: 103s alpha=0.3189682402870834; 103s kappa=0.3233533371893831; 103s 103s Tree givenTree=(256:0.0125904692435069,(822:0.03174476570809336,159:0.004697634911122133)Node2:0.003783383031658003,((113:0.02290965815032718,9939:0.09715473646398903)Node6:0.001963738303768692,(6760:0.0871900946662589,((317:0.04572724580225067,6767:0.08112444672934985)Node12:0.007406354349506197,((135:0.01864200545024668,(529:0.0369543825305891,105r:0.01499426752668652)Node18:0.03035222155464236)Node16:0.007151383664886771,(719:0.03340039755286732,136:0.00716634644269905)Node21:0.05752461268867921)Node15:0.01788686285916396)Node11:0.01883448548779759)Node9:0.02369757404525938)Node5:0.02500400557281433); 103s 103s Using the seed: 103s 1746184599 103s Category variable name: TRUE 103s Site Rate 103s 0 0.00000 103s 1 0.00000 103s 2 0.00000 103s 3 0.00000 103s 4 0.00001 103s 5 0.00001 103s 6 0.00001 103s 7 0.00003 103s 8 0.00003 103s 9 0.00004 103s 10 0.00004 103s 11 0.00005 103s 12 0.00006 103s 13 0.00007 103s 14 0.00007 103s 15 0.00017 103s 16 0.00020 103s 17 0.00030 103s 18 0.00032 103s 19 0.00038 103s 20 0.00069 103s 21 0.00077 103s 22 0.00083 103s 23 0.00084 103s 24 0.00091 103s 25 0.00102 103s 26 0.00121 103s 27 0.00171 103s 28 0.00188 103s 29 0.00194 103s 30 0.00208 103s 31 0.00211 103s 32 0.00217 103s 33 0.00221 103s 34 0.00264 103s 35 0.00340 103s 36 0.00374 103s 37 0.00414 103s 38 0.00509 103s 39 0.00572 103s 40 0.00638 103s 41 0.00642 103s 42 0.00816 103s 43 0.00930 103s 44 0.00950 103s 45 0.01072 103s 46 0.01370 103s 47 0.01374 103s 48 0.01408 103s 49 0.01548 103s 50 0.01650 103s 51 0.01660 103s 52 0.01867 103s 53 0.01869 103s 54 0.01892 103s 55 0.01969 103s 56 0.02013 103s 57 0.02182 103s 58 0.02335 103s 59 0.02348 103s 60 0.02370 103s 61 0.02485 103s 62 0.02507 103s 63 0.02859 103s 64 0.03145 103s 65 0.03243 103s 66 0.03662 103s 67 0.03835 103s 68 0.03977 103s 69 0.04031 103s 70 0.04116 103s 71 0.04221 103s 72 0.04356 103s 73 0.04838 103s 74 0.05054 103s 75 0.05395 103s 76 0.05413 103s 77 0.05449 103s 78 0.05809 103s 79 0.05997 103s 80 0.06506 103s 81 0.06755 103s 82 0.06757 103s 83 0.06815 103s 84 0.06837 103s 85 0.06956 103s 86 0.07286 103s 87 0.07348 103s 88 0.07706 103s 89 0.07787 103s 90 0.08240 103s 91 0.08299 103s 92 0.08376 103s 93 0.08598 103s 94 0.08620 103s 95 0.08852 103s 96 0.08879 103s 97 0.09983 103s 98 0.10164 103s 99 0.10681 103s 100 0.10702 103s 101 0.11246 103s 102 0.11265 103s 103 0.11414 103s 104 0.11544 103s 105 0.12549 103s 106 0.14368 103s 107 0.14415 103s 108 0.15008 103s 109 0.15180 103s 110 0.15318 103s 111 0.16086 103s 112 0.16107 103s 113 0.16405 103s 114 0.16500 103s 115 0.16588 103s 116 0.16741 103s 117 0.17713 103s 118 0.17747 103s 119 0.18044 103s 120 0.18454 103s 121 0.19531 103s 122 0.19588 103s 123 0.20138 103s 124 0.20259 103s 125 0.20935 103s 126 0.21002 103s 127 0.21753 103s 128 0.22254 103s 129 0.22600 103s 130 0.22847 103s 131 0.24889 103s 132 0.25170 103s 133 0.25232 103s 134 0.25477 103s 135 0.25865 103s 136 0.26025 103s 137 0.26317 103s 138 0.26615 103s 139 0.27264 103s 140 0.27397 103s 141 0.27749 103s 142 0.29043 103s 143 0.31238 103s 144 0.32683 103s 145 0.33142 103s 146 0.34853 103s 147 0.35483 103s 148 0.35668 103s 149 0.36204 103s 150 0.36208 103s 151 0.37748 103s 152 0.37881 103s 153 0.38537 103s 154 0.39415 103s 155 0.40763 103s 156 0.43652 103s 157 0.44332 103s 158 0.46337 103s 159 0.46907 103s 160 0.47057 103s 161 0.47177 103s 162 0.48324 103s 163 0.51326 103s 164 0.51439 103s 165 0.52920 103s 166 0.53867 103s 167 0.54819 103s 168 0.55022 103s 169 0.56148 103s 170 0.56979 103s 171 0.57731 103s 172 0.57778 103s 173 0.58270 103s 174 0.58657 103s 175 0.59464 103s 176 0.60262 103s 177 0.60832 103s 178 0.64242 103s 179 0.64805 103s 180 0.67552 103s 181 0.68840 103s 182 0.69648 103s 183 0.71046 103s 184 0.72392 103s 185 0.80223 103s 186 0.80718 103s 187 0.81054 103s 188 0.81954 103s 189 0.82827 103s 190 0.83071 103s 191 0.85689 103s 192 0.86618 103s 193 0.87387 103s 194 0.87674 103s 195 0.92083 103s 196 0.93955 103s 197 0.95464 103s 198 0.95649 103s 199 0.96668 103s 200 0.97906 103s 201 1.01210 103s 202 1.01709 103s 203 1.02400 103s 204 1.03014 103s 205 1.03146 103s 206 1.04030 103s 207 1.06577 103s 208 1.07581 103s 209 1.13842 103s 210 1.15496 103s 211 1.17412 103s 212 1.18415 103s 213 1.18433 103s 214 1.18949 103s 215 1.22031 103s 216 1.26295 103s 217 1.26392 103s 218 1.26875 103s 219 1.27250 103s 220 1.30926 103s 221 1.35013 103s 222 1.40451 103s 223 1.41724 103s 224 1.43525 103s 225 1.49767 103s 226 1.53245 103s 227 1.53653 103s 228 1.57172 103s 229 1.65578 103s 230 1.66248 103s 231 1.73782 103s 232 1.74748 103s 233 1.78097 103s 234 1.81476 103s 235 1.83017 103s 236 1.83192 103s 237 1.89919 103s 238 1.92224 103s 239 1.95777 103s 240 1.96617 103s 241 2.00626 103s 242 2.02462 103s 243 2.05914 103s 244 2.26416 103s 245 2.37005 103s 246 2.56102 103s 247 2.59273 103s 248 2.72346 103s 249 2.84283 103s 250 3.06064 103s 251 3.11322 103s 252 3.26938 103s 253 3.29003 103s 254 3.29345 103s 255 3.62700 103s 256 3.84148 103s 257 3.97092 103s 258 4.02364 103s 259 4.45792 103s 260 4.47453 103s 261 4.64859 103s 262 4.66059 103s 263 5.11639 103s 264 5.91975 103s 265 6.23672 103s 266 6.94553 103s 267 7.02200 103s 268 8.15938 103s 269 8.99379 103s 270 11.42475 103s 271 11.53828 103s 272 21.27008 103s 103s Mean = 0.9770990868462381 103s Var = 4.250494762925442 (1/alpha) = 3.135108370350486 103s + for i in *.bf 103s + '[' -f REV.bf ']' 103s + hyphy REV.bf 103s Log Likelihood = -1099.56653884928; 103s Tree givenTree=(256:0.01860402157369883,(822:0.02270203360589199,159:0.01094574774079271)Node2:0.003780101348180968,((113:0.01829166693394507,9939:0.07804702963665409)Node6:0.00745694312444042,(6760:0.07116621486097498,((317:0.03718908363543502,6767:0.07207157029598205)Node12:0.01018712590338517,((135:0.02037136336270045,(529:0.03424155837402473,105r:0.01130306446387673)Node18:0.02851211787624382)Node16:0.006574155278528049,(719:0.02831061788714248,136:0.009598487289384724)Node21:0.0440397072212266)Node15:0.01655916794574484)Node11:0.01315254475852026)Node9:0.02916035391082011)Node5:0.0137228884596951); 103s + for i in *.bf 103s + '[' -f REVshared.bf ']' 103s + hyphy REVshared.bf 103s Log Likelihood = -1156.62566882473; 103s Global Parameters: 103s AT=0.3612557717095673; 103s GT=0.4593298130117818; 103s CG=0.2458008750740302; 103s AG=1.841067885990832; 103s CT=1.198319596499986; 103s 103s Tree givenTree=(256:0.01207777355185686,(822:0.02972252751746349,159:0.00466983039031213)Node2:0.003489685034773888,((113:0.02209311613253883,9939:0.0798032618862848)Node6:0.004706754530751828,(6760:0.07207977756348634,((317:0.03906388632189382,6767:0.07101307589696332)Node12:0.01082398971097901,((135:0.02052071197747108,(529:0.03439888059496386,105r:0.01468354185491729)Node18:0.02466715963577982)Node16:0.005559323743095656,(719:0.02874522995643912,136:0.009475097392133506)Node21:0.0491206975183563)Node15:0.01582856760827148)Node11:0.01427609200343989)Node9:0.02298222981620111)Node5:0.02145840071070667); 103s + for i in *.bf 103s + '[' -f ReplicateConstraint1.bf ']' 103s + hyphy ReplicateConstraint1.bf 103s 1).Unconstrained HKY85 103s 103s Log Likelihood = -1152.88; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.317.trvs 103s Parameter 2 : hivTree.317.trst 103s Parameter 3 : hivTree.6767.trvs 103s Parameter 4 : hivTree.6767.trst 103s Parameter 5 : hivTree.Node2.trvs 103s Parameter 6 : hivTree.Node2.trst 103s Parameter 7 : hivTree.135.trvs 103s Parameter 8 : hivTree.135.trst 103s Parameter 9 : hivTree.529.trvs 103s Parameter 10 : hivTree.529.trst 103s Parameter 11 : hivTree.105r.trvs 103s Parameter 12 : hivTree.105r.trst 103s Parameter 13 : hivTree.Node8.trvs 103s Parameter 14 : hivTree.Node8.trst 103s Parameter 15 : hivTree.iNode1.trvs 103s Parameter 16 : hivTree.iNode1.trst 103s Parameter 17 : hivTree.719.trvs 103s Parameter 18 : hivTree.719.trst 103s Parameter 19 : hivTree.136.trvs 103s Parameter 20 : hivTree.136.trst 103s Parameter 21 : hivTree.Node11.trvs 103s Parameter 22 : hivTree.Node11.trst 103s Parameter 23 : hivTree.Node5.trvs 103s Parameter 24 : hivTree.Node5.trst 103s Parameter 25 : hivTree.Node1.trvs 103s Parameter 26 : hivTree.Node1.trst 103s Parameter 27 : hivTree.6760.trvs 103s Parameter 28 : hivTree.6760.trst 103s Parameter 29 : hivTree.113.trvs 103s Parameter 30 : hivTree.113.trst 103s Parameter 31 : hivTree.9939.trvs 103s Parameter 32 : hivTree.9939.trst 103s Parameter 33 : hivTree.Node16.trvs 103s Parameter 34 : hivTree.Node16.trst 103s Parameter 35 : hivTree.256.trvs 103s Parameter 36 : hivTree.256.trst 103s Parameter 37 : hivTree.822.trvs 103s Parameter 38 : hivTree.822.trst 103s Parameter 39 : hivTree.159.trvs 103s Parameter 40 : hivTree.159.trst 103s Parameter 41 : hivTree.Node21.trvs 103s Parameter 42 : hivTree.Node21.trst 103s Parameter 43 : hivTree.iNode2.trvs 103s Parameter 44 : hivTree.iNode2.trst 103s Parameter 45 : hivTree.Node15.trvs 103s Parameter 46 : hivTree.Node15.trst 103s 103s 2).HKY85 constrained to F81 103s 103s Log Likelihood = -1187.55; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.317.trvs 103s Parameter 2 : hivTree.6767.trvs 103s Parameter 3 : hivTree.Node2.trvs 103s Parameter 4 : hivTree.135.trvs 103s Parameter 5 : hivTree.529.trvs 103s Parameter 6 : hivTree.105r.trvs 103s Parameter 7 : hivTree.Node8.trvs 103s Parameter 8 : hivTree.iNode1.trvs 103s Parameter 9 : hivTree.719.trvs 103s Parameter 10 : hivTree.136.trvs 103s Parameter 11 : hivTree.Node11.trvs 103s Parameter 12 : hivTree.Node5.trvs 103s Parameter 13 : hivTree.Node1.trvs 103s Parameter 14 : hivTree.6760.trvs 103s Parameter 15 : hivTree.113.trvs 103s Parameter 16 : hivTree.9939.trvs 103s Parameter 17 : hivTree.Node16.trvs 103s Parameter 18 : hivTree.256.trvs 103s Parameter 19 : hivTree.822.trvs 103s Parameter 20 : hivTree.159.trvs 103s Parameter 21 : hivTree.Node21.trvs 103s Parameter 22 : hivTree.iNode2.trvs 103s Parameter 23 : hivTree.Node15.trvs 103s 103s Constrained Parameters List 103s 103s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 103s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 103s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 103s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 103s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 103s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 103s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 103s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 103s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 103s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 103s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 103s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 103s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 103s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 103s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 103s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 103s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 103s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 103s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 103s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 103s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 103s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 103s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 103s 103s 3).HKY85 constrained to F81 on internal branches 103s 103s Log Likelihood = -1167.99; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.Node2.trvs 103s Parameter 2 : hivTree.Node8.trvs 103s Parameter 3 : hivTree.iNode1.trvs 103s Parameter 4 : hivTree.Node11.trvs 103s Parameter 5 : hivTree.Node5.trvs 103s Parameter 6 : hivTree.Node1.trvs 103s Parameter 7 : hivTree.Node16.trvs 103s Parameter 8 : hivTree.Node21.trvs 103s Parameter 9 : hivTree.iNode2.trvs 103s Parameter 10 : hivTree.Node15.trvs 103s Parameter 11 : hivTree.317.trst 103s Parameter 12 : hivTree.317.trvs 103s Parameter 13 : hivTree.6767.trvs 103s Parameter 14 : hivTree.6767.trst 103s Parameter 15 : hivTree.135.trst 103s Parameter 16 : hivTree.135.trvs 103s Parameter 17 : hivTree.529.trvs 103s Parameter 18 : hivTree.529.trst 103s Parameter 19 : hivTree.105r.trst 103s Parameter 20 : hivTree.105r.trvs 103s Parameter 21 : hivTree.719.trvs 103s Parameter 22 : hivTree.719.trst 103s Parameter 23 : hivTree.136.trvs 103s Parameter 24 : hivTree.136.trst 103s Parameter 25 : hivTree.6760.trvs 103s Parameter 26 : hivTree.6760.trst 103s Parameter 27 : hivTree.113.trvs 103s Parameter 28 : hivTree.113.trst 103s Parameter 29 : hivTree.9939.trst 103s Parameter 30 : hivTree.9939.trvs 103s Parameter 31 : hivTree.256.trvs 103s Parameter 32 : hivTree.256.trst 103s Parameter 33 : hivTree.822.trvs 103s Parameter 34 : hivTree.822.trst 103s Parameter 35 : hivTree.159.trst 103s Parameter 36 : hivTree.159.trvs 103s 103s Constrained Parameters List 103s 103s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 103s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 103s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 103s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 103s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 103s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 103s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 103s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 103s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 103s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 103s 103s 4).HKY85 with shared ratio. 103s 103s Log Likelihood = -1165.7; 103s 103s Independent Parameters List 103s 103s Parameter 1 : R 103s Parameter 2 : hivTree.317.trst 103s Parameter 3 : hivTree.6767.trst 103s Parameter 4 : hivTree.Node2.trst 103s Parameter 5 : hivTree.135.trst 103s Parameter 6 : hivTree.529.trst 103s Parameter 7 : hivTree.105r.trst 103s Parameter 8 : hivTree.Node8.trst 103s Parameter 9 : hivTree.iNode1.trst 103s Parameter 10 : hivTree.719.trst 103s Parameter 11 : hivTree.136.trst 103s Parameter 12 : hivTree.Node11.trst 103s Parameter 13 : hivTree.Node5.trst 103s Parameter 14 : hivTree.Node1.trst 103s Parameter 15 : hivTree.6760.trst 103s Parameter 16 : hivTree.113.trst 103s Parameter 17 : hivTree.9939.trst 103s Parameter 18 : hivTree.Node16.trst 103s Parameter 19 : hivTree.256.trst 103s Parameter 20 : hivTree.822.trst 103s Parameter 21 : hivTree.159.trst 103s Parameter 22 : hivTree.Node21.trst 103s Parameter 23 : hivTree.iNode2.trst 103s Parameter 24 : hivTree.Node15.trst 103s 103s Constrained Parameters List 103s 103s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 103s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 103s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 103s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 103s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 103s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 103s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 103s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 103s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 103s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 103s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 103s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 103s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 103s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 103s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 103s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 103s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 103s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 103s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 103s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 103s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 103s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 103s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 103s + '[' -f ReplicateConstraint2.bf ']' 103s + hyphy ReplicateConstraint2.bf 103s 1).Unconstrained HKY85 103s 103s Log Likelihood = -1152.88; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.317.trvs 103s Parameter 2 : hivTree.317.trst 103s Parameter 3 : hivTree.6767.trvs 103s Parameter 4 : hivTree.6767.trst 103s Parameter 5 : hivTree.Node2.trvs 103s Parameter 6 : hivTree.Node2.trst 103s Parameter 7 : hivTree.135.trvs 103s Parameter 8 : hivTree.135.trst 103s Parameter 9 : hivTree.529.trvs 103s Parameter 10 : hivTree.529.trst 103s Parameter 11 : hivTree.105r.trvs 103s Parameter 12 : hivTree.105r.trst 103s Parameter 13 : hivTree.Node8.trvs 103s Parameter 14 : hivTree.Node8.trst 103s Parameter 15 : hivTree.iNode1.trvs 103s Parameter 16 : hivTree.iNode1.trst 103s Parameter 17 : hivTree.719.trvs 103s Parameter 18 : hivTree.719.trst 103s Parameter 19 : hivTree.136.trvs 103s Parameter 20 : hivTree.136.trst 103s Parameter 21 : hivTree.Node11.trvs 103s Parameter 22 : hivTree.Node11.trst 103s Parameter 23 : hivTree.Node5.trvs 103s Parameter 24 : hivTree.Node5.trst 103s Parameter 25 : hivTree.Node1.trvs 103s Parameter 26 : hivTree.Node1.trst 103s Parameter 27 : hivTree.6760.trvs 103s Parameter 28 : hivTree.6760.trst 103s Parameter 29 : hivTree.113.trvs 103s Parameter 30 : hivTree.113.trst 103s Parameter 31 : hivTree.9939.trvs 103s Parameter 32 : hivTree.9939.trst 103s Parameter 33 : hivTree.Node16.trvs 103s Parameter 34 : hivTree.Node16.trst 103s Parameter 35 : hivTree.256.trvs 103s Parameter 36 : hivTree.256.trst 103s Parameter 37 : hivTree.822.trvs 103s Parameter 38 : hivTree.822.trst 103s Parameter 39 : hivTree.159.trvs 103s Parameter 40 : hivTree.159.trst 103s Parameter 41 : hivTree.Node21.trvs 103s Parameter 42 : hivTree.Node21.trst 103s Parameter 43 : hivTree.iNode2.trvs 103s Parameter 44 : hivTree.iNode2.trst 103s Parameter 45 : hivTree.Node15.trvs 103s Parameter 46 : hivTree.Node15.trst 103s 103s 2).HKY85 constrained to F81 on the "iNode1" subtree 103s 103s Log Likelihood = -1157.82; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.135.trvs 103s Parameter 2 : hivTree.529.trvs 103s Parameter 3 : hivTree.105r.trvs 103s Parameter 4 : hivTree.Node8.trvs 103s Parameter 5 : hivTree.317.trvs 103s Parameter 6 : hivTree.317.trst 103s Parameter 7 : hivTree.6767.trst 103s Parameter 8 : hivTree.6767.trvs 103s Parameter 9 : hivTree.Node2.trst 103s Parameter 10 : hivTree.Node2.trvs 103s Parameter 11 : hivTree.iNode1.trvs 103s Parameter 12 : hivTree.iNode1.trst 103s Parameter 13 : hivTree.719.trvs 103s Parameter 14 : hivTree.719.trst 103s Parameter 15 : hivTree.136.trvs 103s Parameter 16 : hivTree.136.trst 103s Parameter 17 : hivTree.Node11.trvs 103s Parameter 18 : hivTree.Node11.trst 103s Parameter 19 : hivTree.Node5.trvs 103s Parameter 20 : hivTree.Node5.trst 103s Parameter 21 : hivTree.Node1.trvs 103s Parameter 22 : hivTree.Node1.trst 103s Parameter 23 : hivTree.6760.trvs 103s Parameter 24 : hivTree.6760.trst 103s Parameter 25 : hivTree.113.trvs 103s Parameter 26 : hivTree.113.trst 103s Parameter 27 : hivTree.9939.trvs 103s Parameter 28 : hivTree.9939.trst 103s Parameter 29 : hivTree.Node16.trvs 103s Parameter 30 : hivTree.Node16.trst 103s Parameter 31 : hivTree.256.trvs 103s Parameter 32 : hivTree.256.trst 103s Parameter 33 : hivTree.822.trvs 103s Parameter 34 : hivTree.822.trst 103s Parameter 35 : hivTree.159.trvs 103s Parameter 36 : hivTree.159.trst 103s Parameter 37 : hivTree.Node21.trvs 103s Parameter 38 : hivTree.Node21.trst 103s Parameter 39 : hivTree.iNode2.trvs 103s Parameter 40 : hivTree.iNode2.trst 103s Parameter 41 : hivTree.Node15.trvs 103s Parameter 42 : hivTree.Node15.trst 103s 103s Constrained Parameters List 103s 103s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 103s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 103s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 103s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 103s 103s 3).HKY85 constrained to F81 on the "iNode1" branch 103s 103s Log Likelihood = -1152.88; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.317.trvs 103s Parameter 2 : hivTree.317.trst 103s Parameter 3 : hivTree.6767.trvs 103s Parameter 4 : hivTree.6767.trst 103s Parameter 5 : hivTree.Node2.trvs 103s Parameter 6 : hivTree.Node2.trst 103s Parameter 7 : hivTree.135.trvs 103s Parameter 8 : hivTree.135.trst 103s Parameter 9 : hivTree.529.trvs 103s Parameter 10 : hivTree.529.trst 103s Parameter 11 : hivTree.105r.trvs 103s Parameter 12 : hivTree.105r.trst 103s Parameter 13 : hivTree.Node8.trvs 103s Parameter 14 : hivTree.Node8.trst 103s Parameter 15 : hivTree.iNode1.trvs 103s Parameter 16 : hivTree.iNode1.trst 103s Parameter 17 : hivTree.719.trvs 103s Parameter 18 : hivTree.719.trst 103s Parameter 19 : hivTree.136.trvs 103s Parameter 20 : hivTree.136.trst 103s Parameter 21 : hivTree.Node11.trvs 103s Parameter 22 : hivTree.Node11.trst 103s Parameter 23 : hivTree.Node5.trvs 103s Parameter 24 : hivTree.Node5.trst 103s Parameter 25 : hivTree.Node1.trvs 103s Parameter 26 : hivTree.Node1.trst 103s Parameter 27 : hivTree.6760.trvs 103s Parameter 28 : hivTree.6760.trst 103s Parameter 29 : hivTree.113.trvs 103s Parameter 30 : hivTree.113.trst 103s Parameter 31 : hivTree.9939.trvs 103s Parameter 32 : hivTree.9939.trst 103s Parameter 33 : hivTree.Node16.trvs 103s Parameter 34 : hivTree.Node16.trst 103s Parameter 35 : hivTree.256.trvs 103s Parameter 36 : hivTree.256.trst 103s Parameter 37 : hivTree.822.trvs 103s Parameter 38 : hivTree.822.trst 103s Parameter 39 : hivTree.159.trvs 103s Parameter 40 : hivTree.159.trst 103s Parameter 41 : hivTree.Node21.trvs 103s Parameter 42 : hivTree.Node21.trst 103s Parameter 43 : hivTree.iNode2.trvs 103s Parameter 44 : hivTree.iNode2.trst 103s Parameter 45 : hivTree.Node15.trvs 103s Parameter 46 : hivTree.Node15.trst 103s 103s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 103s 103s Log Likelihood = -1152.88; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.317.trvs 103s Parameter 2 : hivTree.317.trst 103s Parameter 3 : hivTree.6767.trvs 103s Parameter 4 : hivTree.6767.trst 103s Parameter 5 : hivTree.Node2.trvs 103s Parameter 6 : hivTree.Node2.trst 103s Parameter 7 : hivTree.135.trvs 103s Parameter 8 : hivTree.135.trst 103s Parameter 9 : hivTree.529.trvs 103s Parameter 10 : hivTree.529.trst 103s Parameter 11 : hivTree.105r.trvs 103s Parameter 12 : hivTree.105r.trst 103s Parameter 13 : hivTree.Node8.trvs 103s Parameter 14 : hivTree.Node8.trst 103s Parameter 15 : hivTree.iNode1.trvs 103s Parameter 16 : hivTree.iNode1.trst 103s Parameter 17 : hivTree.719.trvs 103s Parameter 18 : hivTree.719.trst 103s Parameter 19 : hivTree.136.trvs 103s Parameter 20 : hivTree.136.trst 103s Parameter 21 : hivTree.Node11.trvs 103s Parameter 22 : hivTree.Node11.trst 103s Parameter 23 : hivTree.Node5.trvs 103s Parameter 24 : hivTree.Node5.trst 103s Parameter 25 : hivTree.Node1.trvs 103s Parameter 26 : hivTree.Node1.trst 103s Parameter 27 : hivTree.6760.trvs 103s Parameter 28 : hivTree.6760.trst 103s Parameter 29 : hivTree.113.trvs 103s Parameter 30 : hivTree.113.trst 103s Parameter 31 : hivTree.9939.trvs 103s Parameter 32 : hivTree.9939.trst 103s Parameter 33 : hivTree.Node16.trvs 103s Parameter 34 : hivTree.Node16.trst 103s Parameter 35 : hivTree.256.trvs 103s Parameter 36 : hivTree.256.trst 103s Parameter 37 : hivTree.822.trvs 103s Parameter 38 : hivTree.822.trst 103s Parameter 39 : hivTree.159.trvs 103s Parameter 40 : hivTree.159.trst 103s Parameter 41 : hivTree.Node21.trvs 103s Parameter 42 : hivTree.Node21.trst 103s Parameter 43 : hivTree.iNode2.trvs 103s Parameter 44 : hivTree.iNode2.trst 103s Parameter 45 : hivTree.Node15.trvs 103s Parameter 46 : hivTree.Node15.trst 103s 103s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 103s 103s Log Likelihood = -1152.88; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.317.trvs 103s Parameter 2 : hivTree.317.trst 103s Parameter 3 : hivTree.6767.trvs 103s Parameter 4 : hivTree.6767.trst 103s Parameter 5 : hivTree.Node2.trvs 103s Parameter 6 : hivTree.Node2.trst 103s Parameter 7 : hivTree.135.trvs 103s Parameter 8 : hivTree.135.trst 103s Parameter 9 : hivTree.529.trvs 103s Parameter 10 : hivTree.529.trst 103s Parameter 11 : hivTree.105r.trvs 103s Parameter 12 : hivTree.105r.trst 103s Parameter 13 : hivTree.Node8.trvs 103s Parameter 14 : hivTree.Node8.trst 103s Parameter 15 : hivTree.iNode1.trvs 103s Parameter 16 : hivTree.iNode1.trst 103s Parameter 17 : hivTree.719.trvs 103s Parameter 18 : hivTree.719.trst 103s Parameter 19 : hivTree.136.trvs 103s Parameter 20 : hivTree.136.trst 103s Parameter 21 : hivTree.Node11.trvs 103s Parameter 22 : hivTree.Node11.trst 103s Parameter 23 : hivTree.Node5.trvs 103s Parameter 24 : hivTree.Node5.trst 103s Parameter 25 : hivTree.Node1.trvs 103s Parameter 26 : hivTree.Node1.trst 103s Parameter 27 : hivTree.6760.trvs 103s Parameter 28 : hivTree.6760.trst 103s Parameter 29 : hivTree.113.trvs 103s Parameter 30 : hivTree.113.trst 103s Parameter 31 : hivTree.9939.trvs 103s Parameter 32 : hivTree.9939.trst 103s Parameter 33 : hivTree.Node16.trvs 103s Parameter 34 : hivTree.Node16.trst 103s Parameter 35 : hivTree.256.trvs 103s Parameter 36 : hivTree.256.trst 103s Parameter 37 : hivTree.822.trvs 103s Parameter 38 : hivTree.822.trst 103s Parameter 39 : hivTree.159.trvs 103s Parameter 40 : hivTree.159.trst 103s Parameter 41 : hivTree.Node21.trvs 103s Parameter 42 : hivTree.Node21.trst 103s Parameter 43 : hivTree.iNode2.trvs 103s Parameter 44 : hivTree.iNode2.trst 103s Parameter 45 : hivTree.Node15.trvs 103s Parameter 46 : hivTree.Node15.trst 103s 103s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 103s 103s Log Likelihood = -1157.82; 103s 103s Independent Parameters List 103s 103s Parameter 1 : hivTree.135.trst 103s Parameter 2 : hivTree.529.trst 103s Parameter 3 : hivTree.105r.trst 103s Parameter 4 : hivTree.Node8.trst 103s Parameter 5 : hivTree.317.trvs 103s Parameter 6 : hivTree.317.trst 103s Parameter 7 : hivTree.6767.trst 103s Parameter 8 : hivTree.6767.trvs 103s Parameter 9 : hivTree.Node2.trst 103s Parameter 10 : hivTree.Node2.trvs 103s Parameter 11 : hivTree.iNode1.trvs 103s Parameter 12 : hivTree.iNode1.trst 103s Parameter 13 : hivTree.719.trvs 103s Parameter 14 : hivTree.719.trst 103s Parameter 15 : hivTree.136.trvs 103s Parameter 16 : hivTree.136.trst 103s Parameter 17 : hivTree.Node11.trvs 103s Parameter 18 : hivTree.Node11.trst 103s Parameter 19 : hivTree.Node5.trvs 103s Parameter 20 : hivTree.Node5.trst 103s Parameter 21 : hivTree.Node1.trvs 103s Parameter 22 : hivTree.Node1.trst 103s Parameter 23 : hivTree.6760.trvs 103s Parameter 24 : hivTree.6760.trst 103s Parameter 25 : hivTree.113.trvs 103s Parameter 26 : hivTree.113.trst 103s Parameter 27 : hivTree.9939.trvs 103s Parameter 28 : hivTree.9939.trst 103s Parameter 29 : hivTree.Node16.trvs 103s Parameter 30 : hivTree.Node16.trst 103s Parameter 31 : hivTree.256.trvs 103s Parameter 32 : hivTree.256.trst 103s Parameter 33 : hivTree.822.trvs 103s Parameter 34 : hivTree.822.trst 103s Parameter 35 : hivTree.159.trvs 103s Parameter 36 : hivTree.159.trst 103s Parameter 37 : hivTree.Node21.trvs 103s Parameter 38 : hivTree.Node21.trst 103s Parameter 39 : hivTree.iNode2.trvs 103s Parameter 40 : hivTree.iNode2.trst 103s Parameter 41 : hivTree.Node15.trvs 103s Parameter 42 : hivTree.Node15.trst 103s 103s Constrained Parameters List 103s 103s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 103s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 103s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 103s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 103s + '[' -f aa.bf ']' 103s + hyphy aa.bf 103s Log Likelihood = -1134.7315805815; 103s Tree theTree=(((Langur:0.07430857625872316,Baboon:0.03833182311542524)Node2:0.02337958943947592,Human:0.05950610080091293)Node1:0.02005975218269314,Rat:0.2458687008284235,(Cow:0.2551838821559702,Horse:0.5630260009356776)Node7:0.07055352020902278); 103s + for i in *.bf 103s + '[' -f definitions2.bf ']' 103s + hyphy definitions2.bf 103s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 103s 103s Sample by MEAN: 103s 103s Sample mean = 0.5 (sample variance = 0.2450374540764348) 103s 103s Rate[0]= 0.06847689 (weight=0.2500000) 103s Rate[1]= 0.23837593 (weight=0.2500000) 103s Rate[2]= 0.50000000 (weight=0.2500000) 103s Rate[3]= 1.19314718 (weight=0.2500000) 103s ------------------------------------------------ 103s 103s Sample by MEDIAN: 103s 103s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 103s 103s Rate[0]= 0.06676570 (weight=0.2500000) 103s Rate[1]= 0.23500181 (weight=0.2500000) 103s Rate[2]= 0.49041463 (weight=0.2500000) 103s Rate[3]= 1.03972077 (weight=0.2500000) 103s ------------------------------------------------ 103s 103s Sample by SCALED_MEDIAN: 103s 103s Sample mean = 0.5 (sample variance = 0.2154404122636025) 103s 103s Rate[0]= 0.07289218 (weight=0.2500000) 103s Rate[1]= 0.25656580 (weight=0.2500000) 103s Rate[2]= 0.53541552 (weight=0.2500000) 103s Rate[3]= 1.13512650 (weight=0.2500000) 103s ------------------------------------------------ 103s 103s Sample by MEAN (numerical averaging): 103s 103s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 103s 103s Rate[0]= 0.06846096 (weight=0.2500000) 103s Rate[1]= 0.23834015 (weight=0.2500000) 103s Rate[2]= 0.49996411 (weight=0.2500000) 103s Rate[3]= 1.19314889 (weight=0.2500000) 103s ------------------------------------------------ 103s 103s Sample by MEAN (numerical CDF and averaging): 103s 103s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 103s 103s Rate[0]= 0.06849282 (weight=0.2500000) 103s Rate[1]= 0.23835613 (weight=0.2500000) 103s Rate[2]= 0.49994751 (weight=0.2500000) 103s Rate[3]= 1.19311765 (weight=0.2500000) 103s ------------------------------------------------ 103s 2). Equiprobable rates sampled from Exponential with lambda = 2 103s 103s Sample by MEDIAN (3 rate classes): 103s 103s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 103s 103s Rate[0]= 0.09116078 (weight=0.3333333) 103s Rate[1]= 0.34657359 (weight=0.3333333) 103s Rate[2]= 0.89587973 (weight=0.3333333) 103s ------------------------------------------------ 103s 103s Sample by MEDIAN (9 rate classes): 103s 103s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 103s 103s Rate[0]= 0.02857921 (weight=0.1111111) 103s Rate[1]= 0.09116078 (weight=0.1111111) 103s Rate[2]= 0.16271120 (weight=0.1111111) 103s Rate[3]= 0.24623824 (weight=0.1111111) 103s Rate[4]= 0.34657359 (weight=0.1111111) 103s Rate[5]= 0.47223080 (weight=0.1111111) 103s Rate[6]= 0.64046692 (weight=0.1111111) 103s Rate[7]= 0.89587973 (weight=0.1111111) 103s Rate[8]= 1.44518588 (weight=0.1111111) 103s ------------------------------------------------ 103s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 103s 103s Sample by MEAN (10 rate classes): 103s 103s Sample mean = 1 (sample variance = 0.1057310289486733) 103s 103s Rate[0]= 0.52447499 (weight=0.1000000) 103s Rate[1]= 0.67866972 (weight=0.1000000) 103s Rate[2]= 0.77209919 (weight=0.1000000) 103s Rate[3]= 0.85214884 (weight=0.1000000) 103s Rate[4]= 0.92850815 (weight=0.1000000) 103s Rate[5]= 1.00664500 (weight=0.1000000) 103s Rate[6]= 1.09192933 (weight=0.1000000) 103s Rate[7]= 1.19267960 (weight=0.1000000) 103s Rate[8]= 1.32858029 (weight=0.1000000) 103s Rate[9]= 1.62426489 (weight=0.1000000) 103s ------------------------------------------------ 103s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 103s 103s Sample by MEAN (10 rate classes): 103s 103s Sample mean = 2 (sample variance = 0.04259071282256012) 103s 103s Rate[0]= 1.66431246 (weight=0.1000000) 103s Rate[1]= 1.79212822 (weight=0.1000000) 103s Rate[2]= 1.86123411 (weight=0.1000000) 103s Rate[3]= 1.91722052 (weight=0.1000000) 103s Rate[4]= 1.96832799 (weight=0.1000000) 103s Rate[5]= 2.01862937 (weight=0.1000000) 103s Rate[6]= 2.07152664 (weight=0.1000000) 103s Rate[7]= 2.13166629 (weight=0.1000000) 103s Rate[8]= 2.20930216 (weight=0.1000000) 103s Rate[9]= 2.36565224 (weight=0.1000000) 103s ------------------------------------------------ 103s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 103s 103s Sample by MEAN (8 rate classes): 103s 103s Sample mean = 0.5 (sample variance = 0.09375000225643569) 103s 103s Rate[0]= 0.06250000 (weight=0.1250000) 103s Rate[1]= 0.18750000 (weight=0.1250000) 103s Rate[2]= 0.31250001 (weight=0.1250000) 103s Rate[3]= 0.43750001 (weight=0.1250000) 103s Rate[4]= 0.56249993 (weight=0.1250000) 103s Rate[5]= 0.68750001 (weight=0.1250000) 103s Rate[6]= 0.81250002 (weight=0.1250000) 103s Rate[7]= 0.93750002 (weight=0.1250000) 103s ------------------------------------------------ 103s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 103s 103s Sample by MEAN (8 rate classes): 103s 103s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 103s 103s Rate[0]= 2.17658588 (weight=0.1250000) 103s Rate[1]= 2.55230783 (weight=0.1250000) 103s Rate[2]= 2.75432532 (weight=0.1250000) 103s Rate[3]= 2.92101185 (weight=0.1250000) 103s Rate[4]= 3.07898815 (weight=0.1250000) 103s Rate[5]= 3.24567468 (weight=0.1250000) 103s Rate[6]= 3.44769217 (weight=0.1250000) 103s Rate[7]= 3.82341415 (weight=0.1250000) 103s ------------------------------------------------ 103s + for i in *.bf 103s + '[' -f definitions3.bf ']' 103s + hyphy definitions3.bf 103s 103s 103s Sample mean = 1 (sample variance = 0.9920002887656187) 103s 103s Rate[0]= 0.05175536 (weight=0.1000000) 103s Rate[1]= 0.16309623 (weight=0.1000000) 103s Rate[2]= 0.28842380 (weight=0.1000000) 103s Rate[3]= 0.43177086 (weight=0.1000000) 103s Rate[4]= 0.59921784 (weight=0.1000000) 103s Rate[5]= 0.80057298 (weight=0.1000000) 103s Rate[6]= 1.05324451 (weight=0.1000000) 103s Rate[7]= 1.39304259 (weight=0.1000000) 103s Rate[8]= 1.91629073 (weight=0.1000000) 103s Rate[9]= 3.30258509 (weight=0.1000000) 103s ------------------------------------------------ 103s + for i in *.bf 103s + '[' -f displayFunction.bf ']' 103s + hyphy displayFunction.bf 103s + for i in *.bf 103s + '[' -f profile_test.bf ']' 103s + hyphy profile_test.bf 104s 104s Total run time (seconds) : 0.000000 104s Total number of steps : 1500005 104s 104s 1 : s=0; 104s Call count: 1 104s Time (seconds): 1.8e-11 104s 2 : m={5,1}; 104s Call count: 1 104s Time (seconds): 2.2e-11 104s 3 : k=0; 104s Call count: 1 104s Time (seconds): 2e-12 104s 4 : Branch under condition 'k<250000' 104s to 104s s=s+k; 104s else 104s #profilePAUSE, ; 104s Call count: 250001 104s Time (seconds): 3.061900000000996e-08 104s 5 : s=s+k; 104s Call count: 250000 104s Time (seconds): 3.373000000001278e-08 104s 6 : t=Random(0,5); 104s Call count: 250000 104s Time (seconds): 3.489300000001393e-08 104s 7 : m[t]=m[t]+1; 104s Call count: 250000 104s Time (seconds): 8.2403000000061e-08 104s 8 : k=k+1; 104s Call count: 250000 104s Time (seconds): 3.277600000001203e-08 104s 9 : Go to step 4 104s Call count: 250000 104s Time (seconds): 1.100999999999837e-08 104s 10 : #profilePAUSE, ; 104s Call count: 1 104s Time (seconds): 1e-12 104s + for i in *.bf 104s + '[' -f shared.bf ']' 104s + hyphy shared.bf 104s + rm -f '*messages.log*' '*errors.log*' 104s autopkgtest [10:39:02]: test run-unit-tests: -----------------------] 104s run-unit-tests PASS 104s autopkgtest [10:39:02]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 105s autopkgtest [10:39:03]: @@@@@@@@@@@@@@@@@@@@ summary 105s run-unit-tests PASS 120s nova [W] Using flock in prodstack7-arm64 120s Creating nova instance adt-questing-arm64-hyphy-20250502-103717-juju-7f2275-prod-proposed-migration-environment-15-ac1c359d-5339-4d55-9706-19ac779a6f46 from image adt/ubuntu-questing-arm64-server-20250501.img (UUID 137c3127-57d2-4bf2-a106-d904ad6e43f4)... 120s nova [W] Timed out waiting for ba4ffc0e-226d-42a4-8370-6784decc5791 to get deleted.