0s autopkgtest [01:59:40]: starting date and time: 2025-02-16 01:59:40+0000 0s autopkgtest [01:59:40]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:59:40]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y9sp7lgm/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 autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-9.secgroup --name adt-plucky-ppc64el-hyphy-20250216-015940-juju-7f2275-prod-proposed-migration-environment-20-8b3b8b8e-2f87-4740-989d-a101656475f3 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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/ 100s autopkgtest [02:01:20]: testbed dpkg architecture: ppc64el 100s autopkgtest [02:01:20]: testbed apt version: 2.9.28 100s autopkgtest [02:01:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s autopkgtest [02:01:20]: testbed release detected to be: None 101s autopkgtest [02:01:21]: updating testbed package index (apt update) 101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 102s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 102s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 102s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.0 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [842 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 103s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [167 kB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [760 B] 103s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [917 kB] 103s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [4228 B] 104s Fetched 2131 kB in 2s (951 kB/s) 105s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s The following packages will be upgraded: 107s dash gcc-14-base libatomic1 libgcc-s1 libp11-kit0 libstdc++6 libtasn1-6 107s libxdmcp6 107s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 1476 kB of archives. 107s After this operation, 15.4 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el dash ppc64el 0.5.12-12ubuntu1 [114 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libatomic1 ppc64el 14.2.0-17ubuntu1 [10.7 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-base ppc64el 14.2.0-17ubuntu1 [53.6 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++6 ppc64el 14.2.0-17ubuntu1 [886 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-s1 ppc64el 14.2.0-17ubuntu1 [39.2 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libp11-kit0 ppc64el 0.25.5-2ubuntu2 [305 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtasn1-6 ppc64el 4.20.0-2 [55.9 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxdmcp6 ppc64el 1:1.1.5-1 [11.6 kB] 109s Preconfiguring packages ... 109s Fetched 1476 kB in 1s (1202 kB/s) 109s (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 ... 106311 files and directories currently installed.) 109s Preparing to unpack .../dash_0.5.12-12ubuntu1_ppc64el.deb ... 109s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 109s Setting up dash (0.5.12-12ubuntu1) ... 109s (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 ... 106311 files and directories currently installed.) 109s Preparing to unpack .../libatomic1_14.2.0-17ubuntu1_ppc64el.deb ... 109s Unpacking libatomic1:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 109s Preparing to unpack .../gcc-14-base_14.2.0-17ubuntu1_ppc64el.deb ... 109s Unpacking gcc-14-base:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 109s Setting up gcc-14-base:ppc64el (14.2.0-17ubuntu1) ... 110s (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 ... 106311 files and directories currently installed.) 110s Preparing to unpack .../libstdc++6_14.2.0-17ubuntu1_ppc64el.deb ... 110s Unpacking libstdc++6:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 110s Setting up libstdc++6:ppc64el (14.2.0-17ubuntu1) ... 110s (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 ... 106311 files and directories currently installed.) 110s Preparing to unpack .../libgcc-s1_14.2.0-17ubuntu1_ppc64el.deb ... 110s Unpacking libgcc-s1:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 110s Setting up libgcc-s1:ppc64el (14.2.0-17ubuntu1) ... 110s (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 ... 106311 files and directories currently installed.) 110s Preparing to unpack .../libp11-kit0_0.25.5-2ubuntu2_ppc64el.deb ... 110s Unpacking libp11-kit0:ppc64el (0.25.5-2ubuntu2) over (0.25.5-2ubuntu1) ... 110s Preparing to unpack .../libtasn1-6_4.20.0-2_ppc64el.deb ... 110s Unpacking libtasn1-6:ppc64el (4.20.0-2) over (4.19.0-3build1) ... 110s Preparing to unpack .../libxdmcp6_1%3a1.1.5-1_ppc64el.deb ... 110s Unpacking libxdmcp6:ppc64el (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 110s Setting up libxdmcp6:ppc64el (1:1.1.5-1) ... 110s Setting up libp11-kit0:ppc64el (0.25.5-2ubuntu2) ... 110s Setting up libatomic1:ppc64el (14.2.0-17ubuntu1) ... 110s Setting up libtasn1-6:ppc64el (4.20.0-2) ... 110s Processing triggers for libc-bin (2.40-4ubuntu1) ... 110s Processing triggers for man-db (2.13.0-1) ... 111s Processing triggers for debianutils (5.21) ... 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 112s autopkgtest [02:01:32]: upgrading testbed (apt dist-upgrade and autopurge) 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 114s Entering ResolveByKeep 114s 114s The following packages will be upgraded: 114s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 115s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 11.7 MB of archives. 115s After this operation, 358 kB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc-dev-bin ppc64el 2.41-1ubuntu1 [25.3 kB] 115s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc6-dev ppc64el 2.41-1ubuntu1 [2046 kB] 116s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el locales all 2.41-1ubuntu1 [4246 kB] 117s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc6 ppc64el 2.41-1ubuntu1 [3243 kB] 118s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc-bin ppc64el 2.41-1ubuntu1 [742 kB] 118s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el iproute2 ppc64el 6.13.0-1ubuntu1 [1419 kB] 118s Preconfiguring packages ... 119s Fetched 11.7 MB in 4s (3145 kB/s) 119s (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 ... 106311 files and directories currently installed.) 119s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_ppc64el.deb ... 119s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 119s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_ppc64el.deb ... 119s Unpacking libc6-dev:ppc64el (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 119s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 119s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 120s Preparing to unpack .../libc6_2.41-1ubuntu1_ppc64el.deb ... 120s Checking for services that may need to be restarted... 120s Checking init scripts... 120s Checking for services that may need to be restarted... 120s Checking init scripts... 120s Stopping some services possibly affected by the upgrade (will be restarted later): 120s cron: stopping...done. 120s 120s Unpacking libc6:ppc64el (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 121s Setting up libc6:ppc64el (2.41-1ubuntu1) ... 121s Checking for services that may need to be restarted... 121s Checking init scripts... 121s Restarting services possibly affected by the upgrade: 121s cron: restarting...done. 121s 121s Services restarted successfully. 121s (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 ... 106312 files and directories currently installed.) 121s Preparing to unpack .../libc-bin_2.41-1ubuntu1_ppc64el.deb ... 121s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 121s Setting up libc-bin (2.41-1ubuntu1) ... 121s (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 ... 106312 files and directories currently installed.) 121s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_ppc64el.deb ... 122s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 122s Setting up iproute2 (6.13.0-1ubuntu1) ... 122s Setting up locales (2.41-1ubuntu1) ... 122s Installing new version of config file /etc/locale.alias ... 123s Generating locales (this might take a while)... 125s en_US.UTF-8... done 125s Generation complete. 125s Setting up libc-dev-bin (2.41-1ubuntu1) ... 125s Setting up libc6-dev:ppc64el (2.41-1ubuntu1) ... 125s Processing triggers for man-db (2.13.0-1) ... 127s Processing triggers for systemd (257.2-3ubuntu1) ... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Starting pkgProblemResolver with broken count: 0 129s Starting 2 pkgProblemResolver with broken count: 0 129s Done 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s autopkgtest [02:01:52]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 16:32:08 UTC 2025 132s autopkgtest [02:01:52]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 136s Get:1 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (dsc) [2298 B] 136s Get:2 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (tar) [2627 kB] 136s Get:3 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (diff) [17.4 kB] 136s gpgv: Signature made Sat Nov 30 06:13:22 2024 UTC 136s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 136s gpgv: Can't check signature: No public key 136s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.63+dfsg-1build2.dsc: no acceptable signature found 136s autopkgtest [02:01:56]: testing package hyphy version 2.5.63+dfsg-1build2 137s autopkgtest [02:01:57]: build not needed 138s autopkgtest [02:01:58]: test run-unit-tests: preparing testbed 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 140s The following NEW packages will be installed: 140s hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 140s libevent-pthreads-2.1-7t64 libfabric1 libgomp1 libhsa-runtime64-1 libhsakmt1 140s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libllvm17t64 libmunge2 140s libopenmpi40 libpciaccess0 libpmix2t64 librdmacm1t64 libucx0 libxnvctrl0 140s ocl-icd-libopencl1 140s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 61.1 MB of archives. 140s After this operation, 269 MB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ppc64el hyphy-common all 2.5.63+dfsg-1build2 [628 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-17ubuntu1 [161 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libevent-pthreads-2.1-7t64 ppc64el 2.1.12-stable-10 [8026 B] 141s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el librdmacm1t64 ppc64el 55.0-1ubuntu1 [80.5 kB] 141s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libfabric1 ppc64el 1.17.0-3ubuntu1 [692 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhwloc15 ppc64el 2.11.2-1build1 [220 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmunge2 ppc64el 0.5.16-1 [17.3 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpciaccess0 ppc64el 0.17-3build1 [21.4 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu4 [12.6 kB] 142s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1build1 [42.9 kB] 142s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhwloc-plugins ppc64el 2.11.2-1build1 [17.5 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libpmix2t64 ppc64el 5.0.6-3 [759 kB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libllvm17t64 ppc64el 1:17.0.6-20 [27.0 MB] 145s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3build2 [15.3 MB] 146s Get:15 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhsakmt1 ppc64el 5.7.0-1build1 [76.4 kB] 146s Get:16 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-2build1 [330 kB] 146s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libamdhip64-5 ppc64el 5.7.1-5 [9354 kB] 146s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libibumad3 ppc64el 55.0-1ubuntu1 [31.7 kB] 146s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libibmad5 ppc64el 55.0-1ubuntu1 [45.7 kB] 146s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libucx0 ppc64el 1.17.0+ds-3build1 [1224 kB] 146s Get:21 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmpi40 ppc64el 5.0.6-4 [2613 kB] 146s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el hyphy-mpi ppc64el 2.5.63+dfsg-1build2 [1241 kB] 146s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el hyphy-pt ppc64el 2.5.63+dfsg-1build2 [1214 kB] 147s Fetched 61.1 MB in 6s (10.4 MB/s) 147s Selecting previously unselected package hyphy-common. 147s (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 ... 106313 files and directories currently installed.) 147s Preparing to unpack .../00-hyphy-common_2.5.63+dfsg-1build2_all.deb ... 147s Unpacking hyphy-common (2.5.63+dfsg-1build2) ... 147s Selecting previously unselected package libgomp1:ppc64el. 147s Preparing to unpack .../01-libgomp1_14.2.0-17ubuntu1_ppc64el.deb ... 147s Unpacking libgomp1:ppc64el (14.2.0-17ubuntu1) ... 147s Selecting previously unselected package libevent-pthreads-2.1-7t64:ppc64el. 147s Preparing to unpack .../02-libevent-pthreads-2.1-7t64_2.1.12-stable-10_ppc64el.deb ... 147s Unpacking libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10) ... 147s Selecting previously unselected package librdmacm1t64:ppc64el. 147s Preparing to unpack .../03-librdmacm1t64_55.0-1ubuntu1_ppc64el.deb ... 147s Unpacking librdmacm1t64:ppc64el (55.0-1ubuntu1) ... 147s Selecting previously unselected package libfabric1:ppc64el. 147s Preparing to unpack .../04-libfabric1_1.17.0-3ubuntu1_ppc64el.deb ... 147s Unpacking libfabric1:ppc64el (1.17.0-3ubuntu1) ... 147s Selecting previously unselected package libhwloc15:ppc64el. 147s Preparing to unpack .../05-libhwloc15_2.11.2-1build1_ppc64el.deb ... 147s Unpacking libhwloc15:ppc64el (2.11.2-1build1) ... 147s Selecting previously unselected package libmunge2:ppc64el. 147s Preparing to unpack .../06-libmunge2_0.5.16-1_ppc64el.deb ... 147s Unpacking libmunge2:ppc64el (0.5.16-1) ... 147s Selecting previously unselected package libpciaccess0:ppc64el. 147s Preparing to unpack .../07-libpciaccess0_0.17-3build1_ppc64el.deb ... 147s Unpacking libpciaccess0:ppc64el (0.17-3build1) ... 147s Selecting previously unselected package libxnvctrl0:ppc64el. 147s Preparing to unpack .../08-libxnvctrl0_510.47.03-0ubuntu4_ppc64el.deb ... 147s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ... 147s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 147s Preparing to unpack .../09-ocl-icd-libopencl1_2.3.2-1build1_ppc64el.deb ... 147s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1build1) ... 147s Selecting previously unselected package libhwloc-plugins:ppc64el. 147s Preparing to unpack .../10-libhwloc-plugins_2.11.2-1build1_ppc64el.deb ... 147s Unpacking libhwloc-plugins:ppc64el (2.11.2-1build1) ... 147s Selecting previously unselected package libpmix2t64:ppc64el. 147s Preparing to unpack .../11-libpmix2t64_5.0.6-3_ppc64el.deb ... 147s Unpacking libpmix2t64:ppc64el (5.0.6-3) ... 147s Selecting previously unselected package libllvm17t64:ppc64el. 147s Preparing to unpack .../12-libllvm17t64_1%3a17.0.6-20_ppc64el.deb ... 147s Unpacking libllvm17t64:ppc64el (1:17.0.6-20) ... 148s Selecting previously unselected package libamd-comgr2:ppc64el. 148s Preparing to unpack .../13-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_ppc64el.deb ... 148s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build2) ... 149s Selecting previously unselected package libhsakmt1:ppc64el. 149s Preparing to unpack .../14-libhsakmt1_5.7.0-1build1_ppc64el.deb ... 149s Unpacking libhsakmt1:ppc64el (5.7.0-1build1) ... 149s Selecting previously unselected package libhsa-runtime64-1. 149s Preparing to unpack .../15-libhsa-runtime64-1_5.7.1-2build1_ppc64el.deb ... 149s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 149s Selecting previously unselected package libamdhip64-5. 149s Preparing to unpack .../16-libamdhip64-5_5.7.1-5_ppc64el.deb ... 149s Unpacking libamdhip64-5 (5.7.1-5) ... 149s Selecting previously unselected package libibumad3:ppc64el. 149s Preparing to unpack .../17-libibumad3_55.0-1ubuntu1_ppc64el.deb ... 149s Unpacking libibumad3:ppc64el (55.0-1ubuntu1) ... 149s Selecting previously unselected package libibmad5:ppc64el. 149s Preparing to unpack .../18-libibmad5_55.0-1ubuntu1_ppc64el.deb ... 149s Unpacking libibmad5:ppc64el (55.0-1ubuntu1) ... 149s Selecting previously unselected package libucx0:ppc64el. 149s Preparing to unpack .../19-libucx0_1.17.0+ds-3build1_ppc64el.deb ... 149s Unpacking libucx0:ppc64el (1.17.0+ds-3build1) ... 149s Selecting previously unselected package libopenmpi40:ppc64el. 149s Preparing to unpack .../20-libopenmpi40_5.0.6-4_ppc64el.deb ... 149s Unpacking libopenmpi40:ppc64el (5.0.6-4) ... 149s Selecting previously unselected package hyphy-mpi. 149s Preparing to unpack .../21-hyphy-mpi_2.5.63+dfsg-1build2_ppc64el.deb ... 149s Unpacking hyphy-mpi (2.5.63+dfsg-1build2) ... 149s Selecting previously unselected package hyphy-pt. 149s Preparing to unpack .../22-hyphy-pt_2.5.63+dfsg-1build2_ppc64el.deb ... 149s Unpacking hyphy-pt (2.5.63+dfsg-1build2) ... 149s Setting up libpciaccess0:ppc64el (0.17-3build1) ... 149s Setting up libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-10) ... 149s Setting up libibumad3:ppc64el (55.0-1ubuntu1) ... 149s Setting up libibmad5:ppc64el (55.0-1ubuntu1) ... 149s Setting up hyphy-common (2.5.63+dfsg-1build2) ... 149s Setting up libgomp1:ppc64el (14.2.0-17ubuntu1) ... 149s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ... 149s Setting up libmunge2:ppc64el (0.5.16-1) ... 149s Setting up libllvm17t64:ppc64el (1:17.0.6-20) ... 149s Setting up libhwloc15:ppc64el (2.11.2-1build1) ... 149s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1build1) ... 149s Setting up librdmacm1t64:ppc64el (55.0-1ubuntu1) ... 149s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build2) ... 149s Setting up libhsakmt1:ppc64el (5.7.0-1build1) ... 149s Setting up libfabric1:ppc64el (1.17.0-3ubuntu1) ... 149s Setting up hyphy-pt (2.5.63+dfsg-1build2) ... 149s Setting up libhwloc-plugins:ppc64el (2.11.2-1build1) ... 149s Setting up libpmix2t64:ppc64el (5.0.6-3) ... 149s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 149s Setting up libamdhip64-5 (5.7.1-5) ... 149s Setting up libucx0:ppc64el (1.17.0+ds-3build1) ... 149s Setting up libopenmpi40:ppc64el (5.0.6-4) ... 149s Setting up hyphy-mpi (2.5.63+dfsg-1build2) ... 149s Processing triggers for libc-bin (2.41-1ubuntu1) ... 150s Processing triggers for man-db (2.13.0-1) ... 152s autopkgtest [02:02:12]: test run-unit-tests: [----------------------- 152s + for i in *.bf 152s + '[' -f ExonIntron.bf ']' 152s + hyphy ExonIntron.bf 155s Log Likelihood = -1113.34527453458; 155s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134823267562931,(ZMUBIS27F:0,(ZMU29160:0.05439790489821116,ZMU29161:0.03972438373992062)Node8:0.0120170168645435)Node6:0)Node4:0.0245939235537273,BLYMUB1:0.01186169059896943); 155s Tree exon2Tree=(BLYMUB2:0.0354219796970709,(RICRMA630:0.0293592151757737,(ZMUBIS27F:0.07548368613771465,(ZMU29160:0.09106731885578374,ZMU29161:0.02597632203803231)Node8:0.01154237701352565)Node6:0.04929618916406537)Node4:0.02930900118342779,BLYMUB1:0.02204924942508823); 155s Tree intronTree=(BLYMUB2:0.03119337513404881,(RICRMA630:0.04156843575576281,(ZMUBIS27F:0.02044013723342076,(ZMU29160:0.02068575660834807,ZMU29161:0.01019356230091215)Node8:0.02068834836820207)Node6:0)Node4:0,BLYMUB1:0.01036374494579065); 155s + for i in *.bf 155s + '[' -f F81.bf ']' 155s + hyphy F81.bf 155s Log Likelihood = -1187.54703158321; 155s Tree givenTree=(256:0.01194114581051671,(822:0.02944524189026885,159:0.00447162179178419)Node2:0.00364976627649821,((113:0.02245290969048733,9939:0.0762883347834151)Node6:0.005077459343970057,(6760:0.06900624302668132,((317:0.03752839365922606,6767:0.07083856772688221)Node12:0.0122969483901559,((135:0.02046660329336416,(529:0.03337018701846098,105r:0.01321522040669223)Node18:0.02585864946908883)Node16:0.005409584256016949,(719:0.02964827459315724,136:0.008234924891279817)Node21:0.048833191511885)Node15:0.01526164964713513)Node11:0.01379988381860039)Node9:0.02422104087079634)Node5:0.02148432108838633); 155s + for i in *.bf 155s + '[' -f F81relrate.bf ']' 155s + hyphy F81relrate.bf 155s 155s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001001210834; 155s Tree threeTaxaTree=(a:0.08502373447434355,b:0.07338780662543803,c:0.1653961179929538); 155s 155s 155s 1). With the outgroup at taxon #1, the P-value is:0.002155082746832959 155s Log Likelihood = -948.707263619764; 155s Tree threeTaxaTree=(a:0.08228181923420894,b:0.1193752617575549,c:0.1193752617575549); 155s 155s 155s 2). With the outgroup at taxon #2, the P-value is:0.008353493534213663 155s Log Likelihood = -947.479040372903; 155s Tree threeTaxaTree=(a:0.1251255673295682,b:0.07126113984093221,c:0.1251255673295682); 155s 155s 155s 3). With the outgroup at taxon #3, the P-value is:0.6669142488255959 155s Log Likelihood = -944.093617637427; 155s Tree threeTaxaTree=(a:0.07920391148349309,b:0.07920391148349309,c:0.1653766783991298); 155s + for i in *.bf 155s + '[' -f F81relratio.bf ']' 155s + hyphy F81relratio.bf 155s 155s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059868159; 155s Tree fourTaxaTree1=((1:0.1129194713343888,2:0.1073510556030551)Node1:0.09979510227278432,3:0.3469419722230219,4:0.3218829818793753); 155s Tree fourTaxaTree2=((1:0.08582648228819281,2:0.09340546267930305)Node1:0.07362500992789969,3:0.393232777156252,4:0.3801450393722444); 155s 155s 155s 1). Relative ratio constraint; the P-value is:0.6933541995545587 155s Log Likelihood = -2575.74610909507; 155s Global Parameters: 155s R=1.0072908836713; 155s 155s Tree fourTaxaTree1=((1:0.09948361489134727,2:0.09943033885448659)Node1:0.08696825595984072,3:0.3687235526329564,4:0.3489176977337752); 155s Tree fourTaxaTree2=((1:0.1000737077365053,2:0.1000201156897349)Node1:0.08748411322592244,3:0.3709106578209576,4:0.3509873233420385); 155s + for i in *.bf 155s + '[' -f HKY85.bf ']' 155s + hyphy HKY85.bf 156s Log Likelihood = -1152.88077642324; 156s Tree givenTree=(256:0.01162364210421407,(822:0.02980324828706117,159:0.004016335903882491)Node2:0.003749549710913066,((113:0.02130049465534279,9939:0.07787424049947565)Node6:0.004321341660836612,(6760:0.07316332167019128,((317:0.03810262127730785,6767:0.07101128297725369)Node12:0.006272466557278564,((135:0.01787883966930189,(529:0.03258190184912801,105r:0.01513653557074536)Node18:0.02833253021985086)Node16:0.007920142727370703,(719:0.02987702678431454,136:0.008041352869123468)Node21:0.04860052510964809)Node15:0.01598535547059258)Node11:0.01658093012917157)Node9:0.02665163631630434)Node5:0.02296003610980581); 156s + for i in *.bf 156s + '[' -f HKY852blocks.bf ']' 156s + hyphy HKY852blocks.bf 156s 156s ----- RESULTS ----- 156s Log Likelihood = -6801.91478504774; 156s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050228016325972,((((((ZMU60511:0.01039826137197994,ZMU60510:0.02379428156791784)Node8:0.08352366683238749,OSRAC2:0.1884847250802242)Node7:0.05837875237664083,(OSRAC1:0.01536683214325785,SVSOAC1:0.07339619237423527)Node12:0.072973151223813)Node6:0,((OSRAC3:0.07322564238275787,ZMU60507:0.0650275298451046)Node16:0.07979210877889346,ZMU60509:0.1288362454505455)Node15:0.001261914830653511)Node5:0.08267712581822155,(MZEACT1G:0.1142443487523255,OSRAC7:0.03419168935239281)Node20:0)Node4:0.1058665947294054,ZMU60508:0.0169802402435398)Node3:0.05976261727764272); 156s Tree actinTree2=(ZMU60513:0.01013562824790695,ZMU60514:0.02362726563834485,((((((ZMU60511:0.03959062875819274,ZMU60510:0.02870922089895338)Node8:0.04599411141309144,OSRAC2:0.1281475798570719)Node7:0.02274402466776166,(OSRAC1:0.04039556700375126,SVSOAC1:0.05532691847122169)Node12:0.0905660504363473)Node6:0.02100637972579765,((OSRAC3:0.1082307215319248,ZMU60507:0.07346563783448669)Node16:0.05601707673699548,ZMU60509:0.1117447283489773)Node15:0.02915977836687979)Node5:0.04980522416791706,(MZEACT1G:0.1070210243025308,OSRAC7:0.09561870818322175)Node20:0.02267612948724274)Node4:0.04830877376292424,ZMU60508:0.02346278373752455)Node3:0.05651941809924885); 156s + for i in *.bf 156s + '[' -f HKY852blocks2models.bf ']' 156s + hyphy HKY852blocks2models.bf 157s 157s ----- RESULTS ----- 157s Log Likelihood = -6049.33416171633; 157s Tree actinTree1=(ZMU60513:0.01368051563924064,ZMU60514:0.06663244952564902,((((((ZMU60511:0.1014763335833407,ZMU60510:0.08937058885941587)Node8:0.2111617848898169,OSRAC2:0.3683753733728789)Node7:0.06396095845113894,(OSRAC1:0.04314962701034052,SVSOAC1:0.2450394915511599)Node12:0.4086834572886894)Node6:0.1002853648751293,((OSRAC3:0.1862424794925966,ZMU60507:0.3287076578666533)Node16:0.1590960573127765,ZMU60509:0.4445969712610973)Node15:0.04672103028952192)Node5:0.189604074623353,(MZEACT1G:0.3244333586136061,OSRAC7:0.2477748419096852)Node20:0.009365880330604736)Node4:0.2662694910030111,ZMU60508:0.01033363136712426)Node3:0.2232449322168354); 157s Tree actinTree2=(ZMU60513:0.004497551076857547,ZMU60514:0.00448329870379788,((((((ZMU60511:0.004483159913161686,ZMU60510:0.005993930349196082)Node8:0.004874111343135114,OSRAC2:0.04747030223542358)Node7:0.003177370113389075,(OSRAC1:0.01209871877505705,SVSOAC1:0.007446306752153478)Node12:0.02729634549210651)Node6:0,((OSRAC3:0.04645206466703183,ZMU60507:0.009176909538951727)Node16:0.0104527362091823,ZMU60509:0.0244818454152267)Node15:0)Node5:0.01926842942607595,(MZEACT1G:0.03380901569738938,OSRAC7:0.03062886930111947)Node20:0.006211244916759595)Node4:0.007801616186974007,ZMU60508:0.004488650944168376)Node3:0.01512046799575061); 157s + for i in *.bf 157s + '[' -f HKY85relrate.bf ']' 157s + hyphy HKY85relrate.bf 157s 157s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371754591971; 157s Tree threeTaxaTree=(a:0.08470616750756002,b:0.07476331027190458,c:0.1740134198443868); 157s 157s 157s 1). Outgroup at taxon #1 157s a). Transition rate test. P-Value = 0.02098233635026459 157s Log Likelihood = -924.035884024639; 157s Tree threeTaxaTree=(a:0.08099120434783051,b:0.1064970047832805,c:0.1431287317678666); 157s 157s b). Transversion rate test. P-Value = 0.03655161545797225 157s Log Likelihood = -923.557345912356; 157s Tree threeTaxaTree=(a:0.08437179509623652,b:0.09106657097270322,c:0.157751916529313); 157s 157s c). Both rates test. P-Value = 0.006324016976586244 157s Log Likelihood = -926.435155267191; 157s Tree threeTaxaTree=(a:0.08054162717334669,b:0.1248196470986539,c:0.1248196470986539); 157s 157s 157s 2). Outgroup at taxon #2 157s a). Transition rate test. P-Value = 0.02758045337607318 157s Log Likelihood = -923.798806027197; 157s Tree threeTaxaTree=(a:0.1158362270038986,b:0.07098641273264134,c:0.1443231474154938); 157s 157s b). Transversion rate test. P-Value = 0.110646314493098 157s Log Likelihood = -922.644237437577; 157s Tree threeTaxaTree=(a:0.09760331148856001,b:0.07463654105981143,c:0.1608968060640496); 157s 157s c). Both rates test. P-Value = 0.02199506592879741 157s Log Likelihood = -925.188691718764; 157s Tree threeTaxaTree=(a:0.1299134981133936,b:0.07078648354561046,c:0.1299134981133936); 157s 157s 157s 3). Outgroup at taxon #3 157s a). Transition rate test. P-Value = 0.9291997182804549 157s Log Likelihood = -921.375701909991; 157s Tree threeTaxaTree=(a:0.08354356488283134,b:0.07588178145055254,c:0.1740455423951901); 157s 157s b). Transversion rate test. P-Value = 0.5919916735597195 157s Log Likelihood = -921.515376904819; 157s Tree threeTaxaTree=(a:0.08115137204190902,b:0.07834954142678607,c:0.1740030848572789); 157s 157s c). Both rates test. P-Value = 0.8615442246726074 157s Log Likelihood = -921.520783481793; 157s Tree threeTaxaTree=(a:0.07974264193281742,b:0.07974264193281742,c:0.1740977410651071); 157s + for i in *.bf 157s + '[' -f HKY85relratio.bf ']' 157s + hyphy HKY85relratio.bf 157s 157s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78441247106; 157s Tree fourTaxaTree1=((1:0.1137753070915355,2:0.110923572068774)Node1:0.1041248401545123,3:0.3523533291918795,4:0.3311995969783809); 157s Tree fourTaxaTree2=((1:0.0860382650075945,2:0.09351277716626748)Node1:0.08022847963542346,3:0.3859538903435252,4:0.3896405702912022); 157s 157s 157s 1). Relative ratio constraint on transitions; the P-value is:0.573854939578496 157s Log Likelihood = -2541.23688975347; 157s Global Parameters: 157s R=0.8579071346165509; 157s 157s Tree fourTaxaTree1=((1:0.108662468573263,2:0.09420710782123035)Node1:0.11159754962384,3:0.3553174735230037,4:0.3551357165672897); 157s Tree fourTaxaTree2=((1:0.09039858455962528,2:0.1091735565885345)Node1:0.07301058557697321,3:0.3839750614875228,4:0.3655235188774553); 157s 157s 157s 2). Relative ratio constraint on transversions; the P-value is:0.5738492716891384 157s Log Likelihood = -2541.23690643039; 157s Global Parameters: 157s R=0.8583726047293592; 157s 157s Tree fourTaxaTree1=((1:0.1086704866604071,2:0.09419058084323317)Node1:0.1116417907155742,3:0.3553177572190648,4:0.3549098850702043); 157s Tree fourTaxaTree2=((1:0.0903992146486727,2:0.1091887442629099)Node1:0.07309291367947511,3:0.3840653530248642,4:0.3655405743404384); 157s 157s 157s 3). Relative ratio constraint on both rates; the P-value is:0.6565824418208199 157s Log Likelihood = -2543.1909083878; 157s Global Parameters: 157s R=0.9971350744523683; 157s 157s Tree fourTaxaTree1=((1:0.10045063931832,2:0.1006557466218245)Node1:0.09255949975124426,3:0.3713172813563495,4:0.3580988462218703); 157s Tree fourTaxaTree2=((1:0.1003462690459828,2:0.1007099465603393)Node1:0.09290936974086419,3:0.3699887235726969,4:0.3577877680647013); 157s + for i in *.bf 157s + '[' -f HKY85shared.bf ']' 157s + hyphy HKY85shared.bf 157s Log Likelihood = -1165.70261216452; 157s Global Parameters: 157s R=2.985270111313039; 157s 157s Tree givenTree=(256:0.01208887834810965,(822:0.02962497685536022,159:0.004654004356629589)Node2:0.003521675182559771,((113:0.02180335276810001,9939:0.07937939791548564)Node6:0.004910492767676866,(6760:0.07155691643272612,((317:0.03797626454359052,6767:0.07151084045562267)Node12:0.01177117133035185,((135:0.02024393405110816,(529:0.03402215758818016,105r:0.01304776452217465)Node18:0.02631597095118411)Node16:0.005812235226829088,(719:0.02975107090861264,136:0.008128038064313623)Node21:0.04879740775611686)Node15:0.01556125089690037)Node11:0.01396730114004749)Node9:0.02326100835533916)Node5:0.02146650804037714); 157s + for i in *.bf 157s + '[' -f JC69.bf ']' 157s + hyphy JC69.bf 157s Log Likelihood = -1227.4512465621; 157s Tree givenTree=(256:0.01210314714915355,(822:0.02895919170619479,159:0.004660419979370349)Node2:0.003646944276138766,((113:0.02417187311808544,9939:0.07264010622973317)Node6:0.005841276466211582,(6760:0.06387903934602145,((317:0.04026899103627595,6767:0.06821500288806152)Node12:0.01443705918822943,((135:0.02431082223329727,(529:0.03327971740340237,105r:0.01296537960773594)Node18:0.0198783860976395)Node16:0.00361320494782841,(719:0.02785313695935753,136:0.009997027773531036)Node21:0.05116978658235061)Node15:0.01670127397604663)Node11:0.008455166735885979)Node9:0.02635808511771688)Node5:0.02074711301387467); 157s + for i in *.bf 157s + '[' -f K2P.bf ']' 157s + hyphy K2P.bf 157s Log Likelihood = -1198.26189385562; 157s Tree givenTree=(256:0.01177284359454655,(822:0.02926420051801124,159:0.00429051344152916)Node2:0.003666029123241471,((113:0.02366812229156449,9939:0.07261944383784633)Node6:0.003382357489212112,(6760:0.06224212580876966,((317:0.04074378050300317,6767:0.06830506522729138)Node12:0.01244537967266995,((135:0.02260274232468177,(529:0.03395246634634628,105r:0.01240375213258666)Node18:0.02142035398802438)Node16:0.004488785191949653,(719:0.02880975695117095,136:0.008845132574248534)Node21:0.05084376898398974)Node15:0.01733791665694857)Node11:0.01111378532762037)Node9:0.02819644543689198)Node5:0.02370264722255687); 157s + for i in *.bf 157s + '[' -f K2Pshared.bf ']' 157s + hyphy K2Pshared.bf 157s Log Likelihood = -1210.4940471197; 157s Global Parameters: 157s R=2.625794187771459; 157s 157s Tree givenTree=(256:0.01222499913086527,(822:0.02897884477603219,159:0.004781045647509667)Node2:0.003546874563381752,((113:0.02375931697438015,9939:0.07497889571196484)Node6:0.005891745340110638,(6760:0.06492705231751263,((317:0.03971607289912242,6767:0.06952805951610427)Node12:0.01423545272568783,((135:0.02390591837273757,(529:0.03397605182557488,105r:0.01262638012497549)Node18:0.02072334183978022)Node16:0.003968660185345628,(719:0.02814000821125305,136:0.009503865339382732)Node21:0.05082452957836518)Node15:0.01659353390770427)Node11:0.008793165733169515)Node9:0.02627457878597234)Node5:0.02011131840677165); 157s + for i in *.bf 157s + '[' -f MatrixIndexing.bf ']' 157s + hyphy MatrixIndexing.bf 157s 157s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 157s { 157s {0.6283937996785142, 0.574226880579774, 0.5958904008371501, 0.4958474027216079, 0.5620178916868795, 0.281325465366553} 157s {0.9166084970153422, 0.6577365942433795, 0.8256542873162903, 0.4328664043994775, 0.1262284939005572, 0.8017633009706073} 157s {0.942935805987319, 0.3259353610514513, 0.7413901360103372, 0.4457728819562525, 0.1020331832352172, 0.4467673281782231} 157s {0.3177942722844412, 0.5070175601884298, 0.8527221963397977, 0.1836358001883225, 0.2950140576099544, 0.1125300152023626} 157s {0.04171774188096582, 0.7264258628074139, 0.6079196176975779, 0.6072728849498725, 0.9334584663001491, 0.491005091809436} 157s } 157s 157s 2). Accessing a second-row third-column element and a random element. 157s 157s matrix[1][2]=0.8256542873162903 157s matrix[2][3]=0.4457728819562525 157s 157s 3). Accessing the fourth row. 157s 157s matrix[3][-1]= 157s { 157s {0.3177942722844412, 0.5070175601884298, 0.8527221963397977, 0.1836358001883225, 0.2950140576099544, 0.1125300152023626} 157s } 157s 157s 4). Accessing the first column. 157s 157s matrix[-1][0]= 157s { 157s {0.6283937996785142} 157s {0.9166084970153422} 157s {0.942935805987319} 157s {0.3177942722844412} 157s {0.04171774188096582} 157s } 157s 157s 5). Populating a matrix template (below the diagonal). 157s 157s { 157s {0, 0, 0, 0, 0, 0} 157s {1, 0, 0, 0, 0, 0} 157s {1, 1, 0, 0, 0, 0} 157s {1, 1, 1, 0, 0, 0} 157s {1, 1, 1, 1, 0, 0} 157s } 157s 157s 6). Extracting (by row) matrix elements using the template. 157s 157s { 157s {0.9166084970153422, 0.942935805987319, 0.3259353610514513, 0.3177942722844412, 0.5070175601884298, 0.8527221963397977, 0.04171774188096582, 0.7264258628074139, 0.6079196176975779, 0.6072728849498725} 157s } 157s 157s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 157s 157s matrix[{{1,1}}][{{3,2}}]= 157s { 157s {0.6577365942433795, 0.8256542873162903} 157s {0.3259353610514513, 0.7413901360103372} 157s {0.5070175601884298, 0.8527221963397977} 157s } 157s 157s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 157s 157s 157s { 157s {0.3948787674744006, 1.329736510380378, 1.355085369809859, 1.245864646785764, 1.315864110576165, 1.079144017463708} 157s {0.8401711368007245, 0.43261742740688, 1.681705002163771, 1.187373324057732, 1.015933632672403, 1.642824390783285} 157s {0.8891279342129549, 0.1062338595837399, 0.5496593337734264, 1.198713462287583, 1.010410770481111, 1.199601045527508} 157s {0.1009931994967976, 0.257066806339428, 0.7271351441305686, 0.03372210711080551, 1.087033294187489, 1.012663004321444} 157s {0.00174036998764689, 0.5276945341554958, 0.3695662615815692, 0.3687803567953411, 0.8713447083074265, 1.241086000182793} 157s } 157s + for i in *.bf 157s + '[' -f MolecularClockF81.bf ']' 157s + hyphy MolecularClockF81.bf 158s 158s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124511857; 158s Tree theTree=(HVRNASS:0.02575001006727418,(RICRSS3:0.05627633328762239,((ZMSUCS1:0.07162821887278371,(OSRSS1A:0.06060085946218943,(TASUCSYN1:0.02788050936657385,HVSSYNMR:0.02037103884312378)Internal1:0.0518150443892484)Node9:0.02013887522292579)Node7:0.1581214771267317,(MZESUS1:0.07667096361620969,ORRSS2:0.05436191932477639)Internal2:0.0250625831462922)Node6:0.03254927751537996)Node4:0.05901172504007546,TAAJ153:0.01372502151703622); 158s 158s 158s 1). Global Molecular Clock; the P-value is:0 158s Log Likelihood = -11927.6152775937; 158s Tree theTree=(HVRNASS:0.02157619046851307,(RICRSS3:0.1233417587079404,((ZMSUCS1:0.05657749839448778,(OSRSS1A:0.04750827503404448,(TASUCSYN1:0.01823836395960033,HVSSYNMR:0.01823836395960033)Internal1:0.02926991107444416)Node9:0.009069223360443289)Node7:0.05763969203208495,(MZESUS1:0.07013415442519537,ORRSS2:0.07013415442519537)Internal2:0.04408303600137736)Node6:0.009124568281367658)Node4:0.02715740203504393,TAAJ153:0.1504991607429843); 158s 158s 158s 2). Molecular Clock starting at Internal1; the P-value is:0.1603812833179199 158s Log Likelihood = -11476.6977648833; 158s Tree theTree=(HVRNASS:0.02573844080055846,(RICRSS3:0.05631378722825358,((ZMSUCS1:0.07167038566390826,(OSRSS1A:0.06052200635802626,(TASUCSYN1:0.02412007231361854,HVSSYNMR:0.02412007231361854)Internal1:0.05180642537635661)Node9:0.0201883297086285)Node7:0.1580854003791167,(MZESUS1:0.07661279650026552,ORRSS2:0.05440972359229714)Internal2:0.02509732969882329)Node6:0.0325168079804978)Node4:0.05896716802881881,TAAJ153:0.01372945746287497); 158s 158s 158s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610219041140615 158s Log Likelihood = -11479.8412511516; 158s Tree theTree=(HVRNASS:0.02577426459885131,(RICRSS3:0.05653201674210224,((ZMSUCS1:0.07147876170797385,(OSRSS1A:0.06061733122772596,(TASUCSYN1:0.0241210689236839,HVSSYNMR:0.0241210689236839)Internal1:0.05166406791820187)Node9:0.02036487462865511)Node7:0.15805304097391,(MZESUS1:0.06553595600184853,ORRSS2:0.06553595600184853)Internal2:0.02502384937938512)Node6:0.03235653783451369)Node4:0.05874167705615473,TAAJ153:0.01370014984421321); 158s + for i in *.bf 158s + '[' -f MolecularClockHKY85.bf ']' 158s + hyphy MolecularClockHKY85.bf 158s 158s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013460392; 158s Tree theTree=(HVRNASS:0.02588160632147346,(RICRSS3:0.0572778684596349,((ZMSUCS1:0.07269327372186647,(OSRSS1A:0.0609450804058153,(TASUCSYN1:0.02742638806862635,HVSSYNMR:0.02082212300808158)Node11:0.05284393071956665)Node9:0.0205133207273288)Node7:0.1589993998237395,(MZESUS1:0.0776115598439106,ORRSS2:0.05413722402424973)Node14:0.02601477859096467)Node6:0.03166860032777715)Node4:0.06040819412805244,TAAJ153:0.01384597543418121); 158s 158s 158s 1). Global Molecular Clock on transition rates; the P-value is:0 158s Log Likelihood = -11434.7015977526; 158s Tree theTree=(HVRNASS:0.02320093401089936,(RICRSS3:0.08335067901706707,((ZMSUCS1:0.06367225887273886,(OSRSS1A:0.05485628826669928,(TASUCSYN1:0.02325704398171348,HVSSYNMR:0.01890693680324564)Node11:0.04017289050278598)Node9:0.01328246085249365)Node7:0.1273883753935214,(MZESUS1:0.07240481752545966,ORRSS2:0.06226830772267086)Node14:0.03461823303613802)Node6:0.02068741864401786)Node4:0.0389907753383775,TAAJ153:0.08892019886757008); 158s 158s 158s 2). Global Molecular Clock on transversion rates; the P-value is:0 158s Log Likelihood = -11497.3782617505; 158s Tree theTree=(HVRNASS:0.02483374513652973,(RICRSS3:0.09400094407167731,((ZMSUCS1:0.06900016104859703,(OSRSS1A:0.05468863253005631,(TASUCSYN1:0.02276824967429499,HVSSYNMR:0.02033937952106976)Node11:0.04372671057034873)Node9:0.01674390794464558)Node7:0.09971331739371127,(MZESUS1:0.07447754873023903,ORRSS2:0.06133180497234395)Node14:0.03387020446896427)Node6:0.0207983606617849)Node4:0.05007189982013122,TAAJ153:0.07305925449121629); 158s 158s 158s 3). Global Molecular Clock on both rates; the P-value is:0 158s Log Likelihood = -11703.6261703773; 158s Tree theTree=(HVRNASS:0.02209883092205303,(RICRSS3:0.1239713482833267,((ZMSUCS1:0.05799306332227502,(OSRSS1A:0.04854097618749115,(TASUCSYN1:0.01832817383271238,HVSSYNMR:0.01832817383271238)Node11:0.03021280235477877)Node9:0.009452087134783863)Node7:0.05732323219672406,(MZESUS1:0.07024684477730039,ORRSS2:0.07024684477730039)Node14:0.04506945074169867)Node6:0.008655052764327631)Node4:0.02801791989035858,TAAJ153:0.1519892681736853); 158s + for i in *.bf 158s + '[' -f Non-Rev.bf ']' 158s + hyphy Non-Rev.bf 159s Log Likelihood = -1152.77812251564; 159s Global Parameters: 159s GC=0.289067307028803; 159s CG=0.1904240824981787; 159s GA=2.011882198546015; 159s CT=1.283120946971504; 159s GT=0.09087921466998093; 159s CA=0.9387046193012704; 159s AT=0.4544321465273802; 159s AG=1.674965084750759; 159s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2598488914276564; 159s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.091471346706904; 159s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.8311586605467571; 159s 159s Tree givenTree=(256:0.01349106478864757,(822:0.02843205613798875,159:0.006179166286229741)Node2:0.003442655517948683,((113:0.02189254954167687,9939:0.0792345214566952)Node6:0.004959905053622178,(6760:0.07317442271203901,((317:0.04010750426410323,6767:0.0699217273625604)Node12:0.01159113270456289,((135:0.02154504520136196,(529:0.034963132008916,105r:0.01411264612132075)Node18:0.02381660149544254)Node16:0.005282763277421917,(719:0.02873662770138922,136:0.009483754793295832)Node21:0.04925439366590691)Node15:0.0163435219898851)Node11:0.01282250835601035)Node9:0.02190884693802695)Node5:0.0202641203535744); 159s + for i in *.bf 159s + '[' -f PBootstrapHetRates.bf ']' 159s + hyphy PBootstrapHetRates.bf 159s 159s ----ORIGINAL DATA---- 159s Log Likelihood = -1127.31557547954; 159s Global Parameters: 159s alpha=0.3190382613540808; 159s kappa=0.3234807836183294; 159s 159s Tree givenTree=(256:0.01259121359252053,(822:0.0317490620768969,159:0.004696743579906825)Node2:0.003784048729206787,((113:0.02291226872087342,9939:0.09714380821313676)Node6:0.001957332618505038,(6760:0.08722089326584566,((317:0.04574858524494918,6767:0.08109947508885514)Node12:0.00739750920232705,((135:0.01862859698647743,(529:0.03694189404102555,105r:0.01500636906954054)Node18:0.03036654087556295)Node16:0.007153345176218504,(719:0.03342588770911525,136:0.007167817165440045)Node21:0.05748873597681853)Node15:0.01789059310065867)Node11:0.01883873536686844)Node9:0.02369093664481948)Node5:0.02502054241288417); 159s 159s Using the seed: 159s 1739674709 159s Category variable name: TRUE 159s Site Rate 159s 0 0.00000 159s 1 0.00000 159s 2 0.00000 159s 3 0.00000 159s 4 0.00001 159s 5 0.00001 159s 6 0.00001 159s 7 0.00001 159s 8 0.00002 159s 9 0.00003 159s 10 0.00003 159s 11 0.00005 159s 12 0.00007 159s 13 0.00007 159s 14 0.00011 159s 15 0.00013 159s 16 0.00013 159s 17 0.00016 159s 18 0.00017 159s 19 0.00024 159s 20 0.00024 159s 21 0.00026 159s 22 0.00066 159s 23 0.00091 159s 24 0.00107 159s 25 0.00130 159s 26 0.00148 159s 27 0.00157 159s 28 0.00159 159s 29 0.00171 159s 30 0.00176 159s 31 0.00197 159s 32 0.00264 159s 33 0.00265 159s 34 0.00281 159s 35 0.00300 159s 36 0.00344 159s 37 0.00447 159s 38 0.00464 159s 39 0.00552 159s 40 0.00581 159s 41 0.00587 159s 42 0.00605 159s 43 0.00716 159s 44 0.00735 159s 45 0.00741 159s 46 0.00821 159s 47 0.00846 159s 48 0.00881 159s 49 0.00888 159s 50 0.01022 159s 51 0.01029 159s 52 0.01166 159s 53 0.01281 159s 54 0.01286 159s 55 0.01294 159s 56 0.01406 159s 57 0.01494 159s 58 0.01521 159s 59 0.01610 159s 60 0.01641 159s 61 0.01658 159s 62 0.01788 159s 63 0.01807 159s 64 0.01881 159s 65 0.02367 159s 66 0.02369 159s 67 0.02486 159s 68 0.02510 159s 69 0.02686 159s 70 0.02803 159s 71 0.03224 159s 72 0.03414 159s 73 0.04117 159s 74 0.04193 159s 75 0.04456 159s 76 0.04553 159s 77 0.04946 159s 78 0.05325 159s 79 0.05569 159s 80 0.05966 159s 81 0.06137 159s 82 0.06217 159s 83 0.06244 159s 84 0.06463 159s 85 0.06544 159s 86 0.06550 159s 87 0.06684 159s 88 0.06878 159s 89 0.07032 159s 90 0.07230 159s 91 0.07388 159s 92 0.07775 159s 93 0.07947 159s 94 0.07971 159s 95 0.08374 159s 96 0.08399 159s 97 0.08558 159s 98 0.09715 159s 99 0.10235 159s 100 0.10701 159s 101 0.10703 159s 102 0.10763 159s 103 0.11112 159s 104 0.11314 159s 105 0.12650 159s 106 0.12671 159s 107 0.12948 159s 108 0.13104 159s 109 0.13320 159s 110 0.13770 159s 111 0.14660 159s 112 0.15112 159s 113 0.15177 159s 114 0.15848 159s 115 0.16049 159s 116 0.16160 159s 117 0.16311 159s 118 0.16471 159s 119 0.16732 159s 120 0.17056 159s 121 0.17242 159s 122 0.17924 159s 123 0.18278 159s 124 0.18551 159s 125 0.18824 159s 126 0.19265 159s 127 0.19460 159s 128 0.19726+ for i in *.bf 159s + '[' -f REV.bf ']' 159s + hyphy REV.bf 159s 159s 129 0.20131 159s 130 0.20157 159s 131 0.23358 159s 132 0.23627 159s 133 0.23762 159s 134 0.23921 159s 135 0.24040 159s 136 0.24709 159s 137 0.25720 159s 138 0.25875 159s 139 0.26564 159s 140 0.26863 159s 141 0.27115 159s 142 0.28011 159s 143 0.28151 159s 144 0.28337 159s 145 0.28370 159s 146 0.28463 159s 147 0.28464 159s 148 0.28685 159s 149 0.29878 159s 150 0.30767 159s 151 0.31132 159s 152 0.31399 159s 153 0.33411 159s 154 0.33802 159s 155 0.34030 159s 156 0.35440 159s 157 0.36670 159s 158 0.37540 159s 159 0.39817 159s 160 0.39961 159s 161 0.40378 159s 162 0.40655 159s 163 0.40850 159s 164 0.41437 159s 165 0.41818 159s 166 0.42672 159s 167 0.42760 159s 168 0.43042 159s 169 0.43262 159s 170 0.44908 159s 171 0.45440 159s 172 0.46804 159s 173 0.47305 159s 174 0.47351 159s 175 0.47864 159s 176 0.48170 159s 177 0.50484 159s 178 0.51073 159s 179 0.51774 159s 180 0.53966 159s 181 0.55257 159s 182 0.55409 159s 183 0.55676 159s 184 0.58658 159s 185 0.63546 159s 186 0.66959 159s 187 0.67781 159s 188 0.67862 159s 189 0.71181 159s 190 0.72712 159s 191 0.73038 159s 192 0.74694 159s 193 0.78047 159s 194 0.78585 159s 195 0.79330 159s 196 0.84897 159s 197 0.85060 159s 198 0.86761 159s 199 0.90832 159s 200 0.91019 159s 201 0.97348 159s 202 1.02080 159s 203 1.02593 159s 204 1.06304 159s 205 1.08306 159s 206 1.08732 159s 207 1.12123 159s 208 1.16941 159s 209 1.18596 159s 210 1.20790 159s 211 1.23039 159s 212 1.24446 159s 213 1.27184 159s 214 1.28474 159s 215 1.33055 159s 216 1.36730 159s 217 1.41155 159s 218 1.41507 159s 219 1.46323 159s 220 1.47949 159s 221 1.48370 159s 222 1.48909 159s 223 1.49064 159s 224 1.51437 159s 225 1.66820 159s 226 1.68468 159s 227 1.68594 159s 228 1.69828 159s 229 1.74285 159s 230 1.75711 159s 231 1.82676 159s 232 1.83285 159s 233 1.85935 159s 234 1.96362 159s 235 2.03262 159s 236 2.04063 159s 237 2.04947 159s 238 2.08038 159s 239 2.10494 159s 240 2.10928 159s 241 2.12674 159s 242 2.16476 159s 243 2.22656 159s 244 2.24942 159s 245 2.35525 159s 246 2.50021 159s 247 2.50965 159s 248 2.56722 159s 249 2.61029 159s 250 2.68321 159s 251 2.74935 159s 252 2.96365 159s 253 2.97731 159s 254 3.15832 159s 255 3.22502 159s 256 3.26024 159s 257 3.61310 159s 258 3.68595 159s 259 3.69144 159s 260 3.71941 159s 261 3.76394 159s 262 4.64103 159s 263 4.93588 159s 264 5.10925 159s 265 5.22006 159s 266 5.22706 159s 267 5.56451 159s 268 5.85399 159s 269 7.82813 159s 270 7.89734 159s 271 9.78392 159s 272 13.83640 159s 159s Mean = 0.8681870192925496 159s Var = 2.552831565993694 (1/alpha) = 3.134420291020086 159s Log Likelihood = -1099.56654310363; 159s Tree givenTree=(256:0.01860538216157994,(822:0.02270294264862114,159:0.01094295281526419)Node2:0.003780125301190473,((113:0.01829133950928346,9939:0.0780294857458131)Node6:0.007454163686343501,(6760:0.07116808035147786,((317:0.03720628958387322,6767:0.07205711578316218)Node12:0.01019711247501063,((135:0.0203710282523365,(529:0.03423747335232681,105r:0.01129635937370129)Node18:0.02853147714387708)Node16:0.006570771307468816,(719:0.0282965875929688,136:0.009598218472943404)Node21:0.04403507429475615)Node15:0.01656703458156233)Node11:0.01314958375939888)Node9:0.02914838883914652)Node5:0.01372249227603786); 159s + for i in *.bf 159s + '[' -f REVshared.bf ']' 159s + hyphy REVshared.bf 159s Log Likelihood = -1156.62537454769; 159s Global Parameters: 159s AT=0.3657150792881375; 159s GT=0.4638401612022407; 159s CG=0.2489144096963367; 159s AG=1.863059141856964; 159s CT=1.208184615934091; 159s 159s Tree givenTree=(256:0.01208008296894431,(822:0.02974416354112736,159:0.004671989004169355)Node2:0.003487891940605732,((113:0.02209372329169652,9939:0.07979185592439336)Node6:0.004713625359717363,(6760:0.07208833295494536,((317:0.03910508962614788,6767:0.07108002404764888)Node12:0.01085400204409226,((135:0.02052223081982936,(529:0.03437669549093346,105r:0.01466087330498022)Node18:0.0246715427501873)Node16:0.005564851309212862,(719:0.02875126047930013,136:0.009456314541356765)Node21:0.04910010317275702)Node15:0.01585104101299624)Node11:0.01426327852159722)Node9:0.02297211024933358)Node5:0.02145251361064765); 159s + for i in *.bf 159s + '[' -f ReplicateConstraint1.bf ']' 159s + hyphy ReplicateConstraint1.bf 159s 1).Unconstrained HKY85 159s 159s Log Likelihood = -1152.88; 159s 159s Independent Parameters List 159s 159s Parameter 1 : hivTree.317.trvs 159s Parameter 2 : hivTree.317.trst 159s Parameter 3 : hivTree.6767.trvs 159s Parameter 4 : hivTree.6767.trst 159s Parameter 5 : hivTree.Node2.trvs 159s Parameter 6 : hivTree.Node2.trst 159s Parameter 7 : hivTree.135.trvs 159s Parameter 8 : hivTree.135.trst 159s Parameter 9 : hivTree.529.trvs 159s Parameter 10 : hivTree.529.trst 159s Parameter 11 : hivTree.105r.trvs 159s Parameter 12 : hivTree.105r.trst 159s Parameter 13 : hivTree.Node8.trvs 159s Parameter 14 : hivTree.Node8.trst 159s Parameter 15 : hivTree.iNode1.trvs 159s Parameter 16 : hivTree.iNode1.trst 159s Parameter 17 : hivTree.719.trvs 159s Parameter 18 : hivTree.719.trst 159s Parameter 19 : hivTree.136.trvs 159s Parameter 20 : hivTree.136.trst 159s Parameter 21 : hivTree.Node11.trvs 159s Parameter 22 : hivTree.Node11.trst 159s Parameter 23 : hivTree.Node5.trvs 159s Parameter 24 : hivTree.Node5.trst 159s Parameter 25 : hivTree.Node1.trvs 159s Parameter 26 : hivTree.Node1.trst 159s Parameter 27 : hivTree.6760.trvs 159s Parameter 28 : hivTree.6760.trst 159s Parameter 29 : hivTree.113.trvs 159s Parameter 30 : hivTree.113.trst 159s Parameter 31 : hivTree.9939.trvs 159s Parameter 32 : hivTree.9939.trst 159s Parameter 33 : hivTree.Node16.trvs 159s Parameter 34 : hivTree.Node16.trst 159s Parameter 35 : hivTree.256.trvs 159s Parameter 36 : hivTree.256.trst 159s Parameter 37 : hivTree.822.trvs 159s Parameter 38 : hivTree.822.trst 159s Parameter 39 : hivTree.159.trvs 159s Parameter 40 : hivTree.159.trst 159s Parameter 41 : hivTree.Node21.trvs 159s Parameter 42 : hivTree.Node21.trst 159s Parameter 43 : hivTree.iNode2.trvs 159s Parameter 44 : hivTree.iNode2.trst 159s Parameter 45 : hivTree.Node15.trvs 159s Parameter 46 : hivTree.Node15.trst 159s 159s 2).HKY85 constrained to F81 159s 159s Log Likelihood = -1187.55; 159s 159s Independent Parameters List 159s 159s Parameter 1 : hivTree.317.trvs 159s Parameter 2 : hivTree.6767.trvs 159s Parameter 3 : hivTree.Node2.trvs 159s Parameter 4 : hivTree.135.trvs 159s Parameter 5 : hivTree.529.trvs 159s Parameter 6 : hivTree.105r.trvs 159s Parameter 7 : hivTree.Node8.trvs 159s Parameter 8 : hivTree.iNode1.trvs 159s Parameter 9 : hivTree.719.trvs 159s Parameter 10 : hivTree.136.trvs 159s Parameter 11 : hivTree.Node11.trvs 159s Parameter 12 : hivTree.Node5.trvs 159s Parameter 13 : hivTree.Node1.trvs 159s Parameter 14 : hivTree.6760.trvs 159s Parameter 15 : hivTree.113.trvs 159s Parameter 16 : hivTree.9939.trvs 159s Parameter 17 : hivTree.Node16.trvs 159s Parameter 18 : hivTree.256.trvs 159s Parameter 19 : hivTree.822.trvs 159s Parameter 20 : hivTree.159.trvs 159s Parameter 21 : hivTree.Node21.trvs 159s Parameter 22 : hivTree.iNode2.trvs 159s Parameter 23 : hivTree.Node15.trvs 159s 159s Constrained Parameters List 159s 159s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 159s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 159s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 159s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 159s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 159s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 159s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 159s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 159s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 159s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 159s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 159s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 159s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 159s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 159s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 159s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 159s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 159s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 159s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 159s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 159s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 159s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 159s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 159s 159s 3).HKY85 constrained to F81 on internal branches 159s 159s Log Likelihood = -1167.99; 159s 159s Independent Parameters List 159s 159s Parameter 1 : hivTree.Node2.trvs 159s Parameter 2 : hivTree.Node8.trvs 159s Parameter 3 : hivTree.iNode1.trvs 159s Parameter 4 : hivTree.Node11.trvs 159s Parameter 5 : hivTree.Node5.trvs 159s Parameter 6 : hivTree.Node1.trvs 159s Parameter 7 : hivTree.Node16.trvs 159s Parameter 8 : hivTree.Node21.trvs 159s Parameter 9 : hivTree.iNode2.trvs 159s Parameter 10 : hivTree.Node15.trvs 159s Parameter 11 : hivTree.317.trst 159s Parameter 12 : hivTree.317.trvs 159s Parameter 13 : hivTree.6767.trvs 159s Parameter 14 : hivTree.6767.trst 159s Parameter 15 : hivTree.135.trst 159s Parameter 16 : hivTree.135.trvs 159s Parameter 17 : hivTree.529.trvs 159s Parameter 18 : hivTree.529.trst 159s Parameter 19 : hivTree.105r.trst 159s Parameter 20 : hivTree.105r.trvs 159s Parameter 21 : hivTree.719.trvs 159s Parameter 22 : hivTree.719.trst 159s Parameter 23 : hivTree.136.trvs 159s Parameter 24 : hivTree.136.trst 159s Parameter 25 : hivTree.6760.trvs 159s Parameter 26 : hivTree.6760.trst 159s Parameter 27 : hivTree.113.trvs 159s Parameter 28 : hivTree.113.trst 159s Parameter 29 : hivTree.9939.trst 159s Parameter 30 : hivTree.9939.trvs 159s Parameter 31 : hivTree.256.trvs 159s Parameter 32 : hivTree.256.trst 159s Parameter 33 : hivTree.822.trvs 159s Parameter 34 : hivTree.822.trst 159s Parameter 35 : hivTree.159.trst 159s Parameter 36 : hivTree.159.trvs 159s 159s Constrained Parameters List 159s 159s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 159s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 159s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 159s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 159s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 159s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 159s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 159s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 159s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 159s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 159s 159s 4).HKY85 with shared ratio. 159s 159s Log Likelihood = -1165.7; 159s 159s Independent Parameters List 159s 159s Parameter 1 : R 159s Parameter 2 : hivTree.317.trst 159s Parameter 3 : hivTree.6767.trst 159s Parameter 4 : hivTree.Node2.trst 159s Parameter 5 : hivTree.135.trst 159s Parameter 6 : hivTree.529.trst 159s Parameter 7 : hivTree.105r.trst 159s Parameter 8 : hivTree.Node8.trst 159s Parameter 9 : hivTree.iNode1.trst 159s Parameter 10 : hivTree.719.trst 159s Parameter 11 : hivTree.136.trst 159s Parameter 12 : hivTree.Node11.trst 159s Parameter 13 : hivTree.Node5.trst 159s Parameter 14 : hivTree.Node1.trst 159s Parameter 15 : hivTree.6760.trst 159s Parameter 16 : hivTree.113.trst 159s Parameter 17 : hivTree.9939.trst 159s Parameter 18 : hivTree.Node16.trst 159s Parameter 19 : hivTree.256.trst 159s Parameter 20 : hivTree.822.trst 159s Parameter 21 : hivTree.159.trst 159s Parameter 22 : hivTree.Node21.trst 159s Parameter 23 : hivTree.iNode2.trst 159s Parameter 24 : hivTree.Node15.trst 159s 159s Constrained Parameters List 159s 159s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 159s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 159s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 159s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 159s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 159s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 159s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 159s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 159s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 159s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 159s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 159s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 159s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 159s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 159s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 159s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 159s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 159s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 159s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 159s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 159s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 159s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 159s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 159s + '[' -f ReplicateConstraint2.bf ']' 159s + hyphy ReplicateConstraint2.bf 159s 1).Unconstrained HKY85 159s 159s Log Likelihood = -1152.88; 159s 159s Independent Parameters List 159s 159s Parameter 1 : hivTree.317.trvs 159s Parameter 2 : hivTree.317.trst 159s Parameter 3 : hivTree.6767.trvs 159s Parameter 4 : hivTree.6767.trst 159s Parameter 5 : hivTree.Node2.trvs 159s Parameter 6 : hivTree.Node2.trst 159s Parameter 7 : hivTree.135.trvs 159s Parameter 8 : hivTree.135.trst 159s Parameter 9 : hivTree.529.trvs 159s Parameter 10 : hivTree.529.trst 159s Parameter 11 : hivTree.105r.trvs 159s Parameter 12 : hivTree.105r.trst 159s Parameter 13 : hivTree.Node8.trvs 159s Parameter 14 : hivTree.Node8.trst 159s Parameter 15 : hivTree.iNode1.trvs 159s Parameter 16 : hivTree.iNode1.trst 159s Parameter 17 : hivTree.719.trvs 159s Parameter 18 : hivTree.719.trst 159s Parameter 19 : hivTree.136.trvs 159s Parameter 20 : hivTree.136.trst 159s Parameter 21 : hivTree.Node11.trvs 159s Parameter 22 : hivTree.Node11.trst 159s Parameter 23 : hivTree.Node5.trvs 159s Parameter 24 : hivTree.Node5.trst 159s Parameter 25 : hivTree.Node1.trvs 159s Parameter 26 : hivTree.Node1.trst 159s Parameter 27 : hivTree.6760.trvs 159s Parameter 28 : hivTree.6760.trst 159s Parameter 29 : hivTree.113.trvs 159s Parameter 30 : hivTree.113.trst 159s Parameter 31 : hivTree.9939.trvs 159s Parameter 32 : hivTree.9939.trst 159s Parameter 33 : hivTree.Node16.trvs 159s Parameter 34 : hivTree.Node16.trst 159s Parameter 35 : hivTree.256.trvs 159s Parameter 36 : hivTree.256.trst 159s Parameter 37 : hivTree.822.trvs 159s Parameter 38 : hivTree.822.trst 159s Parameter 39 : hivTree.159.trvs 159s Parameter 40 : hivTree.159.trst 159s Parameter 41 : hivTree.Node21.trvs 159s Parameter 42 : hivTree.Node21.trst 159s Parameter 43 : hivTree.iNode2.trvs 159s Parameter 44 : hivTree.iNode2.trst 159s Parameter 45 : hivTree.Node15.trvs 160s Parameter 46 : hivTree.Node15.trst 160s 160s 2).HKY85 constrained to F81 on the "iNode1" subtree 160s 160s Log Likelihood = -1157.82; 160s 160s Independent Parameters List 160s 160s Parameter 1 : hivTree.135.trvs 160s Parameter 2 : hivTree.529.trvs 160s Parameter 3 : hivTree.105r.trvs 160s Parameter 4 : hivTree.Node8.trvs 160s Parameter 5 : hivTree.317.trvs 160s Parameter 6 : hivTree.317.trst 160s Parameter 7 : hivTree.6767.trst 160s Parameter 8 : hivTree.6767.trvs 160s Parameter 9 : hivTree.Node2.trst 160s Parameter 10 : hivTree.Node2.trvs 160s Parameter 11 : hivTree.iNode1.trvs 160s Parameter 12 : hivTree.iNode1.trst 160s Parameter 13 : hivTree.719.trvs 160s Parameter 14 : hivTree.719.trst 160s Parameter 15 : hivTree.136.trvs 160s Parameter 16 : hivTree.136.trst 160s Parameter 17 : hivTree.Node11.trvs 160s Parameter 18 : hivTree.Node11.trst 160s Parameter 19 : hivTree.Node5.trvs 160s Parameter 20 : hivTree.Node5.trst 160s Parameter 21 : hivTree.Node1.trvs 160s Parameter 22 : hivTree.Node1.trst 160s Parameter 23 : hivTree.6760.trvs 160s Parameter 24 : hivTree.6760.trst 160s Parameter 25 : hivTree.113.trvs 160s Parameter 26 : hivTree.113.trst 160s Parameter 27 : hivTree.9939.trvs 160s Parameter 28 : hivTree.9939.trst 160s Parameter 29 : hivTree.Node16.trvs 160s Parameter 30 : hivTree.Node16.trst 160s Parameter 31 : hivTree.256.trvs 160s Parameter 32 : hivTree.256.trst 160s Parameter 33 : hivTree.822.trvs 160s Parameter 34 : hivTree.822.trst 160s Parameter 35 : hivTree.159.trvs 160s Parameter 36 : hivTree.159.trst 160s Parameter 37 : hivTree.Node21.trvs 160s Parameter 38 : hivTree.Node21.trst 160s Parameter 39 : hivTree.iNode2.trvs 160s Parameter 40 : hivTree.iNode2.trst 160s Parameter 41 : hivTree.Node15.trvs 160s Parameter 42 : hivTree.Node15.trst 160s 160s Constrained Parameters List 160s 160s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 160s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 160s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 160s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 160s 160s 3).HKY85 constrained to F81 on the "iNode1" branch 160s 160s Log Likelihood = -1152.88; 160s 160s Independent Parameters List 160s 160s Parameter 1 : hivTree.317.trvs 160s Parameter 2 : hivTree.317.trst 160s Parameter 3 : hivTree.6767.trvs 160s Parameter 4 : hivTree.6767.trst 160s Parameter 5 : hivTree.Node2.trvs 160s Parameter 6 : hivTree.Node2.trst 160s Parameter 7 : hivTree.135.trvs 160s Parameter 8 : hivTree.135.trst 160s Parameter 9 : hivTree.529.trvs 160s Parameter 10 : hivTree.529.trst 160s Parameter 11 : hivTree.105r.trvs 160s Parameter 12 : hivTree.105r.trst 160s Parameter 13 : hivTree.Node8.trvs 160s Parameter 14 : hivTree.Node8.trst 160s Parameter 15 : hivTree.iNode1.trvs 160s Parameter 16 : hivTree.iNode1.trst 160s Parameter 17 : hivTree.719.trvs 160s Parameter 18 : hivTree.719.trst 160s Parameter 19 : hivTree.136.trvs 160s Parameter 20 : hivTree.136.trst 160s Parameter 21 : hivTree.Node11.trvs 160s Parameter 22 : hivTree.Node11.trst 160s Parameter 23 : hivTree.Node5.trvs 160s Parameter 24 : hivTree.Node5.trst 160s Parameter 25 : hivTree.Node1.trvs 160s Parameter 26 : hivTree.Node1.trst 160s Parameter 27 : hivTree.6760.trvs 160s Parameter 28 : hivTree.6760.trst 160s Parameter 29 : hivTree.113.trvs 160s Parameter 30 : hivTree.113.trst 160s Parameter 31 : hivTree.9939.trvs 160s Parameter 32 : hivTree.9939.trst 160s Parameter 33 : hivTree.Node16.trvs 160s Parameter 34 : hivTree.Node16.trst 160s Parameter 35 : hivTree.256.trvs 160s Parameter 36 : hivTree.256.trst 160s Parameter 37 : hivTree.822.trvs 160s Parameter 38 : hivTree.822.trst 160s Parameter 39 : hivTree.159.trvs 160s Parameter 40 : hivTree.159.trst 160s Parameter 41 : hivTree.Node21.trvs 160s Parameter 42 : hivTree.Node21.trst 160s Parameter 43 : hivTree.iNode2.trvs 160s Parameter 44 : hivTree.iNode2.trst 160s Parameter 45 : hivTree.Node15.trvs 160s Parameter 46 : hivTree.Node15.trst 160s 160s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 160s 160s Log Likelihood = -1152.88; 160s 160s Independent Parameters List 160s 160s Parameter 1 : hivTree.317.trvs 160s Parameter 2 : hivTree.317.trst 160s Parameter 3 : hivTree.6767.trvs 160s Parameter 4 : hivTree.6767.trst 160s Parameter 5 : hivTree.Node2.trvs 160s Parameter 6 : hivTree.Node2.trst 160s Parameter 7 : hivTree.135.trvs 160s Parameter 8 : hivTree.135.trst 160s Parameter 9 : hivTree.529.trvs 160s Parameter 10 : hivTree.529.trst 160s Parameter 11 : hivTree.105r.trvs 160s Parameter 12 : hivTree.105r.trst 160s Parameter 13 : hivTree.Node8.trvs 160s Parameter 14 : hivTree.Node8.trst 160s Parameter 15 : hivTree.iNode1.trvs 160s Parameter 16 : hivTree.iNode1.trst 160s Parameter 17 : hivTree.719.trvs 160s Parameter 18 : hivTree.719.trst 160s Parameter 19 : hivTree.136.trvs 160s Parameter 20 : hivTree.136.trst 160s Parameter 21 : hivTree.Node11.trvs 160s Parameter 22 : hivTree.Node11.trst 160s Parameter 23 : hivTree.Node5.trvs 160s Parameter 24 : hivTree.Node5.trst 160s Parameter 25 : hivTree.Node1.trvs 160s Parameter 26 : hivTree.Node1.trst 160s Parameter 27 : hivTree.6760.trvs 160s Parameter 28 : hivTree.6760.trst 160s Parameter 29 : hivTree.113.trvs 160s Parameter 30 : hivTree.113.trst 160s Parameter 31 : hivTree.9939.trvs 160s Parameter 32 : hivTree.9939.trst 160s Parameter 33 : hivTree.Node16.trvs 160s Parameter 34 : hivTree.Node16.trst 160s Parameter 35 : hivTree.256.trvs 160s Parameter 36 : hivTree.256.trst 160s Parameter 37 : hivTree.822.trvs 160s Parameter 38 : hivTree.822.trst 160s Parameter 39 : hivTree.159.trvs 160s Parameter 40 : hivTree.159.trst 160s Parameter 41 : hivTree.Node21.trvs 160s Parameter 42 : hivTree.Node21.trst 160s Parameter 43 : hivTree.iNode2.trvs 160s Parameter 44 : hivTree.iNode2.trst 160s Parameter 45 : hivTree.Node15.trvs 160s Parameter 46 : hivTree.Node15.trst 160s 160s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 160s 160s Log Likelihood = -1152.88; 160s 160s Independent Parameters List 160s 160s Parameter 1 : hivTree.317.trvs 160s Parameter 2 : hivTree.317.trst 160s Parameter 3 : hivTree.6767.trvs 160s Parameter 4 : hivTree.6767.trst 160s Parameter 5 : hivTree.Node2.trvs 160s Parameter 6 : hivTree.Node2.trst 160s Parameter 7 : hivTree.135.trvs 160s Parameter 8 : hivTree.135.trst 160s Parameter 9 : hivTree.529.trvs 160s Parameter 10 : hivTree.529.trst 160s Parameter 11 : hivTree.105r.trvs 160s Parameter 12 : hivTree.105r.trst 160s Parameter 13 : hivTree.Node8.trvs 160s Parameter 14 : hivTree.Node8.trst 160s Parameter 15 : hivTree.iNode1.trvs 160s Parameter 16 : hivTree.iNode1.trst 160s Parameter 17 : hivTree.719.trvs 160s Parameter 18 : hivTree.719.trst 160s Parameter 19 : hivTree.136.trvs 160s Parameter 20 : hivTree.136.trst 160s Parameter 21 : hivTree.Node11.trvs 160s Parameter 22 : hivTree.Node11.trst 160s Parameter 23 : hivTree.Node5.trvs 160s Parameter 24 : hivTree.Node5.trst 160s Parameter 25 : hivTree.Node1.trvs 160s Parameter 26 : hivTree.Node1.trst 160s Parameter 27 : hivTree.6760.trvs 160s Parameter 28 : hivTree.6760.trst 160s Parameter 29 : hivTree.113.trvs 160s Parameter 30 : hivTree.113.trst 160s Parameter 31 : hivTree.9939.trvs 160s Parameter 32 : hivTree.9939.trst 160s Parameter 33 : hivTree.Node16.trvs 160s Parameter 34 : hivTree.Node16.trst 160s Parameter 35 : hivTree.256.trvs 160s Parameter 36 : hivTree.256.trst 160s Parameter 37 : hivTree.822.trvs 160s Parameter 38 : hivTree.822.trst 160s Parameter 39 : hivTree.159.trvs 160s Parameter 40 : hivTree.159.trst 160s Parameter 41 : hivTree.Node21.trvs 160s Parameter 42 : hivTree.Node21.trst 160s Parameter 43 : hivTree.iNode2.trvs 160s Parameter 44 : hivTree.iNode2.trst 160s Parameter 45 : hivTree.Node15.trvs 160s Parameter 46 : hivTree.Node15.trst 160s 160s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 160s 160s Log Likelihood = -1157.82; 160s 160s Independent Parameters List 160s 160s Parameter 1 : hivTree.135.trst 160s Parameter 2 : hivTree.529.trst 160s Parameter 3 : hivTree.105r.trst 160s Parameter 4 : hivTree.Node8.trst 160s Parameter 5 : hivTree.317.trvs 160s Parameter 6 : hivTree.317.trst 160s Parameter 7 : hivTree.6767.trst 160s Parameter 8 : hivTree.6767.trvs 160s Parameter 9 : hivTree.Node2.trst 160s Parameter 10 : hivTree.Node2.trvs 160s Parameter 11 : hivTree.iNode1.trvs 160s Parameter 12 : hivTree.iNode1.trst 160s Parameter 13 : hivTree.719.trvs 160s Parameter 14 : hivTree.719.trst 160s Parameter 15 : hivTree.136.trvs 160s Parameter 16 : hivTree.136.trst 160s Parameter 17 : hivTree.Node11.trvs 160s Parameter 18 : hivTree.Node11.trst 160s Parameter 19 : hivTree.Node5.trvs 160s Parameter 20 : hivTree.Node5.trst 160s Parameter 21 : hivTree.Node1.trvs 160s Parameter 22 : hivTree.Node1.trst 160s Parameter 23 : hivTree.6760.trvs 160s Parameter 24 : hivTree.6760.trst 160s Parameter 25 : hivTree.113.trvs 160s Parameter 26 : hivTree.113.trst 160s Parameter 27 : hivTree.9939.trvs 160s Parameter 28 : hivTree.9939.trst 160s Parameter 29 : hivTree.Node16.trvs 160s Parameter 30 : hivTree.Node16.trst 160s Parameter 31 : hivTree.256.trvs 160s Parameter 32 : hivTree.256.trst 160s Parameter 33 : hivTree.822.trvs 160s Parameter 34 : hivTree.822.trst 160s Parameter 35 : hivTree.159.trvs 160s Parameter 36 : hivTree.159.trst 160s Parameter 37 : hivTree.Node21.trvs 160s Parameter 38 : hivTree.Node21.trst 160s Parameter 39 : hivTree.iNode2.trvs 160s Parameter 40 : hivTree.iNode2.trst 160s Parameter 41 : hivTree.Node15.trvs 160s Parameter 42 : hivTree.Node15.trst 160s 160s Constrained Parameters List 160s 160s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 160s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 160s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 160s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 160s + '[' -f aa.bf ']' 160s + hyphy aa.bf 160s Log Likelihood = -1134.73159786158; 160s Tree theTree=(((Langur:0.07428656821870078,Baboon:0.03833724264166073)Node2:0.02338349962027235,Human:0.05948335162646717)Node1:0.02006356709749271,Rat:0.2458393542260101,(Cow:0.255038587209211,Horse:0.5625920223284028)Node7:0.0705988140401653); 160s + for i in *.bf 160s + '[' -f definitions2.bf ']' 160s + hyphy definitions2.bf 160s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 160s 160s Sample by MEAN: 160s 160s Sample mean = 0.5 (sample variance = 0.2450374540764348) 160s 160s Rate[0]= 0.06847689 (weight=0.2500000) 160s Rate[1]= 0.23837593 (weight=0.2500000) 160s Rate[2]= 0.50000000 (weight=0.2500000) 160s Rate[3]= 1.19314718 (weight=0.2500000) 160s ------------------------------------------------ 160s 160s Sample by MEDIAN: 160s 160s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 160s 160s Rate[0]= 0.06676570 (weight=0.2500000) 160s Rate[1]= 0.23500181 (weight=0.2500000) 160s Rate[2]= 0.49041463 (weight=0.2500000) 160s Rate[3]= 1.03972077 (weight=0.2500000) 160s ------------------------------------------------ 160s 160s Sample by SCALED_MEDIAN: 160s 160s Sample mean = 0.5 (sample variance = 0.2154404122636025) 160s 160s Rate[0]= 0.07289218 (weight=0.2500000) 160s Rate[1]= 0.25656580 (weight=0.2500000) 160s Rate[2]= 0.53541552 (weight=0.2500000) 160s Rate[3]= 1.13512650 (weight=0.2500000) 160s ------------------------------------------------ 160s 160s Sample by MEAN (numerical averaging): 160s 160s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 160s 160s Rate[0]= 0.06846096 (weight=0.2500000) 160s Rate[1]= 0.23834015 (weight=0.2500000) 160s Rate[2]= 0.49996411 (weight=0.2500000) 160s Rate[3]= 1.19314889 (weight=0.2500000) 160s ------------------------------------------------ 160s 160s Sample by MEAN (numerical CDF and averaging): 160s 160s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 160s 160s Rate[0]= 0.06849282 (weight=0.2500000) 160s Rate[1]= 0.23835613 (weight=0.2500000) 160s Rate[2]= 0.49994751 (weight=0.2500000) 160s Rate[3]= 1.19311765 (weight=0.2500000) 160s ------------------------------------------------ 160s 2). Equiprobable rates sampled from Exponential with lambda = 2 160s 160s Sample by MEDIAN (3 rate classes): 160s 160s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 160s 160s Rate[0]= 0.09116078 (weight=0.3333333) 160s Rate[1]= 0.34657359 (weight=0.3333333) 160s Rate[2]= 0.89587973 (weight=0.3333333) 160s ------------------------------------------------ 160s 160s Sample by MEDIAN (9 rate classes): 160s 160s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 160s 160s Rate[0]= 0.02857921 (weight=0.1111111) 160s Rate[1]= 0.09116078 (weight=0.1111111) 160s Rate[2]= 0.16271120 (weight=0.1111111) 160s Rate[3]= 0.24623824 (weight=0.1111111) 160s Rate[4]= 0.34657359 (weight=0.1111111) 160s Rate[5]= 0.47223080 (weight=0.1111111) 160s Rate[6]= 0.64046692 (weight=0.1111111) 160s Rate[7]= 0.89587973 (weight=0.1111111) 160s Rate[8]= 1.44518588 (weight=0.1111111) 160s ------------------------------------------------ 160s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 160s 160s Sample by MEAN (10 rate classes): 160s 160s Sample mean = 1 (sample variance = 0.1057310289486733) 160s 160s Rate[0]= 0.52447499 (weight=0.1000000) 160s Rate[1]= 0.67866972 (weight=0.1000000) 160s Rate[2]= 0.77209919 (weight=0.1000000) 160s Rate[3]= 0.85214884 (weight=0.1000000) 160s Rate[4]= 0.92850815 (weight=0.1000000) 160s Rate[5]= 1.00664500 (weight=0.1000000) 160s Rate[6]= 1.09192933 (weight=0.1000000) 160s Rate[7]= 1.19267960 (weight=0.1000000) 160s Rate[8]= 1.32858029 (weight=0.1000000) 160s Rate[9]= 1.62426489 (weight=0.1000000) 160s ------------------------------------------------ 160s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 160s 160s Sample by MEAN (10 rate classes): 160s 160s Sample mean = 2 (sample variance = 0.04259071282256012) 160s 160s Rate[0]= 1.66431246 (weight=0.1000000) 160s Rate[1]= 1.79212822 (weight=0.1000000) 160s Rate[2]= 1.86123411 (weight=0.1000000) 160s Rate[3]= 1.91722052 (weight=0.1000000) 160s Rate[4]= 1.96832799 (weight=0.1000000) 160s Rate[5]= 2.01862937 (weight=0.1000000) 160s Rate[6]= 2.07152664 (weight=0.1000000) 160s Rate[7]= 2.13166629 (weight=0.1000000) 160s Rate[8]= 2.20930216 (weight=0.1000000) 160s Rate[9]= 2.36565224 (weight=0.1000000) 160s ------------------------------------------------ 160s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 160s 160s Sample by MEAN (8 rate classes): 160s 160s Sample mean = 0.5 (sample variance = 0.09375000225643569) 160s 160s Rate[0]= 0.06250000 (weight=0.1250000) 160s Rate[1]= 0.18750000 (weight=0.1250000) 160s Rate[2]= 0.31250001 (weight=0.1250000) 160s Rate[3]= 0.43750001 (weight=0.1250000) 160s Rate[4]= 0.56249993 (weight=0.1250000) 160s Rate[5]= 0.68750001 (weight=0.1250000) 160s Rate[6]= 0.81250002 (weight=0.1250000) 160s Rate[7]= 0.93750002 (weight=0.1250000) 160s ------------------------------------------------ 160s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 160s 160s Sample by MEAN (8 rate classes): 160s 160s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 160s 160s Rate[0]= 2.17658588 (weight=0.1250000) 160s Rate[1]= 2.55230783 (weight=0.1250000) 160s Rate[2]= 2.75432532 (weight=0.1250000) 160s Rate[3]= 2.92101185 (weight=0.1250000) 160s Rate[4]= 3.07898815 (weight=0.1250000) 160s Rate[5]= 3.24567468 (weight=0.1250000) 160s Rate[6]= 3.44769217 (weight=0.1250000) 160s Rate[7]= 3.82341415 (weight=0.1250000) 160s ------------------------------------------------ 160s + for i in *.bf 160s + '[' -f definitions3.bf ']' 160s + hyphy definitions3.bf 160s 160s 160s Sample mean = + for i in *.bf 160s + '[' -f displayFunction.bf ']' 160s + hyphy displayFunction.bf 160s 1 (sample variance = 0.9920002887656187) 160s 160s Rate[0]= 0.05175536 (weight=0.1000000) 160s Rate[1]= 0.16309623 (weight=0.1000000) 160s Rate[2]= 0.28842380 (weight=0.1000000) 160s Rate[3]= 0.43177086 (weight=0.1000000) 160s Rate[4]= 0.59921784 (weight=0.1000000) 160s Rate[5]= 0.80057298 (weight=0.1000000) 160s Rate[6]= 1.05324451 (weight=0.1000000) 160s Rate[7]= 1.39304259 (weight=0.1000000) 160s Rate[8]= 1.91629073 (weight=0.1000000) 160s Rate[9]= 3.30258509 (weight=0.1000000) 160s ------------------------------------------------ 160s + for i in *.bf 160s + '[' -f profile_test.bf ']' 160s + hyphy profile_test.bf 160s 160s Total run time (seconds) : 0.000000 160s Total number of steps : 1500005 160s 160s 1 : s=0; 160s Call count: 1 160s Time (seconds): 1.8e-11 160s 2 : m={5,1}; 160s Call count: 1 160s Time (seconds): 1.8e-11 160s 3 : k=0; 160s Call count: 1 160s Time (seconds): 2e-12 160s 4 : Branch under condition 'k<250000' 160s to 160s s=s+k; 160s else 160s #profilePAUSE, ; 160s Call count: 250001 160s Time (seconds): 5.997000000002869e-08 160s 5 : s=s+k; 160s Call count: 250000 160s Time (seconds): 4.883600000002457e-08 160s 6 : t=Random(0,5); 160s Call count: 250000 160s Time (seconds): 6.281700000003056e-08 160s 7 : m[t]=m[t]+1; 160s Call count: 250000 160s Time (seconds): 1.676020000001099e-07 160s 8 : k=k+1; 160s Call count: 250000 160s Time (seconds): 8.539200000004166e-08 160s 9 : Go to step 4 160s Call count: 250000 160s Time (seconds): 1.414299999999608e-08 160s 10 : #profilePAUSE, ; 160s Call count: 1 160s Time (seconds): 1e-12 160s + for i in *.bf 160s + '[' -f shared.bf ']' 160s + hyphy shared.bf 160s + rm -f '*messages.log*' '*errors.log*' 161s autopkgtest [02:02:21]: test run-unit-tests: -----------------------] 161s autopkgtest [02:02:21]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 161s run-unit-tests PASS 162s autopkgtest [02:02:22]: @@@@@@@@@@@@@@@@@@@@ summary 162s run-unit-tests PASS 179s nova [W] Using flock in prodstack6-ppc64el 179s Creating nova instance adt-plucky-ppc64el-hyphy-20250216-015940-juju-7f2275-prod-proposed-migration-environment-20-8b3b8b8e-2f87-4740-989d-a101656475f3 from image adt/ubuntu-plucky-ppc64el-server-20250215.img (UUID 6b0563e5-c35c-4c0f-8fb5-aae43570455f)... 179s nova [W] Timed out waiting for 15d08a76-5644-4b62-8c1f-eb2735946df2 to get deleted.