0s autopkgtest [20:06:23]: starting date and time: 2025-02-15 20:06:23+0000 0s autopkgtest [20:06:23]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [20:06:23]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pw9aksih/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade hyphy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-23.secgroup --name adt-plucky-amd64-hyphy-20250215-200623-juju-7f2275-prod-proposed-migration-environment-2-501970f2-1fb4-48d8-b61f-1fddceb5ac0c --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 50s autopkgtest [20:07:13]: testbed dpkg architecture: amd64 51s autopkgtest [20:07:14]: testbed apt version: 2.9.28 51s autopkgtest [20:07:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [20:07:14]: testbed release detected to be: None 52s autopkgtest [20:07:15]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 53s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 53s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [820 kB] 53s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.0 kB] 53s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [82.9 kB] 53s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 53s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 53s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [844 kB] 53s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [303 kB] 53s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 53s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB] 53s Fetched 2329 kB in 1s (2457 kB/s) 54s Reading package lists... 54s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 55s The following packages will be upgraded: 55s libtasn1-6 55s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 51.2 kB of archives. 55s After this operation, 22.5 kB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 56s Fetched 51.2 kB in 0s (187 kB/s) 56s (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 ... 108914 files and directories currently installed.) 56s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 56s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 56s Setting up libtasn1-6:amd64 (4.20.0-2) ... 56s Processing triggers for libc-bin (2.40-4ubuntu1) ... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 57s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 57s autopkgtest [20:07:20]: upgrading testbed (apt dist-upgrade and autopurge) 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 58s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 58s Starting 2 pkgProblemResolver with broken count: 0 58s Done 58s Entering ResolveByKeep 58s 58s The following packages will be upgraded: 58s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 59s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Need to get 11.8 MB of archives. 59s After this operation, 746 kB of additional disk space will be used. 59s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 59s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 59s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 59s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 59s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 59s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 60s Preconfiguring packages ... 60s Fetched 11.8 MB in 1s (12.2 MB/s) 60s (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 ... 108914 files and directories currently installed.) 60s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 60s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 60s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 60s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 60s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 60s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 60s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 60s Checking for services that may need to be restarted... 60s Checking init scripts... 60s Checking for services that may need to be restarted... 60s Checking init scripts... 60s Stopping some services possibly affected by the upgrade (will be restarted later): 60s cron: stopping...done. 60s 60s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 61s Setting up libc6:amd64 (2.41-1ubuntu1) ... 61s Checking for services that may need to be restarted... 61s Checking init scripts... 61s Restarting services possibly affected by the upgrade: 61s cron: restarting...done. 61s 61s Services restarted successfully. 61s (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 ... 108915 files and directories currently installed.) 61s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 61s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 61s Setting up libc-bin (2.41-1ubuntu1) ... 61s (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 ... 108915 files and directories currently installed.) 61s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 61s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 61s Setting up iproute2 (6.13.0-1ubuntu1) ... 62s Setting up locales (2.41-1ubuntu1) ... 62s Installing new version of config file /etc/locale.alias ... 62s Generating locales (this might take a while)... 63s en_US.UTF-8... done 63s Generation complete. 63s Setting up libc-dev-bin (2.41-1ubuntu1) ... 63s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 63s Processing triggers for man-db (2.13.0-1) ... 64s Processing triggers for systemd (257.2-3ubuntu1) ... 65s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Starting pkgProblemResolver with broken count: 0 66s Starting 2 pkgProblemResolver with broken count: 0 66s Done 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s autopkgtest [20:07:32]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 69s autopkgtest [20:07:32]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 72s Get:1 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (dsc) [2298 B] 72s Get:2 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (tar) [2627 kB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (diff) [17.4 kB] 72s gpgv: Signature made Sat Nov 30 06:13:22 2024 UTC 72s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 72s gpgv: Can't check signature: No public key 72s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.63+dfsg-1build2.dsc: no acceptable signature found 73s autopkgtest [20:07:36]: testing package hyphy version 2.5.63+dfsg-1build2 73s autopkgtest [20:07:36]: build not needed 74s autopkgtest [20:07:37]: test run-unit-tests: preparing testbed 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Starting pkgProblemResolver with broken count: 0 75s Starting 2 pkgProblemResolver with broken count: 0 75s Done 75s The following NEW packages will be installed: 75s hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 75s libevent-pthreads-2.1-7t64 libfabric1 libgomp1 libhsa-runtime64-1 libhsakmt1 75s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libllvm17t64 libmunge2 75s libopenmpi40 libpciaccess0 libpmix2t64 libpsm-infinipath1 libpsm2-2 75s librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 76s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 61.1 MB of archives. 76s After this operation, 256 MB of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 hyphy-common all 2.5.63+dfsg-1build2 [628 kB] 76s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-17ubuntu1 [148 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 76s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 76s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 55.0-1ubuntu1 [71.5 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3ubuntu1 [658 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.2-1build1 [193 kB] 77s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 77s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 77s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 77s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 77s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.11.2-1build1 [16.0 kB] 77s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-3 [714 kB] 77s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-20 [26.0 MB] 79s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 80s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 80s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 80s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 80s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 55.0-1ubuntu1 [29.7 kB] 80s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 55.0-1ubuntu1 [42.7 kB] 80s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 81s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.6-4 [2523 kB] 81s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 hyphy-mpi amd64 2.5.63+dfsg-1build2 [1967 kB] 81s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 hyphy-pt amd64 2.5.63+dfsg-1build2 [1921 kB] 81s Fetched 61.1 MB in 5s (11.3 MB/s) 81s Selecting previously unselected package hyphy-common. 81s (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 ... 108916 files and directories currently installed.) 81s Preparing to unpack .../00-hyphy-common_2.5.63+dfsg-1build2_all.deb ... 81s Unpacking hyphy-common (2.5.63+dfsg-1build2) ... 81s Selecting previously unselected package libgomp1:amd64. 81s Preparing to unpack .../01-libgomp1_14.2.0-17ubuntu1_amd64.deb ... 81s Unpacking libgomp1:amd64 (14.2.0-17ubuntu1) ... 81s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 81s Preparing to unpack .../02-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 81s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 81s Selecting previously unselected package libpsm-infinipath1. 81s Preparing to unpack .../03-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 81s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 81s Selecting previously unselected package libpsm2-2. 81s Preparing to unpack .../04-libpsm2-2_11.2.185-2.1_amd64.deb ... 81s Unpacking libpsm2-2 (11.2.185-2.1) ... 81s Selecting previously unselected package librdmacm1t64:amd64. 81s Preparing to unpack .../05-librdmacm1t64_55.0-1ubuntu1_amd64.deb ... 81s Unpacking librdmacm1t64:amd64 (55.0-1ubuntu1) ... 81s Selecting previously unselected package libfabric1:amd64. 81s Preparing to unpack .../06-libfabric1_1.17.0-3ubuntu1_amd64.deb ... 81s Unpacking libfabric1:amd64 (1.17.0-3ubuntu1) ... 81s Selecting previously unselected package libhwloc15:amd64. 81s Preparing to unpack .../07-libhwloc15_2.11.2-1build1_amd64.deb ... 81s Unpacking libhwloc15:amd64 (2.11.2-1build1) ... 81s Selecting previously unselected package libmunge2:amd64. 81s Preparing to unpack .../08-libmunge2_0.5.16-1_amd64.deb ... 81s Unpacking libmunge2:amd64 (0.5.16-1) ... 81s Selecting previously unselected package libpciaccess0:amd64. 82s Preparing to unpack .../09-libpciaccess0_0.17-3build1_amd64.deb ... 82s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 82s Selecting previously unselected package libxnvctrl0:amd64. 82s Preparing to unpack .../10-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 82s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 82s Selecting previously unselected package ocl-icd-libopencl1:amd64. 82s Preparing to unpack .../11-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 82s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 82s Selecting previously unselected package libhwloc-plugins:amd64. 82s Preparing to unpack .../12-libhwloc-plugins_2.11.2-1build1_amd64.deb ... 82s Unpacking libhwloc-plugins:amd64 (2.11.2-1build1) ... 82s Selecting previously unselected package libpmix2t64:amd64. 82s Preparing to unpack .../13-libpmix2t64_5.0.6-3_amd64.deb ... 82s Unpacking libpmix2t64:amd64 (5.0.6-3) ... 82s Selecting previously unselected package libllvm17t64:amd64. 82s Preparing to unpack .../14-libllvm17t64_1%3a17.0.6-20_amd64.deb ... 82s Unpacking libllvm17t64:amd64 (1:17.0.6-20) ... 82s Selecting previously unselected package libamd-comgr2:amd64. 82s Preparing to unpack .../15-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 82s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 82s Selecting previously unselected package libhsakmt1:amd64. 82s Preparing to unpack .../16-libhsakmt1_5.7.0-1build1_amd64.deb ... 82s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 82s Selecting previously unselected package libhsa-runtime64-1. 82s Preparing to unpack .../17-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 82s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 82s Selecting previously unselected package libamdhip64-5. 82s Preparing to unpack .../18-libamdhip64-5_5.7.1-5_amd64.deb ... 82s Unpacking libamdhip64-5 (5.7.1-5) ... 83s Selecting previously unselected package libibumad3:amd64. 83s Preparing to unpack .../19-libibumad3_55.0-1ubuntu1_amd64.deb ... 83s Unpacking libibumad3:amd64 (55.0-1ubuntu1) ... 83s Selecting previously unselected package libibmad5:amd64. 83s Preparing to unpack .../20-libibmad5_55.0-1ubuntu1_amd64.deb ... 83s Unpacking libibmad5:amd64 (55.0-1ubuntu1) ... 83s Selecting previously unselected package libucx0:amd64. 83s Preparing to unpack .../21-libucx0_1.17.0+ds-3build1_amd64.deb ... 83s Unpacking libucx0:amd64 (1.17.0+ds-3build1) ... 83s Selecting previously unselected package libopenmpi40:amd64. 83s Preparing to unpack .../22-libopenmpi40_5.0.6-4_amd64.deb ... 83s Unpacking libopenmpi40:amd64 (5.0.6-4) ... 83s Selecting previously unselected package hyphy-mpi. 83s Preparing to unpack .../23-hyphy-mpi_2.5.63+dfsg-1build2_amd64.deb ... 83s Unpacking hyphy-mpi (2.5.63+dfsg-1build2) ... 83s Selecting previously unselected package hyphy-pt. 83s Preparing to unpack .../24-hyphy-pt_2.5.63+dfsg-1build2_amd64.deb ... 83s Unpacking hyphy-pt (2.5.63+dfsg-1build2) ... 83s Setting up libpciaccess0:amd64 (0.17-3build1) ... 83s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 83s Setting up libibumad3:amd64 (55.0-1ubuntu1) ... 83s Setting up libibmad5:amd64 (55.0-1ubuntu1) ... 83s Setting up hyphy-common (2.5.63+dfsg-1build2) ... 83s Setting up libgomp1:amd64 (14.2.0-17ubuntu1) ... 83s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 83s Setting up libmunge2:amd64 (0.5.16-1) ... 83s Setting up libllvm17t64:amd64 (1:17.0.6-20) ... 83s Setting up libhwloc15:amd64 (2.11.2-1build1) ... 83s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 83s Setting up libpsm2-2 (11.2.185-2.1) ... 83s Setting up librdmacm1t64:amd64 (55.0-1ubuntu1) ... 83s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 83s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 83s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 83s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 83s Setting up libfabric1:amd64 (1.17.0-3ubuntu1) ... 83s Setting up hyphy-pt (2.5.63+dfsg-1build2) ... 83s Setting up libhwloc-plugins:amd64 (2.11.2-1build1) ... 83s Setting up libpmix2t64:amd64 (5.0.6-3) ... 83s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 83s Setting up libamdhip64-5 (5.7.1-5) ... 83s Setting up libucx0:amd64 (1.17.0+ds-3build1) ... 83s Setting up libopenmpi40:amd64 (5.0.6-4) ... 83s Setting up hyphy-mpi (2.5.63+dfsg-1build2) ... 83s Processing triggers for libc-bin (2.41-1ubuntu1) ... 83s Processing triggers for man-db (2.13.0-1) ... 84s autopkgtest [20:07:47]: test run-unit-tests: [----------------------- 85s + for i in *.bf 85s + '[' -f ExonIntron.bf ']' 85s + hyphy ExonIntron.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s Log Likelihood = -1113.34527453453; 85s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134823264742666,(ZMUBIS27F:0,(ZMU29160:0.0543979048651192,ZMU29161:0.03972438403897811)Node8:0.01201701682786049)Node6:0)Node4:0.02459392341219462,BLYMUB1:0.01186169044708103); 85s Tree exon2Tree=(BLYMUB2:0.03542197961822478,(RICRMA630:0.02935921503563649,(ZMUBIS27F:0.07548368577676967,(ZMU29160:0.09106731878945297,ZMU29161:0.02597632188472451)Node8:0.01154237700910456)Node6:0.04929618909211774)Node4:0.02930900114162638,BLYMUB1:0.02204924931130404); 85s Tree intronTree=(BLYMUB2:0.03119337515251674,(RICRMA630:0.04156843578037744,(ZMUBIS27F:0.0204401372723281,(ZMU29160:0.02068575673807109,ZMU29161:0.01019356243541257)Node8:0.02068834848503982)Node6:0)Node4:0,BLYMUB1:0.01036374500587675); 85s + for i in *.bf 85s + '[' -f F81.bf ']' 85s + hyphy F81.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s Log Likelihood = -1187.54703158316; 85s Tree givenTree=(256:0.01194114584269996,(822:0.02944524200406485,159:0.004471621727702883)Node2:0.003649766276848208,((113:0.02245290968696168,9939:0.07628833488968456)Node6:0.005077459423903443,(6760:0.06900624319962295,((317:0.03752839365149217,6767:0.07083856789220619)Node12:0.01229694845527588,((135:0.02046660329422206,(529:0.033370186974953,105r:0.01321522052896401)Node18:0.02585864946809065)Node16:0.005409584208063661,(719:0.02964827453374408,136:0.008234924817714496)Node21:0.04883319135007599)Node15:0.01526164959101132)Node11:0.01379988377559006)Node9:0.02422104099349152)Node5:0.02148432122467328); 85s + for i in *.bf 85s + '[' -f F81relrate.bf ']' 85s + hyphy F81relrate.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s 85s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001001210834; 85s Tree threeTaxaTree=(a:0.08502373447434354,b:0.07338780662543803,c:0.1653961179929532); 85s 85s 85s 1). With the outgroup at taxon #1, the P-value is:0.002155082746832959 85s Log Likelihood = -948.707263619764; 85s Tree threeTaxaTree=(a:0.08228181923420894,b:0.1193752617575549,c:0.1193752617575549); 85s 85s 85s 2). With the outgroup at taxon #2, the P-value is:0.008353493534204115 85s Log Likelihood = -947.479040372904; 85s Tree threeTaxaTree=(a:0.1251255673327281,b:0.07126113981601379,c:0.1251255673327281); 85s 85s 85s 3). With the outgroup at taxon #3, the P-value is:0.66691424887132 85s Log Likelihood = -944.0936176374; 85s Tree threeTaxaTree=(a:0.07920391206007872,b:0.07920391206007872,c:0.1653766792476455); 85s + for i in *.bf 85s + '[' -f F81relratio.bf ']' 85s + hyphy F81relratio.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s + for i in *.bf 85s + '[' -f HKY85.bf ']' 85s + hyphy HKY85.bf 85s 85s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059868191; 85s Tree fourTaxaTree1=((1:0.1129194728687213,2:0.1073510574302118)Node1:0.09979510553959611,3:0.3469419664945096,4:0.3218829828403453); 85s Tree fourTaxaTree2=((1:0.08582648436799857,2:0.09340546433118044)Node1:0.07362500440693939,3:0.3932327768954633,4:0.3801450365999581); 85s 85s 85s 1). Relative ratio constraint; the P-value is:0.6933541995336102 85s Log Likelihood = -2575.74610909545; 85s Global Parameters: 85s R=1.00729087894436; 85s 85s Tree fourTaxaTree1=((1:0.09948361640754592,2:0.09943034029459893)Node1:0.08696825701278402,3:0.3687235533633875,4:0.3489176985747814); 85s Tree fourTaxaTree2=((1:0.100073708792079,2:0.1000201166690223)Node1:0.08748411387457239,3:0.3709106568151394,4:0.3509873225409459); 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s Log Likelihood = -1152.8807764511; 85s Tree givenTree=(256:0.01162364208121404,(822:0.0298032482996139,159:0.004016335948448932)Node2:0.003749549758547418,((113:0.02130049470887995,9939:0.07787423959097547)Node6:0.00432134166140833,(6760:0.0731633214845111,((317:0.03810262081076875,6767:0.07101128285678154)Node12:0.006272466408941219,((135:0.01787883930187171,(529:0.03258190006864846,105r:0.01513653604375252)Node18:0.02833253018772181)Node16:0.007920141355983864,(719:0.02987695722144628,136:0.008042439233754379)Node21:0.04860034722759218)Node15:0.01598535372967415)Node11:0.01658093035485627)Node9:0.02665163614677067)Node5:0.02296003630289992); 85s + for i in *.bf 85s + '[' -f HKY852blocks.bf ']' 85s + hyphy HKY852blocks.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s 85s ----- RESULTS ----- 85s Log Likelihood = -6801.91478399091; 85s Tree actinTree1=(ZMU60513:0,ZMU60514:0.0105022860115478,((((((ZMU60511:0.0103983740198079,ZMU60510:0.02379423263212027)Node8:0.08352408168893914,OSRAC2:0.1884845139595169)Node7:0.05837814314842114,(OSRAC1:0.01536674648346974,SVSOAC1:0.07339321914025002)Node12:0.0729724126243604)Node6:0,((OSRAC3:0.07322437868423916,ZMU60507:0.06502887280030831)Node16:0.07980138377130398,ZMU60509:0.1288399461195618)Node15:0.001258648818386277)Node5:0.08267768586798346,(MZEACT1G:0.1142450335082617,OSRAC7:0.03419097466650178)Node20:0)Node4:0.1058668084498628,ZMU60508:0.01697942376470984)Node3:0.05976214372658487); 85s Tree actinTree2=(ZMU60513:0.01013416289228185,ZMU60514:0.02362827133304094,((((((ZMU60511:0.03958977859246978,ZMU60510:0.02870895254099158)Node8:0.04599291165529495,OSRAC2:0.1281487398904044)Node7:0.02274683091454808,(OSRAC1:0.04038760863463942,SVSOAC1:0.05532913524002903)Node12:0.09056631328962836)Node6:0.02100713118232088,((OSRAC3:0.1082309100734644,ZMU60507:0.07346510325659318)Node16:0.0560191375559436,ZMU60509:0.1117457328158209)Node15:0.0291608248491057)Node5:0.04980514012043324,(MZEACT1G:0.1070211282838932,OSRAC7:0.09561860631771396)Node20:0.02267694909496633)Node4:0.04831147926657874,ZMU60508:0.02346403600619949)Node3:0.05651912531517781); 85s + for i in *.bf 85s + '[' -f HKY852blocks2models.bf ']' 85s + hyphy HKY852blocks2models.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s 85s ----- RESULTS ----- 85s Log Likelihood = -6049.33413104958; 85s Tree actinTree1=(ZMU60513:0.0136821456240327,ZMU60514:0.06663425088318328,((((((ZMU60511:0.1014485769044888,ZMU60510:0.08941529527315095)Node8:0.2113125275483744,OSRAC2:0.3685569981843553)Node7:0.0639483599640059,(OSRAC1:0.04314405075821624,SVSOAC1:0.2447419718145064)Node12:0.4085240941670377)Node6:0.1002847494051549,((OSRAC3:0.1862555640447713,ZMU60507:0.3288957711847951)Node16:0.1591202883825444,ZMU60509:0.4441967612302722)Node15:0.04672448875919261)Node5:0.1895749452316279,(MZEACT1G:0.3243136667958134,OSRAC7:0.2476804752761438)Node20:0.009381033841108246)Node4:0.266229466785495,ZMU60508:0.01033213074724353)Node3:0.2230279650825975); 85s Tree actinTree2=(ZMU60513:0.004497092570363351,ZMU60514:0.004483798406111789,((((((ZMU60511:0.004482186832725611,ZMU60510:0.005995225466141256)Node8:0.004869578543811144,OSRAC2:0.04747012086275841)Node7:0.003177697004913643,(OSRAC1:0.012098722365415,SVSOAC1:0.007445096958111817)Node12:0.02729899474756489)Node6:0,((OSRAC3:0.04645225905854616,ZMU60507:0.009177512759927174)Node16:0.01045406542978229,ZMU60509:0.02448224234251211)Node15:0)Node5:0.01926907550250604,(MZEACT1G:0.03380955513030544,OSRAC7:0.03062846550199231)Node20:0.006214025540760514)Node4:0.007799250774073434,ZMU60508:0.004488629195567876)Node3:0.01512034598775335); 85s + for i in *.bf 85s + '[' -f HKY85relrate.bf ']' 85s + hyphy HKY85relrate.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s 85s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371754592056; 85s Tree threeTaxaTree=(a:0.08470616712490835,b:0.07476331104110312,c:0.174013419819606); 85s 85s 85s 1). Outgroup at taxon #1 85s a). Transition rate test. P-Value = 0.02098233635295554 85s Log Likelihood = -924.035884024613; 85s Tree threeTaxaTree=(a:0.08099120544958245,b:0.1064970052103861,c:0.1431287317913004); 85s 85s b). Transversion rate test. P-Value = 0.03655161546436125 85s Log Likelihood = -923.557345912292; 85s Tree threeTaxaTree=(a:0.08437179548943792,b:0.09106657122333411,c:0.1577519164945806); 85s 85s c). Both rates test. P-Value = 0.006324016977125479 85s Log Likelihood = -926.435155267191; 85s Tree threeTaxaTree=(a:0.08054162717334669,b:0.1248196470986539,c:0.1248196470986539); 85s 85s 85s 2). Outgroup at taxon #2 85s a). Transition rate test. P-Value = 0.02758045337926496 85s Log Likelihood = -923.798806027183; 85s Tree threeTaxaTree=(a:0.1158362260630627,b:0.07098641267473906,c:0.1443231461867119); 85s 85s b). Transversion rate test. P-Value = 0.110646314504248 85s Log Likelihood = -922.644237437583; 85s Tree threeTaxaTree=(a:0.09760331118012684,b:0.0746365413868597,c:0.1608968059672476); 85s 85s c). Both rates test. P-Value = 0.02199506592011558 85s Log Likelihood = -925.188691719244; 85s Tree threeTaxaTree=(a:0.1299134980860552,b:0.07078647771051938,c:0.1299134980860552); 85s 85s 85s 3). Outgroup at taxon #3 85s a). Transition rate test. P-Value = 0.9291997193329261 85s Log Likelihood = -921.375701909959; 85s Tree threeTaxaTree=(a:0.08354356501334997,b:0.07588178145291921,c:0.1740455429104291); 85s 85s b). Transversion rate test. P-Value = 0.5919916735151514 85s Log Likelihood = -921.515376904939; 85s Tree threeTaxaTree=(a:0.08115137182818569,b:0.07834954130614444,c:0.1740030839139619); 85s 85s c). Both rates test. P-Value = 0.8615442246207938 85s Log Likelihood = -921.520783481938; 85s Tree threeTaxaTree=(a:0.07974264151890507,b:0.07974264151890507,c:0.1740977410499742); 85s + for i in *.bf 85s + '[' -f HKY85relratio.bf ']' 85s + hyphy HKY85relratio.bf 85s Using /usr/lib/hyphy/bin/hyphy-avx 85s 85s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78441247112; 85s Tree fourTaxaTree1=((1:0.1137753432483493,2:0.1109236050189239)Node1:0.1041248489452749,3:0.3523533317266987,4:0.331199600422348); 85s Tree fourTaxaTree2=((1:0.08603826701139318,2:0.09351277613638176)Node1:0.08022847824750728,3:0.3859539005695455,4:0.3896405654435391); 86s 86s 86s 1). Relative ratio constraint on transitions; the P-value is:0.5738549386091414 86s Log Likelihood = -2541.23688975638; 86s Global Parameters: 86s R=0.8579071165239532; 86s 86s Tree fourTaxaTree1=((1:0.1086624596942303,2:0.09420709800667647)Node1:0.1115975418561597,3:0.3553174709651912,4:0.3551357070655257); 86s Tree fourTaxaTree2=((1:0.09039857822556413,2:0.1091735479856031)Node1:0.07301057782361876,3:0.3839750476305116,4:0.3655235056100101); 86s 86s 86s 2). Relative ratio constraint on transversions; the P-value is:0.5738361517816171 86s Log Likelihood = -2541.23694503417; 86s Global Parameters: 86s R=0.8588027801662774; 86s 86s Tree fourTaxaTree1=((1:0.1087337683900204,2:0.09418435019331176)Node1:0.1117115080680469,3:0.3552930339890447,4:0.3550019685680007); 86s Tree fourTaxaTree2=((1:0.09042775319179003,2:0.1092509575819726)Node1:0.07318632992910007,3:0.3839467840066154,4:0.3656962456098764); 86s 86s 86s 3). Relative ratio constraint on both rates; the P-value is:0.6565853043708002 86s Log Likelihood = -2543.19089462393; 86s Global Parameters: 86s R=0.9967879999302107; 86s 86s Tree fourTaxaTree1=((1:0.1004743196574104,2:0.1006712011054959)Node1:0.09257223730012826,3:0.3714089266796365,4:0.3580943849562002); 86s Tree fourTaxaTree2=((1:0.1003349252916487,2:0.1006905700770038)Node1:0.09289057670314788,3:0.3699493488703654,4:0.3576557088147451); 86s + for i in *.bf 86s + '[' -f HKY85shared.bf ']' 86s + hyphy HKY85shared.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s Log Likelihood = -1165.70261216452; 86s Global Parameters: 86s R=2.985270111313039; 86s 86s Tree givenTree=(256:0.01208887834815901,(822:0.02962497685427722,159:0.004654004356729274)Node2:0.003521675182559771,((113:0.02180335276760238,9939:0.07937939791587371)Node6:0.004910492767676866,(6760:0.07155691643255428,((317:0.03797626454349588,6767:0.07151084044985624)Node12:0.01177117132944822,((135:0.0202439340510802,(529:0.03402215758826741,105r:0.01304776452220313)Node18:0.02631597095116721)Node16:0.005812235226828101,(719:0.02975107090860332,136:0.00812803806432239)Node21:0.0487974077554183)Node15:0.01556125089703152)Node11:0.01396730114015469)Node9:0.02326100835525552)Node5:0.02146650803956782); 86s + for i in *.bf 86s + '[' -f JC69.bf ']' 86s + hyphy JC69.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s Log Likelihood = -1227.45124656186; 86s Tree givenTree=(256:0.01210314715601103,(822:0.02895919172539597,159:0.004660419962712772)Node2:0.003646944277022842,((113:0.02417187811130204,9939:0.07264010626043545)Node6:0.005841276267488251,(6760:0.06387903947432765,((317:0.0402689912044173,6767:0.06821500325396383)Node12:0.01443705913976238,((135:0.02431082236064348,(529:0.03327971747081741,105r:0.01296537962026748)Node18:0.01987838625842827)Node16:0.003613204940440659,(719:0.02785313707568823,136:0.009997027747744899)Node21:0.05116979204685271)Node15:0.01670127412969276)Node11:0.008455166962596889)Node9:0.02635808518130239)Node5:0.02074711332979767); 86s + for i in *.bf 86s + '[' -f K2P.bf ']' 86s + hyphy K2P.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s Log Likelihood = -1198.26189385495; 86s Tree givenTree=(256:0.01177284359460724,(822:0.02926420042581505,159:0.004290513736525809)Node2:0.003666029123726261,((113:0.02366812236207649,9939:0.07261944383728258)Node6:0.003382357557467079,(6760:0.06224213120219273,((317:0.04074378042354266,6767:0.06830506620031575)Node12:0.01244537972185381,((135:0.02260274238146858,(529:0.03395246655084691,105r:0.01240375196225558)Node18:0.02142035442572977)Node16:0.004488785195180413,(719:0.02880975681576832,136:0.008845132022720012)Node21:0.05084376886979997)Node15:0.01733791687183826)Node11:0.01111378509935902)Node9:0.02819644522391989)Node5:0.02370264713467913); 86s + for i in *.bf 86s + '[' -f K2Pshared.bf ']' 86s + hyphy K2Pshared.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s Log Likelihood = -1210.49415319464; 86s Global Parameters: 86s R=2.617877703050858; 86s 86s Tree givenTree=(256:0.01222252409647712,(822:0.02896401725502035,159:0.0047803093553595)Node2:0.003546561133800182,((113:0.02375952686910732,9939:0.07494123484052866)Node6:0.0058906858724509,(6760:0.06493002047872463,((317:0.03970995143577984,6767:0.06949604874815728)Node12:0.0142324803639633,((135:0.02389935732638408,(529:0.0339620761369963,105r:0.01262776767970488)Node18:0.02071514078898529)Node16:0.003966885131087294,(719:0.02813863196348805,136:0.009502482796709844)Node21:0.05080141666996246)Node15:0.01659083039177516)Node11:0.00879847833422477)Node9:0.02627038150507176)Node5:0.02011072172082169); 86s + for i in *.bf 86s + '[' -f MatrixIndexing.bf ']' 86s + hyphy MatrixIndexing.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s 86s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 86s { 86s {0.8611533965126503, 0.4191844557456636, 0.78765204311061, 0.1502263446222586, 0.9959290851829409, 0.5503457634594165} 86s {0.2521429765625258, 0.1011039731328152, 0.336958552323505, 0.5625733734487028, 0.3770817302579716, 0.5796220159576325} 86s {0.1021022387086652, 0.8527768556617147, 0.9326274331967875, 0.9020053876801406, 0.6249293630535084, 0.05406247662707755} 86s {0.02620731131783857, 0.3512361467236737, 0.5545193253910446, 0.2966676955802058, 0.3224824965750991, 0.8195649154529825} 86s {0.6542918671980248, 0.8250730861502404, 0.6198701571253757, 0.1249153360549629, 0.9917215004078396, 0.9188368930292402} 86s } 86s 86s 2). Accessing a second-row third-column element and a random element. 86s 86s matrix[1][2]=0.336958552323505 86s matrix[2][3]=0.9020053876801406 86s 86s 3). Accessing the fourth row. 86s 86s matrix[3][-1]= 86s { 86s {0.02620731131783857, 0.3512361467236737, 0.5545193253910446, 0.2966676955802058, 0.3224824965750991, 0.8195649154529825} 86s } 86s 86s 4). Accessing the first column. 86s 86s matrix[-1][0]= 86s { 86s {0.8611533965126503} 86s {0.2521429765625258} 86s {0.1021022387086652} 86s {0.02620731131783857} 86s {0.6542918671980248} 86s } 86s 86s 5). Populating a matrix template (below the diagonal). 86s 86s { 86s {0, 0, 0, 0, 0, 0} 86s {1, 0, 0, 0, 0, 0} 86s {1, 1, 0, 0, 0, 0} 86s {1, 1, 1, 0, 0, 0} 86s {1, 1, 1, 1, 0, 0} 86s } 86s 86s 6). Extracting (by row) matrix elements using the template. 86s 86s { 86s {0.2521429765625258, 0.1021022387086652, 0.8527768556617147, 0.02620731131783857, 0.3512361467236737, 0.5545193253910446, 0.6542918671980248, 0.8250730861502404, 0.6198701571253757, 0.1249153360549629} 86s } 86s 86s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 86s 86s matrix[{{1,1}}][{{3,2}}]= 86s { 86s {0.1011039731328152, 0.336958552323505} 86s {0.8527768556617147, 0.9326274331967875} 86s {0.3512361467236737, 0.5545193253910446} 86s } 86s 86s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 86s 86s 86s { 86s {0.741585172325274, 1.175715607938788, 1.620395741016318, 1.022567954618566, 1.99187474271333, 1.302880459357728} 86s {0.06357608062981045, 0.01022201338324102, 1.113541065983952, 1.316488800513454, 1.142190631294346, 1.33596168138279} 86s {0.01042486714932125, 0.727228365552281, 0.8697939291512284, 1.813613719404001, 1.390536708806464, 1.002922751379053} 86s {0.0006868231665101096, 0.123366830765294, 0.3074916822321392, 0.08801172160086969, 1.103994960597309, 1.671686650641454} 86s {0.4280978474814777, 0.680745597489482, 0.384239011694638, 0.01560384118172432, 0.9835115343711766, 1.844261235991628} 86s } 86s + for i in *.bf 86s + '[' -f MolecularClockF81.bf ']' 86s + hyphy MolecularClockF81.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s 86s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124511853; 86s Tree theTree=(HVRNASS:0.02575000992001696,(RICRSS3:0.05627633325970368,((ZMSUCS1:0.07162821854451373,(OSRSS1A:0.06060085909184281,(TASUCSYN1:0.02788050928673517,HVSSYNMR:0.02037103888178513)Internal1:0.05181504470091592)Node9:0.0201388752140165)Node7:0.1581214781121993,(MZESUS1:0.0766709632125869,ORRSS2:0.05436191919368689)Internal2:0.02506258319086711)Node6:0.03254927716192263)Node4:0.05901172489589786,TAAJ153:0.01372502139042321); 86s 86s 86s 1). Global Molecular Clock; the P-value is:0 86s Log Likelihood = -11927.6152775945; 86s Tree theTree=(HVRNASS:0.02157619050001621,(RICRSS3:0.123341757781444,((ZMSUCS1:0.05657749785917571,(OSRSS1A:0.04750827470212941,(TASUCSYN1:0.01823836386688954,HVSSYNMR:0.01823836386688954)Internal1:0.02926991083523986)Node9:0.009069223157046308)Node7:0.05763969173506601,(MZESUS1:0.07013415360040209,ORRSS2:0.07013415360040209)Internal2:0.04408303599383963)Node6:0.009124568187202274)Node4:0.02715740212935572,TAAJ153:0.1504991599107997); 86s 86s 86s 2). Molecular Clock starting at Internal1; the P-value is:0.1603812828385469 86s Log Likelihood = -11476.6977648851; 86s Tree theTree=(HVRNASS:0.02573844094146125,(RICRSS3:0.0563137871339699,((ZMSUCS1:0.0716703848407636,(OSRSS1A:0.06052200609648575,(TASUCSYN1:0.02412007171388292,HVSSYNMR:0.02412007171388292)Internal1:0.05180642512157242)Node9:0.02018832992932158)Node7:0.1580854007148063,(MZESUS1:0.07661279269927271,ORRSS2:0.05440972409288723)Internal2:0.02509732988446418)Node6:0.03251680758134581)Node4:0.05896716757648389,TAAJ153:0.01372945734068447); 86s 86s 86s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610198592905765 86s Log Likelihood = -11479.8412638503; 86s Tree theTree=(HVRNASS:0.02577626949934585,(RICRSS3:0.05653151541837186,((ZMSUCS1:0.07146574524396022,(OSRSS1A:0.06062672630458839,(TASUCSYN1:0.02412138069532457,HVSSYNMR:0.02412138069532457)Internal1:0.05166825454356137)Node9:0.02036980161852215)Node7:0.1580660019679755,(MZESUS1:0.06553596297695533,ORRSS2:0.06553596297695533)Internal2:0.02501869021797128)Node6:0.03236600635387854)Node4:0.05871283692533161,TAAJ153:0.01369806842377236); 86s + for i in *.bf 86s + '[' -f MolecularClockHKY85.bf ']' 86s + hyphy MolecularClockHKY85.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s 86s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.801342093; 86s Tree theTree=(HVRNASS:0.02587691912749383,(RICRSS3:0.05728330273598947,((ZMSUCS1:0.07269281555359218,(OSRSS1A:0.06094910676618378,(TASUCSYN1:0.02742974575288322,HVSSYNMR:0.02081801119511672)Node11:0.05284334387102224)Node9:0.0205154812926661)Node7:0.1589977181046804,(MZESUS1:0.07762386424784064,ORRSS2:0.05413968943108643)Node14:0.0260138095611969)Node6:0.03166782543907126)Node4:0.06040066936747673,TAAJ153:0.01384257218513097); 86s 86s 86s 1). Global Molecular Clock on transition rates; the P-value is:0 86s Log Likelihood = -11434.7015977526; 86s Tree theTree=(HVRNASS:0.02320093377666508,(RICRSS3:0.08335067907753874,((ZMSUCS1:0.06367225869474381,(OSRSS1A:0.05485628837400268,(TASUCSYN1:0.02325704414756039,HVSSYNMR:0.0189069368764526)Node11:0.04017289048064666)Node9:0.01328246090787509)Node7:0.1273883755917507,(MZESUS1:0.07240481747745382,ORRSS2:0.06226830770340222)Node14:0.03461823304172163)Node6:0.02068741863261955)Node4:0.03899077519482415,TAAJ153:0.08892019846246008); 86s 86s 86s 2). Global Molecular Clock on transversion rates; the P-value is:0 86s Log Likelihood = -11497.3782616367; 86s Tree theTree=(HVRNASS:0.02483377120663421,(RICRSS3:0.09400096808117495,((ZMSUCS1:0.06900022014439625,(OSRSS1A:0.05468843532302373,(TASUCSYN1:0.0227681191139076,HVSSYNMR:0.02033927398312015)Node11:0.04372662545759581)Node9:0.01674415689734263)Node7:0.0997132977051416,(MZESUS1:0.07447752494377287,ORRSS2:0.06133178983540311)Node14:0.03387025707708272)Node6:0.02079835489865799)Node4:0.05007195315719793,TAAJ153:0.0730592542564953); 86s 86s 86s 3). Global Molecular Clock on both rates; the P-value is:0 86s Log Likelihood = -11703.62617038; 86s Tree theTree=(HVRNASS:0.02209883094767406,(RICRSS3:0.123971345685067,((ZMSUCS1:0.0579930613164423,(OSRSS1A:0.04854097508115863,(TASUCSYN1:0.01832817327425516,HVSSYNMR:0.01832817327425516)Node11:0.03021280180690348)Node9:0.009452086235283666)Node7:0.05732323182605422,(MZESUS1:0.07024684227967057,ORRSS2:0.07024684227967057)Node14:0.04506945086282596)Node6:0.008655052542570449)Node4:0.02801791987639635,TAAJ153:0.1519892655614633); 86s + for i in *.bf 86s + '[' -f Non-Rev.bf ']' 86s + hyphy Non-Rev.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s Log Likelihood = -1152.77788413868; 86s Global Parameters: 86s GC=0.2878965015476054; 86s CG=0.1920278794550741; 86s GA=2.012575640829181; 86s CT=1.28591509703919; 86s GT=0.09060941497903398; 86s CA=0.9369445982106634; 86s AT=0.4552741717944004; 86s AG=1.673851652688038; 86s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.260563613483256; 86s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.092653801488938; 86s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.832744149228912; 86s 86s Tree givenTree=(256:0.01350757367397654,(822:0.02842308763163221,159:0.006187823724833804)Node2:0.00343883053584559,((113:0.02185673722727815,9939:0.07937141432558381)Node6:0.004975656729563787,(6760:0.07324190704932776,((317:0.04006168902397533,6767:0.06989378017413259)Node12:0.0115840387106518,((135:0.02158968959787761,(529:0.03501297020553119,105r:0.0141201937960671)Node18:0.02381308472003549)Node16:0.005281310405131212,(719:0.02874077311842878,136:0.009477399348348198)Node21:0.04923282791485612)Node15:0.01636560054114494)Node11:0.01279840155005876)Node9:0.02191385256353895)Node5:0.02023916042631375); 86s + for i in *.bf 86s + '[' -f PBootstrapHetRates.bf ']' 86s + hyphy PBootstrapHetRates.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s 86s ----ORIGINAL DATA---- 86s Log Likelihood = -1127.31557547917; 86s Global Parameters: 86s alpha=0.3190382643796303; 86s kappa=0.323480786769056; 86s 86s Tree givenTree=(256:0.01259121382537815,(822:0.03174906135353765,159:0.004696749055441803)Node2:0.003784051027636173,((113:0.02291226987302801,9939:0.09714380968074078)Node6:0.001957336262686744,(6760:0.0872208952232702,((317:0.04574858519886639,6767:0.08109947576804025)Node12:0.007397509547353489,((135:0.01862859871271914,(529:0.03694189450261745,105r:0.01500636842287409)Node18:0.03036654042762036)Node16:0.00715334703675526,(719:0.0334258877439834,136:0.007167816475717228)Node21:0.05748874066048163)Node15:0.01789059336941416)Node11:0.018838736673502)Node9:0.02369093495084598)Node5:0.02502054401422136); 86s 86s Using the seed: 86s 1739653225 86s Category variable name: TRUE 86s Site Rate 86s 0 0.00000 86s 1 0.00000 86s 2 0.00000 86s 3 0.00000 86s 4 0.00000 86s 5 0.00001 86s 6 0.00001 86s 7 0.00001 86s 8 0.00004 86s 9 0.00006 86s 10 0.00014 86s 11 0.00018 86s 12 0.00028 86s 13 0.00040 86s 14 0.00044 86s 15 0.00048 86s 16 0.00060 86s 17 0.00081 86s 18 0.00085 86s 19 0.00088 86s 20 0.00106 86s 21 0.00126 86s 22 0.00130 86s 23 0.00133 86s 24 0.00137 86s 25 0.00142 86s 26 0.00153 86s 27 0.00164 86s 28 0.00192 86s 29 0.00198 86s 30 0.00202 86s 31 0.00207 86s 32 0.00218 86s 33 0.00220 86s 34 0.00230 86s 35 0.00234 86s 36 0.00247 86s 37 0.00273 86s 38 0.00366 86s 39 0.00423 86s 40 0.00475 86s 41 0.00520 86s 42 0.00547 86s 43 0.00628 86s 44 0.00709 86s 45 0.00744 86s 46 0.00753 86s 47 0.00812 86s 48 0.00847 86s 49 0.00868 86s 50 0.00943 86s 51 0.00981 86s 52 0.01018 86s 53 0.01028 86s 54 0.01098 86s 55 0.01110 86s 56 0.01247 86s 57 0.01358 86s 58 0.01537 86s 59 0.01544 86s 60 0.01551 86s 61 0.01558 86s 62 0.01607 86s 63 0.01864 86s 64 0.02094 86s 65 0.02193 86s 66 0.02246 86s 67 0.02396 86s 68 0.02406 86s 69 0.02480 86s 70 0.02548 86s 71 0.02700 86s 72 0.02729 86s 73 0.02786 86s 74 0.02804 86s 75 0.03166 86s 76 0.03682 86s 77 0.04161 86s 78 0.04261 86s 79 0.04539 86s 80 0.04581 86s 81 0.04599 86s 82 0.04696 86s 83 0.04906 86s 84 0.05156 86s 85 0.05208 86s 86 0.05527 86s 87 0.05810 86s 88 0.06500 86s 89 0.07179 86s 90 0.07427 86s 91 0.07604 86s 92 0.08159 86s 93 0.08445 86s 94 0.08809 86s 95 0.08846 86s 96 0.08923 86s 97 0.09322 86s 98 0.10126 86s 99 0.10179 86s 100 0.10191 86s 101 0.11007 86s 102 0.11111 86s 103 0.11521 86s 104 0.11715 86s 105 0.11908 86s 106 0.12056 86s 107 0.12767 86s 108 0.12939 86s 109 0.12969 86s 110 0.13006 86s 111 0.13188 86s 112 0.14333 86s 113 0.14350 86s 114 0.14377 86s 115 0.14806 86s 116 0.15432 86s 117 0.15729 86s 118 0.15784 86s 119 0.15801 86s 120 0.16098 86s 121 0.16816 86s 122 0.17019 86s 123 0.17266 86s 124 0.17656 86s 125 0.17938 86s 126 0.18193 86s 127 0.19219 86s 128 0.19277 86s 129 0.19560 86s 130 0.19599 86s 131 0.20077 86s 132 0.20411 86s 133 0.21598 86s 134 0.22283 86s 135 0.22927 86s 136 0.23000 86s 137 0.24509 86s 138 0.24795 86s 139 0.26070 86s 140 0.26547 86s 141 0.26725 86s 142 0.26831 86s 143 0.27116 86s 144 0.27208 86s 145 0.27621 86s 146 0.27874 86s 147 0.28203 86s 148 0.28377 86s 149 0.28717 86s 150 0.29324 86s 151 0.29705 86s 152 0.30860 86s 153 0.31060 86s 154 0.31766 86s 155 0.32094 86s 156 0.32844 86s 157 0.32974 86s 158 0.33443 86s 159 0.33718 86s 160 0.34136 86s 161 0.34743 86s 162 0.34854 86s 163 0.36459 86s 164 0.38281 86s 165 0.38345 86s 166 0.38980 86s 167 0.39384 86s 168 0.39488 86s 169 0.39598 86s 170 0.40997 86s 171 0.43111 86s 172 0.43753 86s 173 0.45445 86s 174 0.46232 86s 175 0.46358 86s 176 0.48264 86s 177 0.49394 86s 178 0.49667 86s 179 0.50762 86s 180 0.56232 86s 181 0.56730 86s 182 0.56822 86s 183 0.61394 86s 184 0.63009 86s 185 0.69091 86s 186 0.70557 86s 187 0.70863 86s 188 0.73783 86s 189 0.76028 86s 190 0.77787 86s 191 0.78728 86s 192 0.78919 86s 193 0.81032 86s 194 0.81515 86s 195 0.81575 86s 196 0.83497 86s 197 0.84740 86s 198 0.86347 86s 199 0.87754 86s 200 0.91782 86s 201 0.97938 86s 202 1.00032 86s 203 1.03215 86s 204 1.05567 86s 205 1.08930 86s 206 1.11874 86s 207 1.13488 86s 208 1.13802 86s 209 1.15096 86s 210 1.15615 86s 211 1.17764 86s 212 1.18680 86s 213 1.26932 86s 214 1.28403 86s 215 1.31703 86s 216 1.33269 86s 217 1.35640 86s 218 1.36228 86s 219 1.38738 86s 220 1.39088 86s 221 1.49592 86s 222 1.51398 86s 223 1.56040 86s 224 1.56125 86s 225 1.59863 86s 226 1.93573 86s 227 2.01988 86s 228 2.09188 86s 229 2.13410 86s 230 2.15547 86s 231 2.26344 86s 232 2.29348 86s 233 2.40238 86s 234 2.43945 86s 235 2.47235 86s 236 2.49501 86s 237 2.50696 86s 238 2.52191 86s 239 2.72234 86s 240 2.78249 86s 241 2.80794 86s 242 2.81467 86s 243 2.87338 86s 244 2.88942 86s 245 3.04842 86s 246 3.11905 86s 247 3.12942 86s 248 3.15393 86s 249 3.18675 86s 250 3.29652 86s 251 3.34923 86s 252 3.40774 86s 253 3.97304 86s 254 4.04620 86s 255 4.35837 86s 256 4.40779 86s 257 4.67663 86s 258 4.76488 86s 259 4.81215 86s 260 4.85650 86s 261 5.84853 86s 262 5.87808 86s 263 6.03566 86s 264 6.15927 86s 265 6.34144 86s 266 6.62829 86s 267 7.30394 86s 268 7.33190 86s 269 7.41075 86s 270 7.80113 86s 271 8.16184 86s 272 9.69912 86s 86s Mean = 0.9646081609051356 86s Var = 2.856205412181442 (1/alpha) = 3.134420261295301 86s Log Likelihood = -1099.56654250237; 86s Tree givenTree=(256:0.01860538216592163,(822:0.02270294265010517,159:0.01094295279063959)Node2:0.003780125299159155,((113:0.01828957740878258,9939:0.07803362120391523)Node6:0.007454163698445758,(6760:0.07117756915256836,((317:0.03719474236305448,6767:0.07205711603473006)Node12:0.01019711262477446,((135:0.02037016430094575,(529:0.03423644431361968,105r:0.01129635941382865)Node18:0.02853411094307351)Node16:0.006570770995922345,(719:0.02829658769318103,136:0.009598218497603334)Node21:0.04403605938644621)Node15:0.01656544075209431)Node11:0.01314632215991641)Node9:0.02914838877282535)Node5:0.01372591353217269); 86s + for i in *.bf 86s + '[' -f REV.bf ']' 86s + hyphy REV.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s + for i in *.bf 86s + '[' -f REVshared.bf ']' 86s + hyphy REVshared.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s Log Likelihood = -1156.62547812924; 86s Global Parameters: 86s AT=0.3659305368438306; 86s GT=0.4642708694719478; 86s CG=0.2489094004429558; 86s AG=1.864573921247967; 86s CT=1.209041720129288; 86s 86s Tree givenTree=(256:0.01208398846959864,(822:0.02975092918598913,159:0.00467531992712307)Node2:0.003482408674095348,((113:0.02209990617746585,9939:0.07979806639491439)Node6:0.004702158179013777,(6760:0.07209300945103697,((317:0.03912165145841142,6767:0.07108749338931902)Node12:0.01084597413702608,((135:0.02051433585184169,(529:0.03439236541276284,105r:0.01466399904543574)Node18:0.02467425245294734)Node16:0.005566003025397778,(719:0.02876800901809972,136:0.00945211041963227)Node21:0.0491095876501559)Node15:0.0158425315611777)Node11:0.01426362717141769)Node9:0.02296359852812584)Node5:0.02143618025545869); 86s + for i in *.bf 86s + '[' -f ReplicateConstraint1.bf ']' 86s + hyphy ReplicateConstraint1.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s 1).Unconstrained HKY85 86s 86s Log Likelihood = -1152.88; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.317.trvs 86s Parameter 2 : hivTree.317.trst 86s Parameter 3 : hivTree.6767.trvs 86s Parameter 4 : hivTree.6767.trst 86s Parameter 5 : hivTree.Node2.trvs 86s Parameter 6 : hivTree.Node2.trst 86s Parameter 7 : hivTree.135.trvs 86s Parameter 8 : hivTree.135.trst 86s Parameter 9 : hivTree.529.trvs 86s Parameter 10 : hivTree.529.trst 86s Parameter 11 : hivTree.105r.trvs 86s Parameter 12 : hivTree.105r.trst 86s Parameter 13 : hivTree.Node8.trvs 86s Parameter 14 : hivTree.Node8.trst 86s Parameter 15 : hivTree.iNode1.trvs 86s Parameter 16 : hivTree.iNode1.trst 86s Parameter 17 : hivTree.719.trvs 86s Parameter 18 : hivTree.719.trst 86s Parameter 19 : hivTree.136.trvs 86s Parameter 20 : hivTree.136.trst 86s Parameter 21 : hivTree.Node11.trvs 86s Parameter 22 : hivTree.Node11.trst 86s Parameter 23 : hivTree.Node5.trvs 86s Parameter 24 : hivTree.Node5.trst 86s Parameter 25 : hivTree.Node1.trvs 86s Parameter 26 : hivTree.Node1.trst 86s Parameter 27 : hivTree.6760.trvs 86s Parameter 28 : hivTree.6760.trst 86s Parameter 29 : hivTree.113.trvs 86s Parameter 30 : hivTree.113.trst 86s Parameter 31 : hivTree.9939.trvs 86s Parameter 32 : hivTree.9939.trst 86s Parameter 33 : hivTree.Node16.trvs 86s Parameter 34 : hivTree.Node16.trst 86s Parameter 35 : hivTree.256.trvs 86s Parameter 36 : hivTree.256.trst 86s Parameter 37 : hivTree.822.trvs 86s Parameter 38 : hivTree.822.trst 86s Parameter 39 : hivTree.159.trvs 86s Parameter 40 : hivTree.159.trst 86s Parameter 41 : hivTree.Node21.trvs 86s Parameter 42 : hivTree.Node21.trst 86s Parameter 43 : hivTree.iNode2.trvs 86s Parameter 44 : hivTree.iNode2.trst 86s Parameter 45 : hivTree.Node15.trvs 86s Parameter 46 : hivTree.Node15.trst 86s 86s 2).HKY85 constrained to F81 86s 86s Log Likelihood = -1187.55; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.317.trvs 86s Parameter 2 : hivTree.6767.trvs 86s Parameter 3 : hivTree.Node2.trvs 86s Parameter 4 : hivTree.135.trvs 86s Parameter 5 : hivTree.529.trvs 86s Parameter 6 : hivTree.105r.trvs 86s Parameter 7 : hivTree.Node8.trvs 86s Parameter 8 : hivTree.iNode1.trvs 86s Parameter 9 : hivTree.719.trvs 86s Parameter 10 : hivTree.136.trvs 86s Parameter 11 : hivTree.Node11.trvs 86s Parameter 12 : hivTree.Node5.trvs 86s Parameter 13 : hivTree.Node1.trvs 86s Parameter 14 : hivTree.6760.trvs 86s Parameter 15 : hivTree.113.trvs 86s Parameter 16 : hivTree.9939.trvs 86s Parameter 17 : hivTree.Node16.trvs 86s Parameter 18 : hivTree.256.trvs 86s Parameter 19 : hivTree.822.trvs 86s Parameter 20 : hivTree.159.trvs 86s Parameter 21 : hivTree.Node21.trvs 86s Parameter 22 : hivTree.iNode2.trvs 86s Parameter 23 : hivTree.Node15.trvs 86s 86s Constrained Parameters List 86s 86s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 86s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 86s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 86s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 86s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 86s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 86s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 86s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 86s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 86s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 86s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 86s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 86s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 86s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 86s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 86s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 86s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 86s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 86s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 86s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 86s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 86s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 86s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 86s 86s 3).HKY85 constrained to F81 on internal branches 86s 86s Log Likelihood = -1167.99; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.Node2.trvs 86s Parameter 2 : hivTree.Node8.trvs 86s Parameter 3 : hivTree.iNode1.trvs 86s Parameter 4 : hivTree.Node11.trvs 86s Parameter 5 : hivTree.Node5.trvs 86s Parameter 6 : hivTree.Node1.trvs 86s Parameter 7 : hivTree.Node16.trvs 86s Parameter 8 : hivTree.Node21.trvs 86s Parameter 9 : hivTree.iNode2.trvs 86s Parameter 10 : hivTree.Node15.trvs 86s Parameter 11 : hivTree.317.trst 86s Parameter 12 : hivTree.317.trvs 86s Parameter 13 : hivTree.6767.trvs 86s Parameter 14 : hivTree.6767.trst 86s Parameter 15 : hivTree.135.trst 86s Parameter 16 : hivTree.135.trvs 86s Parameter 17 : hivTree.529.trvs 86s Parameter 18 : hivTree.529.trst 86s Parameter 19 : hivTree.105r.trst 86s Parameter 20 : hivTree.105r.trvs 86s Parameter 21 : hivTree.719.trvs 86s Parameter 22 : hivTree.719.trst 86s Parameter 23 : hivTree.136.trvs 86s Parameter 24 : hivTree.136.trst 86s Parameter 25 : hivTree.6760.trvs 86s Parameter 26 : hivTree.6760.trst 86s Parameter 27 : hivTree.113.trvs 86s Parameter 28 : hivTree.113.trst 86s Parameter 29 : hivTree.9939.trst 86s Parameter 30 : hivTree.9939.trvs 86s Parameter 31 : hivTree.256.trvs 86s Parameter 32 : hivTree.256.trst 86s Parameter 33 : hivTree.822.trvs 86s Parameter 34 : hivTree.822.trst 86s Parameter 35 : hivTree.159.trst 86s Parameter 36 : hivTree.159.trvs 86s 86s Constrained Parameters List 86s 86s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 86s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 86s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 86s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 86s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 86s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 86s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 86s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 86s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 86s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 86s 86s 4).HKY85 with shared ratio. 86s 86s Log Likelihood = -1165.7; 86s 86s Independent Parameters List 86s 86s Parameter 1 : R 86s Parameter 2 : hivTree.317.trst 86s Parameter 3 : hivTree.6767.trst 86s Parameter 4 : hivTree.Node2.trst 86s Parameter 5 : hivTree.135.trst 86s Parameter 6 : hivTree.529.trst 86s Parameter 7 : hivTree.105r.trst 86s Parameter 8 : hivTree.Node8.trst 86s Parameter 9 : hivTree.iNode1.trst 86s Parameter 10 : hivTree.719.trst 86s Parameter 11 : hivTree.136.trst 86s Parameter 12 : hivTree.Node11.trst 86s Parameter 13 : hivTree.Node5.trst 86s Parameter 14 : hivTree.Node1.trst 86s Parameter 15 : hivTree.6760.trst 86s Parameter 16 : hivTree.113.trst 86s Parameter 17 : hivTree.9939.trst 86s Parameter 18 : hivTree.Node16.trst 86s Parameter 19 : hivTree.256.trst 86s Parameter 20 : hivTree.822.trst 86s Parameter 21 : hivTree.159.trst 86s Parameter 22 : hivTree.Node21.trst 86s Parameter 23 : hivTree.iNode2.trst 86s Parameter 24 : hivTree.Node15.trst 86s 86s Constrained Parameters List 86s 86s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 86s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 86s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 86s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 86s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 86s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 86s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 86s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 86s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 86s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 86s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 86s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 86s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 86s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 86s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 86s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 86s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 86s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 86s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 86s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 86s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 86s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 86s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 86s + '[' -f ReplicateConstraint2.bf ']' 86s + hyphy ReplicateConstraint2.bf 86s Using /usr/lib/hyphy/bin/hyphy-avx 86s 1).Unconstrained HKY85 86s 86s Log Likelihood = -1152.88; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.317.trvs 86s Parameter 2 : hivTree.317.trst 86s Parameter 3 : hivTree.6767.trvs 86s Parameter 4 : hivTree.6767.trst 86s Parameter 5 : hivTree.Node2.trvs 86s Parameter 6 : hivTree.Node2.trst 86s Parameter 7 : hivTree.135.trvs 86s Parameter 8 : hivTree.135.trst 86s Parameter 9 : hivTree.529.trvs 86s Parameter 10 : hivTree.529.trst 86s Parameter 11 : hivTree.105r.trvs 86s Parameter 12 : hivTree.105r.trst 86s Parameter 13 : hivTree.Node8.trvs 86s Parameter 14 : hivTree.Node8.trst 86s Parameter 15 : hivTree.iNode1.trvs 86s Parameter 16 : hivTree.iNode1.trst 86s Parameter 17 : hivTree.719.trvs 86s Parameter 18 : hivTree.719.trst 86s Parameter 19 : hivTree.136.trvs 86s Parameter 20 : hivTree.136.trst 86s Parameter 21 : hivTree.Node11.trvs 86s Parameter 22 : hivTree.Node11.trst 86s Parameter 23 : hivTree.Node5.trvs 86s Parameter 24 : hivTree.Node5.trst 86s Parameter 25 : hivTree.Node1.trvs 86s Parameter 26 : hivTree.Node1.trst 86s Parameter 27 : hivTree.6760.trvs 86s Parameter 28 : hivTree.6760.trst 86s Parameter 29 : hivTree.113.trvs 86s Parameter 30 : hivTree.113.trst 86s Parameter 31 : hivTree.9939.trvs 86s Parameter 32 : hivTree.9939.trst 86s Parameter 33 : hivTree.Node16.trvs 86s Parameter 34 : hivTree.Node16.trst 86s Parameter 35 : hivTree.256.trvs 86s Parameter 36 : hivTree.256.trst 86s Parameter 37 : hivTree.822.trvs 86s Parameter 38 : hivTree.822.trst 86s Parameter 39 : hivTree.159.trvs 86s Parameter 40 : hivTree.159.trst 86s Parameter 41 : hivTree.Node21.trvs 86s Parameter 42 : hivTree.Node21.trst 86s Parameter 43 : hivTree.iNode2.trvs 86s Parameter 44 : hivTree.iNode2.trst 86s Parameter 45 : hivTree.Node15.trvs 86s Parameter 46 : hivTree.Node15.trst 86s 86s 2).HKY85 constrained to F81 on the "iNode1" subtree 86s 86s Log Likelihood = -1157.82; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.135.trvs 86s Parameter 2 : hivTree.529.trvs 86s Parameter 3 : hivTree.105r.trvs 86s Parameter 4 : hivTree.Node8.trvs 86s Parameter 5 : hivTree.317.trvs 86s Parameter 6 : hivTree.317.trst 86s Parameter 7 : hivTree.6767.trst 86s Parameter 8 : hivTree.6767.trvs 86s Parameter 9 : hivTree.Node2.trst 86s Parameter 10 : hivTree.Node2.trvs 86s Parameter 11 : hivTree.iNode1.trvs 86s Parameter 12 : hivTree.iNode1.trst 86s Parameter 13 : hivTree.719.trvs 86s Parameter 14 : hivTree.719.trst 86s Parameter 15 : hivTree.136.trvs 86s Parameter 16 : hivTree.136.trst 86s Parameter 17 : hivTree.Node11.trvs 86s Parameter 18 : hivTree.Node11.trst 86s Parameter 19 : hivTree.Node5.trvs 86s Parameter 20 : hivTree.Node5.trst 86s Parameter 21 : hivTree.Node1.trvs 86s Parameter 22 : hivTree.Node1.trst 86s Parameter 23 : hivTree.6760.trvs 86s Parameter 24 : hivTree.6760.trst 86s Parameter 25 : hivTree.113.trvs 86s Parameter 26 : hivTree.113.trst 86s Parameter 27 : hivTree.9939.trvs 86s Parameter 28 : hivTree.9939.trst 86s Parameter 29 : hivTree.Node16.trvs 86s Parameter 30 : hivTree.Node16.trst 86s Parameter 31 : hivTree.256.trvs 86s Parameter 32 : hivTree.256.trst 86s Parameter 33 : hivTree.822.trvs 86s Parameter 34 : hivTree.822.trst 86s Parameter 35 : hivTree.159.trvs 86s Parameter 36 : hivTree.159.trst 86s Parameter 37 : hivTree.Node21.trvs 86s Parameter 38 : hivTree.Node21.trst 86s Parameter 39 : hivTree.iNode2.trvs 86s Parameter 40 : hivTree.iNode2.trst 86s Parameter 41 : hivTree.Node15.trvs 86s Parameter 42 : hivTree.Node15.trst 86s 86s Constrained Parameters List 86s 86s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 86s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 86s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 86s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 86s 86s 3).HKY85 constrained to F81 on the "iNode1" branch 86s 86s Log Likelihood = -1152.88; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.317.trvs 86s Parameter 2 : hivTree.317.trst 86s Parameter 3 : hivTree.6767.trvs 86s Parameter 4 : hivTree.6767.trst 86s Parameter 5 : hivTree.Node2.trvs 86s Parameter 6 : hivTree.Node2.trst 86s Parameter 7 : hivTree.135.trvs 86s Parameter 8 : hivTree.135.trst 86s Parameter 9 : hivTree.529.trvs 86s Parameter 10 : hivTree.529.trst 86s Parameter 11 : hivTree.105r.trvs 86s Parameter 12 : hivTree.105r.trst 86s Parameter 13 : hivTree.Node8.trvs 86s Parameter 14 : hivTree.Node8.trst 86s Parameter 15 : hivTree.iNode1.trvs 86s Parameter 16 : hivTree.iNode1.trst 86s Parameter 17 : hivTree.719.trvs 86s Parameter 18 : hivTree.719.trst 86s Parameter 19 : hivTree.136.trvs 86s Parameter 20 : hivTree.136.trst 86s Parameter 21 : hivTree.Node11.trvs 86s Parameter 22 : hivTree.Node11.trst 86s Parameter 23 : hivTree.Node5.trvs 86s Parameter 24 : hivTree.Node5.trst 86s Parameter 25 : hivTree.Node1.trvs 86s Parameter 26 : hivTree.Node1.trst 86s Parameter 27 : hivTree.6760.trvs 86s Parameter 28 : hivTree.6760.trst 86s Parameter 29 : hivTree.113.trvs 86s Parameter 30 : hivTree.113.trst 86s Parameter 31 : hivTree.9939.trvs 86s Parameter 32 : hivTree.9939.trst 86s Parameter 33 : hivTree.Node16.trvs 86s Parameter 34 : hivTree.Node16.trst 86s Parameter 35 : hivTree.256.trvs 86s Parameter 36 : hivTree.256.trst 86s Parameter 37 : hivTree.822.trvs 86s Parameter 38 : hivTree.822.trst 86s Parameter 39 : hivTree.159.trvs 86s Parameter 40 : hivTree.159.trst 86s Parameter 41 : hivTree.Node21.trvs 86s Parameter 42 : hivTree.Node21.trst 86s Parameter 43 : hivTree.iNode2.trvs 86s Parameter 44 : hivTree.iNode2.trst 86s Parameter 45 : hivTree.Node15.trvs 86s Parameter 46 : hivTree.Node15.trst 86s 86s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 86s 86s Log Likelihood = -1152.88; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.317.trvs 86s Parameter 2 : hivTree.317.trst 86s Parameter 3 : hivTree.6767.trvs 86s Parameter 4 : hivTree.6767.trst 86s Parameter 5 : hivTree.Node2.trvs 86s Parameter 6 : hivTree.Node2.trst 86s Parameter 7 : hivTree.135.trvs 86s Parameter 8 : hivTree.135.trst 86s Parameter 9 : hivTree.529.trvs 86s Parameter 10 : hivTree.529.trst 86s Parameter 11 : hivTree.105r.trvs 86s Parameter 12 : hivTree.105r.trst 86s Parameter 13 : hivTree.Node8.trvs 86s Parameter 14 : hivTree.Node8.trst 86s Parameter 15 : hivTree.iNode1.trvs 86s Parameter 16 : hivTree.iNode1.trst 86s Parameter 17 : hivTree.719.trvs 86s Parameter 18 : hivTree.719.trst 86s Parameter 19 : hivTree.136.trvs 86s Parameter 20 : hivTree.136.trst 86s Parameter 21 : hivTree.Node11.trvs 86s Parameter 22 : hivTree.Node11.trst 86s Parameter 23 : hivTree.Node5.trvs 86s Parameter 24 : hivTree.Node5.trst 86s Parameter 25 : hivTree.Node1.trvs 86s Parameter 26 : hivTree.Node1.trst 86s Parameter 27 : hivTree.6760.trvs 86s Parameter 28 : hivTree.6760.trst 86s Parameter 29 : hivTree.113.trvs 86s Parameter 30 : hivTree.113.trst 86s Parameter 31 : hivTree.9939.trvs 86s Parameter 32 : hivTree.9939.trst 86s Parameter 33 : hivTree.Node16.trvs 86s Parameter 34 : hivTree.Node16.trst 86s Parameter 35 : hivTree.256.trvs 86s Parameter 36 : hivTree.256.trst 86s Parameter 37 : hivTree.822.trvs 86s Parameter 38 : hivTree.822.trst 86s Parameter 39 : hivTree.159.trvs 86s Parameter 40 : hivTree.159.trst 86s Parameter 41 : hivTree.Node21.trvs 86s Parameter 42 : hivTree.Node21.trst 86s Parameter 43 : hivTree.iNode2.trvs 86s Parameter 44 : hivTree.iNode2.trst 86s Parameter 45 : hivTree.Node15.trvs 86s Parameter 46 : hivTree.Node15.trst 86s 86s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 86s 86s Log Likelihood = -1152.88; 86s 86s Independent Parameters List 86s 86s Parameter 1 : hivTree.317.trvs 86s Parameter 2 : hivTree.317.trst 86s Parameter 3 : hivTree.6767.trvs 86s Parameter 4 : hivTree.6767.trst 86s Parameter 5 : hivTree.Node2.trvs 86s Parameter 6 : hivTree.Node2.trst 86s Parameter 7 : hivTree.135.trvs 86s Parameter 8 : hivTree.135.trst 86s Parameter 9 : hivTree.529.trvs 86s Parameter 10 : hivTree.529.trst 86s Parameter 11 : hivTree.105r.trvs 86s Parameter 12 : hivTree.105r.trst 86s Parameter 13 : hivTree.Node8.trvs 86s Parameter 14 : hivTree.Node8.trst 86s Parameter 15 : hivTree.iNode1.trvs 86s Parameter 16 : hivTree.iNode1.trst 86s Parameter 17 : hivTree.719.trvs 86s Parameter 18 : hivTree.719.trst 86s Parameter 19 : hivTree.136.trvs 86s Parameter 20 : hivTree.136.trst 86s Parameter 21 : hivTree.Node11.trvs 86s Parameter 22 : hivTree.Node11.trst 86s Parameter 23 : hivTree.Node5.trvs 86s Parameter 24 : hivTree.Node5.trst 86s Parameter 25 : hivTree.Node1.trvs 86s Parameter 26 : hivTree.Node1.trst 86s Parameter 27 : hivTree.6760.trvs 86s Parameter 28 : hivTree.6760.trst 86s Parameter 29 : hivTree.113.trvs 86s Parameter 30 : hivTree.113.trst 86s Parameter 31 : hivTree.9939.trvs 86s Parameter 32 : hivTree.9939.trst 86s Parameter 33 : hivTree.Node16.trvs 86s Parameter 34 : hivTree.Node16.trst 86s Parameter 35 : hivTree.256.trvs 86s Parameter 36 : hivTree.256.trst 86s Parameter 37 : hivTree.822.trvs 86s Parameter 38 : hivTree.822.trst 86s Parameter 39 : hivTree.159.trvs 86s Parameter 40 : hivTree.159.trst 86s Parameter 41 : hivTree.Node21.trvs 86s Parameter 42 : hivTree.Node21.trst 86s Parameter 43 : hivTree.iNode2.trvs 86s Parameter 44 : hivTree.iNode2.trst 86s Parameter 45 : hivTree.Node15.trvs 87s Parameter 46 : hivTree.Node15.trst+ for i in *.bf 87s + '[' -f aa.bf ']' 87s + hyphy aa.bf 87s 87s 87s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 87s 87s Log Likelihood = -1157.82; 87s 87s Independent Parameters List 87s 87s Parameter 1 : hivTree.135.trst 87s Parameter 2 : hivTree.529.trst 87s Parameter 3 : hivTree.105r.trst 87s Parameter 4 : hivTree.Node8.trst 87s Parameter 5 : hivTree.317.trvs 87s Parameter 6 : hivTree.317.trst 87s Parameter 7 : hivTree.6767.trst 87s Parameter 8 : hivTree.6767.trvs 87s Parameter 9 : hivTree.Node2.trst 87s Parameter 10 : hivTree.Node2.trvs 87s Parameter 11 : hivTree.iNode1.trvs 87s Parameter 12 : hivTree.iNode1.trst 87s Parameter 13 : hivTree.719.trvs 87s Parameter 14 : hivTree.719.trst 87s Parameter 15 : hivTree.136.trvs 87s Parameter 16 : hivTree.136.trst 87s Parameter 17 : hivTree.Node11.trvs 87s Parameter 18 : hivTree.Node11.trst 87s Parameter 19 : hivTree.Node5.trvs 87s Parameter 20 : hivTree.Node5.trst 87s Parameter 21 : hivTree.Node1.trvs 87s Parameter 22 : hivTree.Node1.trst 87s Parameter 23 : hivTree.6760.trvs 87s Parameter 24 : hivTree.6760.trst 87s Parameter 25 : hivTree.113.trvs 87s Parameter 26 : hivTree.113.trst 87s Parameter 27 : hivTree.9939.trvs 87s Parameter 28 : hivTree.9939.trst 87s Parameter 29 : hivTree.Node16.trvs 87s Parameter 30 : hivTree.Node16.trst 87s Parameter 31 : hivTree.256.trvs 87s Parameter 32 : hivTree.256.trst 87s Parameter 33 : hivTree.822.trvs 87s Parameter 34 : hivTree.822.trst 87s Parameter 35 : hivTree.159.trvs 87s Parameter 36 : hivTree.159.trst 87s Parameter 37 : hivTree.Node21.trvs 87s Parameter 38 : hivTree.Node21.trst 87s Parameter 39 : hivTree.iNode2.trvs 87s Parameter 40 : hivTree.iNode2.trst 87s Parameter 41 : hivTree.Node15.trvs 87s Parameter 42 : hivTree.Node15.trst 87s 87s Constrained Parameters List 87s 87s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 87s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 87s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 87s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trstUsing /usr/lib/hyphy/bin/hyphy-avx 87s Log Likelihood = -1134.73159786164; 87s Tree theTree=(((Langur:0.07428656826252425,Baboon:0.03833724267473084)Node2:0.02338350071469701,Human:0.05948335123013283)Node1:0.02006356750543715,Rat:0.2458393538674523,(Cow:0.2550385870728282,Horse:0.5625920217215449)Node7:0.07059881410023654); 87s + for i in *.bf 87s + '[' -f definitions2.bf ']' 87s + hyphy definitions2.bf 87s Using /usr/lib/hyphy/bin/hyphy-avx 87s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 87s 87s Sample by MEAN: 87s 87s Sample mean = 0.5 (sample variance = 0.2450374540764348) 87s 87s Rate[0]= 0.06847689 (weight=0.2500000) 87s Rate[1]= 0.23837593 (weight=0.2500000) 87s Rate[2]= 0.50000000 (weight=0.2500000) 87s Rate[3]= 1.19314718 (weight=0.2500000) 87s ------------------------------------------------ 87s 87s Sample by MEDIAN: 87s 87s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 87s 87s Rate[0]= 0.06676570 (weight=0.2500000) 87s Rate[1]= 0.23500181 (weight=0.2500000) 87s Rate[2]= 0.49041463 (weight=0.2500000) 87s Rate[3]= 1.03972077 (weight=0.2500000) 87s ------------------------------------------------ 87s 87s Sample by SCALED_MEDIAN: 87s 87s Sample mean = 0.5 (sample variance = 0.2154404122636025) 87s 87s Rate[0]= 0.07289218 (weight=0.2500000) 87s Rate[1]= 0.25656580 (weight=0.2500000) 87s Rate[2]= 0.53541552 (weight=0.2500000) 87s Rate[3]= 1.13512650 (weight=0.2500000) 87s ------------------------------------------------ 87s 87s Sample by MEAN (numerical averaging): 87s 87s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 87s 87s Rate[0]= 0.06846096 (weight=0.2500000) 87s Rate[1]= 0.23834015 (weight=0.2500000) 87s Rate[2]= 0.49996411 (weight=0.2500000) 87s Rate[3]= 1.19314889 (weight=0.2500000) 87s ------------------------------------------------ 87s 87s Sample by MEAN (numerical CDF and averaging): 87s 87s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 87s 87s Rate[0]= 0.06849282 (weight=0.2500000) 87s Rate[1]= 0.23835613 (weight=0.2500000) 87s Rate[2]= 0.49994751 (weight=0.2500000) 87s Rate[3]= 1.19311765 (weight=0.2500000) 87s ------------------------------------------------ 87s 2). Equiprobable rates sampled from Exponential with lambda = 2 87s 87s Sample by MEDIAN (3 rate classes): 87s 87s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 87s 87s Rate[0]= 0.09116078 (weight=0.3333333) 87s Rate[1]= 0.34657359 (weight=0.3333333) 87s Rate[2]= 0.89587973 (weight=0.3333333) 87s ------------------------------------------------ 87s 87s Sample by MEDIAN (9 rate classes): 87s 87s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 87s 87s Rate[0]= 0.02857921 (weight=0.1111111) 87s Rate[1]= 0.09116078 (weight=0.1111111) 87s Rate[2]= 0.16271120 (weight=0.1111111) 87s Rate[3]= 0.24623824 (weight=0.1111111) 87s Rate[4]= 0.34657359 (weight=0.1111111) 87s Rate[5]= 0.47223080 (weight=0.1111111) 87s Rate[6]= 0.64046692 (weight=0.1111111) 87s Rate[7]= 0.89587973 (weight=0.1111111) 87s Rate[8]= 1.44518588 (weight=0.1111111) 87s ------------------------------------------------ 87s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 87s 87s Sample by MEAN (10 rate classes): 87s 87s Sample mean = 1 (sample variance = 0.1057310289486733) 87s 87s Rate[0]= 0.52447499 (weight=0.1000000) 87s Rate[1]= 0.67866972 (weight=0.1000000) 87s Rate[2]= 0.77209919 (weight=0.1000000) 87s Rate[3]= 0.85214884 (weight=0.1000000) 87s Rate[4]= 0.92850815 (weight=0.1000000) 87s Rate[5]= 1.00664500 (weight=0.1000000) 87s Rate[6]= 1.09192933 (weight=0.1000000) 87s Rate[7]= 1.19267960 (weight=0.1000000) 87s Rate[8]= 1.32858029 (weight=0.1000000) 87s Rate[9]= 1.62426489 (weight=0.1000000) 87s ------------------------------------------------ 87s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 87s 87s Sample by MEAN (10 rate classes): 87s 87s Sample mean = 2 (sample variance = 0.04259071282256012) 87s 87s Rate[0]= 1.66431246 (weight=0.1000000) 87s Rate[1]= 1.79212822 (weight=0.1000000) 87s Rate[2]= 1.86123411 (weight=0.1000000) 87s Rate[3]= 1.91722052 (weight=0.1000000) 87s Rate[4]= 1.96832799 (weight=0.1000000) 87s Rate[5]= 2.01862937 (weight=0.1000000) 87s Rate[6]= 2.07152664 (weight=0.1000000) 87s Rate[7]= 2.13166629 (weight=0.1000000) 87s Rate[8]= 2.20930216 (weight=0.1000000) 87s Rate[9]= 2.36565224 (weight=0.1000000) 87s ------------------------------------------------ 87s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 87s 87s Sample by MEAN (8 rate classes): 87s 87s Sample mean = 0.5 (sample variance = 0.09375000225643569) 87s 87s Rate[0]= 0.06250000 (weight=0.1250000) 87s Rate[1]= 0.18750000 (weight=0.1250000) 87s Rate[2]= 0.31250001 (weight=0.1250000) 87s Rate[3]= 0.43750001 (weight=0.1250000) 87s Rate[4]= 0.56249993 (weight=0.1250000) 87s Rate[5]= 0.68750001 (weight=0.1250000) 87s Rate[6]= 0.81250002 (weight=0.1250000) 87s Rate[7]= 0.93750002 (weight=0.1250000) 87s ------------------------------------------------ 87s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 87s 87s Sample by MEAN (8 rate classes): 87s 87s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 87s 87s Rate[0]= 2.17658588 (weight=0.1250000) 87s Rate[1]= 2.55230783 (weight=0.1250000) 87s Rate[2]= 2.75432532 (weight=+ for i in *.bf 87s + '[' -f definitions3.bf ']' 87s + hyphy definitions3.bf 87s 0.1250000) 87s Rate[3]= 2.92101185 (weight=0.1250000) 87s Rate[4]= 3.07898815 (weight=0.1250000) 87s Rate[5]= 3.24567468 (weight=0.1250000) 87s Rate[6]= 3.44769217 (weight=0.1250000) 87s Rate[7]= 3.82341415 (weight=0.1250000) 87s ------------------------------------------------ 87s Using /usr/lib/hyphy/bin/hyphy-avx 87s 87s 87s Sample mean = 1 (sample variance = 0.9920002887656187) 87s 87s Rate[0]= 0.05175536 (weight=0.1000000) 87s Rate[1]= 0.16309623 (weight=0.1000000) 87s Rate[2]= 0.28842380 (weight=0.1000000) 87s Rate[3]= 0.43177086 (weight=0.1000000) 87s Rate[4]= 0.59921784 (weight=0.1000000) 87s Rate[5]= 0.80057298 (weight=0.1000000) 87s Rate[6]= 1.05324451 (weight=0.1000000) 87s Rate[7]= 1.39304259 (weight=0.1000000) 87s Rate[8]= 1.91629073 (weight=0.1000000) 87s Rate[9]= 3.30258509 (weight=0.1000000) 87s ------------------------------------------------ 87s + for i in *.bf 87s + '[' -f displayFunction.bf ']' 87s + hyphy displayFunction.bf 87s Using /usr/lib/hyphy/bin/hyphy-avx 87s + for i in *.bf 87s + '[' -f profile_test.bf ']' 87s + hyphy profile_test.bf 87s Using /usr/lib/hyphy/bin/hyphy-avx 87s 87s Total run time (seconds) : 0.000000 87s Total number of steps : 1500005 87s 87s 1 : s=0; 87s Call count: 1 87s Time (seconds): 1.6e-11 87s 2 : m={5,1}; 87s Call count: 1 87s Time (seconds): 1.5e-11 87s 3 : k=0; 87s Call count: 1 87s Time (seconds): 2e-12 87s 4 : Branch under condition 'k<250000' 87s to 87s s=s+k; 87s else 87s #profilePAUSE, ; 87s Call count: 250001 87s Time (seconds): 2.305300000000241e-08 87s 5 : s=s+k; 87s Call count: 250000 87s Time (seconds): 2.375700000000307e-08 87s 6 : t=Random(0,5); 87s Call count: 250000 87s Time (seconds): 2.388400000000319e-08 87s 7 : m[t]=m[t]+1; 87s Call count: 250000 87s Time (seconds): 5.991700000003845e-08 87s 8 : k=k+1; 87s Call count: 250000 87s Time (seconds): 2.343900000000311e-08 87s 9 : Go to step 4 87s Call count: 250000 87s Time (seconds): 8.329000000000314e-09 87s 10 : #profilePAUSE, ; 87s Call count: 1 87s Time (seconds): 2e-12 87s + for i in *.bf 87s + '[' -f shared.bf ']' 87s + hyphy shared.bf 87s Using /usr/lib/hyphy/bin/hyphy-avx 87s + rm -f '*messages.log*' '*errors.log*' 87s autopkgtest [20:07:50]: test run-unit-tests: -----------------------] 88s autopkgtest [20:07:51]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 88s run-unit-tests PASS 88s autopkgtest [20:07:51]: @@@@@@@@@@@@@@@@@@@@ summary 88s run-unit-tests PASS 106s nova [W] Skipping flock for amd64 106s Creating nova instance adt-plucky-amd64-hyphy-20250215-200623-juju-7f2275-prod-proposed-migration-environment-2-501970f2-1fb4-48d8-b61f-1fddceb5ac0c from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)... 106s nova [W] Timed out waiting for c385bd0f-a02f-4615-b044-0156c385a6e7 to get deleted.