0s autopkgtest [00:10:49]: starting date and time: 2025-02-16 00:10:49+0000 0s autopkgtest [00:10:49]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [00:10:49]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wovi918f/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-43.secgroup --name adt-plucky-arm64-hyphy-20250216-001049-juju-7f2275-prod-proposed-migration-environment-2-e7302dbe-2406-42d9-b667-3ce5fa2f63a2 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/ 268s autopkgtest [00:15:17]: testbed dpkg architecture: arm64 269s autopkgtest [00:15:18]: testbed apt version: 2.9.28 269s autopkgtest [00:15:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 269s autopkgtest [00:15:18]: testbed release detected to be: None 270s autopkgtest [00:15:19]: updating testbed package index (apt update) 271s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 271s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 271s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 271s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 271s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.1 kB] 271s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 271s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 271s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [823 kB] 271s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [163 kB] 271s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 271s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [937 kB] 271s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.0 kB] 272s Fetched 2140 kB in 1s (2124 kB/s) 272s Reading package lists... 273s Reading package lists... 274s Building dependency tree... 274s Reading state information... 275s Calculating upgrade... 276s The following packages will be upgraded: 276s dash libtasn1-6 libxdmcp6 276s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 276s Need to get 151 kB of archives. 276s After this operation, 17.4 kB of additional disk space will be used. 276s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 dash arm64 0.5.12-12ubuntu1 [96.1 kB] 276s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libtasn1-6 arm64 4.20.0-2 [43.9 kB] 276s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [10.7 kB] 276s Preconfiguring packages ... 277s Fetched 151 kB in 0s (362 kB/s) 277s (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 ... 116609 files and directories currently installed.) 277s Preparing to unpack .../dash_0.5.12-12ubuntu1_arm64.deb ... 277s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 277s Setting up dash (0.5.12-12ubuntu1) ... 277s (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 ... 116609 files and directories currently installed.) 277s Preparing to unpack .../libtasn1-6_4.20.0-2_arm64.deb ... 277s Unpacking libtasn1-6:arm64 (4.20.0-2) over (4.19.0-3build1) ... 277s Preparing to unpack .../libxdmcp6_1%3a1.1.5-1_arm64.deb ... 277s Unpacking libxdmcp6:arm64 (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 277s Setting up libxdmcp6:arm64 (1:1.1.5-1) ... 277s Setting up libtasn1-6:arm64 (4.20.0-2) ... 277s Processing triggers for libc-bin (2.40-4ubuntu1) ... 277s Processing triggers for man-db (2.13.0-1) ... 278s Processing triggers for debianutils (5.21) ... 278s Reading package lists... 279s Building dependency tree... 279s Reading state information... 280s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 280s autopkgtest [00:15:29]: upgrading testbed (apt dist-upgrade and autopurge) 280s Reading package lists... 281s Building dependency tree... 281s Reading state information... 282s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 282s Starting 2 pkgProblemResolver with broken count: 0 282s Done 284s Entering ResolveByKeep 284s 285s The following packages will be upgraded: 285s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 285s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 285s Need to get 10.7 MB of archives. 285s After this operation, 358 kB of additional disk space will be used. 285s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu1 [24.0 kB] 285s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu1 [1750 kB] 286s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu1 [4246 kB] 286s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu1 [2910 kB] 286s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu1 [600 kB] 286s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 287s Preconfiguring packages ... 287s Fetched 10.7 MB in 1s (10.3 MB/s) 287s (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 ... 116609 files and directories currently installed.) 287s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_arm64.deb ... 287s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 287s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_arm64.deb ... 287s Unpacking libc6-dev:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 287s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 287s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 288s Preparing to unpack .../libc6_2.41-1ubuntu1_arm64.deb ... 288s Checking for services that may need to be restarted... 288s Checking init scripts... 288s Checking for services that may need to be restarted... 288s Checking init scripts... 288s Stopping some services possibly affected by the upgrade (will be restarted later): 288s cron: stopping...done. 288s 288s Unpacking libc6:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 288s Setting up libc6:arm64 (2.41-1ubuntu1) ... 288s Checking for services that may need to be restarted... 288s Checking init scripts... 288s Restarting services possibly affected by the upgrade: 288s cron: restarting...done. 288s 288s Services restarted successfully. 289s (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 ... 116610 files and directories currently installed.) 289s Preparing to unpack .../libc-bin_2.41-1ubuntu1_arm64.deb ... 289s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 289s Setting up libc-bin (2.41-1ubuntu1) ... 289s (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 ... 116610 files and directories currently installed.) 289s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_arm64.deb ... 289s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 290s Setting up iproute2 (6.13.0-1ubuntu1) ... 290s Setting up locales (2.41-1ubuntu1) ... 290s Installing new version of config file /etc/locale.alias ... 291s Generating locales (this might take a while)... 293s en_US.UTF-8... done 293s Generation complete. 293s Setting up libc-dev-bin (2.41-1ubuntu1) ... 293s Setting up libc6-dev:arm64 (2.41-1ubuntu1) ... 293s Processing triggers for man-db (2.13.0-1) ... 294s Processing triggers for systemd (257.2-3ubuntu1) ... 295s Reading package lists... 295s Building dependency tree... 295s Reading state information... 296s Starting pkgProblemResolver with broken count: 0 296s Starting 2 pkgProblemResolver with broken count: 0 296s Done 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 300s autopkgtest [00:15:49]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 300s autopkgtest [00:15:49]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 303s Get:1 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (dsc) [2298 B] 303s Get:2 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (tar) [2627 kB] 303s Get:3 http://ftpmaster.internal/ubuntu plucky/universe hyphy 2.5.63+dfsg-1build2 (diff) [17.4 kB] 304s gpgv: Signature made Sat Nov 30 06:13:22 2024 UTC 304s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 304s gpgv: Can't check signature: No public key 304s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.63+dfsg-1build2.dsc: no acceptable signature found 304s autopkgtest [00:15:53]: testing package hyphy version 2.5.63+dfsg-1build2 305s autopkgtest [00:15:54]: build not needed 308s autopkgtest [00:15:57]: test run-unit-tests: preparing testbed 308s Reading package lists... 309s Building dependency tree... 309s Reading state information... 309s Starting pkgProblemResolver with broken count: 0 309s Starting 2 pkgProblemResolver with broken count: 0 309s Done 310s The following NEW packages will be installed: 310s hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 310s libevent-pthreads-2.1-7t64 libfabric1 libgomp1 libhsa-runtime64-1 libhsakmt1 310s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libllvm17t64 libmunge2 310s libopenmpi40 libpciaccess0 libpmix2t64 librdmacm1t64 libucx0 libxnvctrl0 310s ocl-icd-libopencl1 310s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 310s Need to get 57.1 MB of archives. 310s After this operation, 239 MB of additional disk space will be used. 310s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 hyphy-common all 2.5.63+dfsg-1build2 [628 kB] 310s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-17ubuntu1 [145 kB] 310s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 310s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 55.0-1ubuntu1 [71.5 kB] 310s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3ubuntu1 [542 kB] 310s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.11.2-1build1 [162 kB] 310s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 310s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 310s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 310s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 310s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.11.2-1build1 [15.8 kB] 311s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.6-3 [666 kB] 311s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-20 [24.9 MB] 313s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 314s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 314s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 314s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB] 315s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 55.0-1ubuntu1 [29.8 kB] 315s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 55.0-1ubuntu1 [43.3 kB] 315s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.17.0+ds-3build1 [1093 kB] 315s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi40 arm64 5.0.6-4 [2416 kB] 315s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 hyphy-mpi arm64 2.5.63+dfsg-1build2 [1112 kB] 315s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 hyphy-pt arm64 2.5.63+dfsg-1build2 [1085 kB] 315s Fetched 57.1 MB in 5s (10.8 MB/s) 315s Selecting previously unselected package hyphy-common. 315s (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 ... 116611 files and directories currently installed.) 315s Preparing to unpack .../00-hyphy-common_2.5.63+dfsg-1build2_all.deb ... 315s Unpacking hyphy-common (2.5.63+dfsg-1build2) ... 316s Selecting previously unselected package libgomp1:arm64. 316s Preparing to unpack .../01-libgomp1_14.2.0-17ubuntu1_arm64.deb ... 316s Unpacking libgomp1:arm64 (14.2.0-17ubuntu1) ... 316s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 316s Preparing to unpack .../02-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 316s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 316s Selecting previously unselected package librdmacm1t64:arm64. 316s Preparing to unpack .../03-librdmacm1t64_55.0-1ubuntu1_arm64.deb ... 316s Unpacking librdmacm1t64:arm64 (55.0-1ubuntu1) ... 316s Selecting previously unselected package libfabric1:arm64. 316s Preparing to unpack .../04-libfabric1_1.17.0-3ubuntu1_arm64.deb ... 316s Unpacking libfabric1:arm64 (1.17.0-3ubuntu1) ... 316s Selecting previously unselected package libhwloc15:arm64. 316s Preparing to unpack .../05-libhwloc15_2.11.2-1build1_arm64.deb ... 316s Unpacking libhwloc15:arm64 (2.11.2-1build1) ... 316s Selecting previously unselected package libmunge2:arm64. 316s Preparing to unpack .../06-libmunge2_0.5.16-1_arm64.deb ... 316s Unpacking libmunge2:arm64 (0.5.16-1) ... 316s Selecting previously unselected package libpciaccess0:arm64. 316s Preparing to unpack .../07-libpciaccess0_0.17-3build1_arm64.deb ... 316s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 316s Selecting previously unselected package libxnvctrl0:arm64. 316s Preparing to unpack .../08-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 316s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 316s Selecting previously unselected package ocl-icd-libopencl1:arm64. 316s Preparing to unpack .../09-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 316s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 316s Selecting previously unselected package libhwloc-plugins:arm64. 316s Preparing to unpack .../10-libhwloc-plugins_2.11.2-1build1_arm64.deb ... 316s Unpacking libhwloc-plugins:arm64 (2.11.2-1build1) ... 316s Selecting previously unselected package libpmix2t64:arm64. 316s Preparing to unpack .../11-libpmix2t64_5.0.6-3_arm64.deb ... 316s Unpacking libpmix2t64:arm64 (5.0.6-3) ... 316s Selecting previously unselected package libllvm17t64:arm64. 316s Preparing to unpack .../12-libllvm17t64_1%3a17.0.6-20_arm64.deb ... 316s Unpacking libllvm17t64:arm64 (1:17.0.6-20) ... 317s Selecting previously unselected package libamd-comgr2:arm64. 317s Preparing to unpack .../13-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 317s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 317s Selecting previously unselected package libhsakmt1:arm64. 317s Preparing to unpack .../14-libhsakmt1_5.7.0-1build1_arm64.deb ... 317s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 317s Selecting previously unselected package libhsa-runtime64-1. 317s Preparing to unpack .../15-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 317s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 317s Selecting previously unselected package libamdhip64-5. 317s Preparing to unpack .../16-libamdhip64-5_5.7.1-5_arm64.deb ... 317s Unpacking libamdhip64-5 (5.7.1-5) ... 317s Selecting previously unselected package libibumad3:arm64. 317s Preparing to unpack .../17-libibumad3_55.0-1ubuntu1_arm64.deb ... 317s Unpacking libibumad3:arm64 (55.0-1ubuntu1) ... 317s Selecting previously unselected package libibmad5:arm64. 317s Preparing to unpack .../18-libibmad5_55.0-1ubuntu1_arm64.deb ... 317s Unpacking libibmad5:arm64 (55.0-1ubuntu1) ... 317s Selecting previously unselected package libucx0:arm64. 317s Preparing to unpack .../19-libucx0_1.17.0+ds-3build1_arm64.deb ... 317s Unpacking libucx0:arm64 (1.17.0+ds-3build1) ... 317s Selecting previously unselected package libopenmpi40:arm64. 318s Preparing to unpack .../20-libopenmpi40_5.0.6-4_arm64.deb ... 318s Unpacking libopenmpi40:arm64 (5.0.6-4) ... 318s Selecting previously unselected package hyphy-mpi. 318s Preparing to unpack .../21-hyphy-mpi_2.5.63+dfsg-1build2_arm64.deb ... 318s Unpacking hyphy-mpi (2.5.63+dfsg-1build2) ... 318s Selecting previously unselected package hyphy-pt. 318s Preparing to unpack .../22-hyphy-pt_2.5.63+dfsg-1build2_arm64.deb ... 318s Unpacking hyphy-pt (2.5.63+dfsg-1build2) ... 318s Setting up libpciaccess0:arm64 (0.17-3build1) ... 318s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 318s Setting up libibumad3:arm64 (55.0-1ubuntu1) ... 318s Setting up libibmad5:arm64 (55.0-1ubuntu1) ... 318s Setting up hyphy-common (2.5.63+dfsg-1build2) ... 318s Setting up libgomp1:arm64 (14.2.0-17ubuntu1) ... 318s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 318s Setting up libmunge2:arm64 (0.5.16-1) ... 318s Setting up libllvm17t64:arm64 (1:17.0.6-20) ... 318s Setting up libhwloc15:arm64 (2.11.2-1build1) ... 318s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 318s Setting up librdmacm1t64:arm64 (55.0-1ubuntu1) ... 318s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 318s Setting up libhsakmt1:arm64 (5.7.0-1build1) ... 318s Setting up libfabric1:arm64 (1.17.0-3ubuntu1) ... 318s Setting up hyphy-pt (2.5.63+dfsg-1build2) ... 318s Setting up libhwloc-plugins:arm64 (2.11.2-1build1) ... 318s Setting up libpmix2t64:arm64 (5.0.6-3) ... 318s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 318s Setting up libamdhip64-5 (5.7.1-5) ... 318s Setting up libucx0:arm64 (1.17.0+ds-3build1) ... 318s Setting up libopenmpi40:arm64 (5.0.6-4) ... 318s Setting up hyphy-mpi (2.5.63+dfsg-1build2) ... 318s Processing triggers for libc-bin (2.41-1ubuntu1) ... 318s Processing triggers for man-db (2.13.0-1) ... 320s autopkgtest [00:16:09]: test run-unit-tests: [----------------------- 320s + for i in *.bf 320s + '[' -f ExonIntron.bf ']' 320s + hyphy ExonIntron.bf 321s Log Likelihood = -1113.34527456867; 321s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134823249406291,(ZMUBIS27F:0,(ZMU29160:0.05439790490966976,ZMU29161:0.0397243840156002)Node8:0.01201701686336866)Node6:0)Node4:0.02458984864262132,BLYMUB1:0.01186169057397155); 321s Tree exon2Tree=(BLYMUB2:0.03542197962164734,(RICRMA630:0.0293592149755165,(ZMUBIS27F:0.07548368596295525,(ZMU29160:0.09106731877653031,ZMU29161:0.02597632170615614)Node8:0.01154237714197667)Node6:0.04929618899065108)Node4:0.02930900096949015,BLYMUB1:0.02204924938596156); 321s Tree intronTree=(BLYMUB2:0.03119337510917415,(RICRMA630:0.04156843579780962,(ZMUBIS27F:0.02044013725984574,(ZMU29160:0.02068575651075207,ZMU29161:0.0101935623024677)Node8:0.02068834837849097)Node6:0)Node4:0,BLYMUB1:0.01036374500758001); 321s + for i in *.bf 321s + '[' -f F81.bf ']' 321s + hyphy F81.bf 321s Log Likelihood = -1187.54703158314; 321s Tree givenTree=(256:0.01194114591373754,(822:0.02944524202488117,159:0.004471621910620015)Node2:0.003649766270171017,((113:0.02245290968891151,9939:0.07628833493441228)Node6:0.00507745946273519,(6760:0.06900624324407222,((317:0.03752839381317082,6767:0.0708385678934737)Node12:0.0122969485056881,((135:0.02046660344281419,(529:0.03337018700273726,105r:0.01321522054451425)Node18:0.02585864946812182)Node16:0.005409584237460074,(719:0.02964827457182188,136:0.008234924918530817)Node21:0.04883319135024773)Node15:0.01526164962674536)Node11:0.01379988380937047)Node9:0.02422104085746439)Node5:0.02148432123134071); 321s + for i in *.bf 321s + '[' -f F81relrate.bf ']' 321s + hyphy F81relrate.bf 321s 321s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001001210834; 321s Tree threeTaxaTree=(a:0.08502373447434355,b:0.07338780662543803,c:0.1653961179929538); 321s 321s 321s 1). With the outgroup at taxon #1, the P-value is:0.00215508274683196 321s Log Likelihood = -948.707263619764; 321s Tree threeTaxaTree=(a:0.08228181919201959,b:0.1193752617687577,c:0.1193752617687577); 321s 321s 321s 2). With the outgroup at taxon #2, the P-value is:0.008353493534544953 321s Log Likelihood = -947.479040372868; 321s Tree threeTaxaTree=(a:0.1251255678882126,b:0.07126113961403335,c:0.1251255678882126); 321s 321s 321s 3). With the outgroup at taxon #3, the P-value is:0.6669142488401969 321s Log Likelihood = -944.093617637419; 321s Tree threeTaxaTree=(a:0.079203911773313,b:0.079203911773313,c:0.1653766790363053); 321s 321s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059868146; 321s Tree fourTaxaTree1=((1:0.1129194699795783,2:0.1073510528520759)Node1:0.09979509926335275,3:0.3469419686896131,4:0.3218829827848902); 321s Tree fourTaxaTree2=((1:0.08582647823069564,2:0.09340546044431464)Node1:0.07362501198948862,3:0.3932327773698152,4:0.3801450397654411); 321s 321s 321s 1). Relative ratio constraint; the P-value is:0.6933541994142367 321s Log Likelihood = -2575.74610909532; 321s Global Parameters: 321s R=1.007290882641435; 321s 321s Tree fourTaxaTree1=((1:0.0994836156075871,2:0.09943033948566604)Node1:0.08696825592979363,3:0.3687235521692194,4:0.3489176973250386); 321s Tree fourTaxaTree2=((1:0.1000737083546772,2:0.1000201162223966)Node1:0.08748411310625245,3:0.3709106569752469,4:0.3509873225720243); 321s + for i in *.bf 321s + '[' -f F81relratio.bf ']' 321s + hyphy F81relratio.bf 321s + for i in *.bf 321s + '[' -f HKY85.bf ']' 321s + hyphy HKY85.bf 321s Log Likelihood = -1152.88077642317; 321s Tree givenTree=(256:0.01162364210421448,(822:0.02980324829311718,159:0.004016335948323236)Node2:0.003749549759386841,((113:0.02130049477488836,9939:0.07787424068794199)Node6:0.004321341712317832,(6760:0.07316332185525985,((317:0.03810262129250685,6767:0.07101128309172208)Node12:0.006272466556908361,((135:0.01787883982597592,(529:0.03258190184741874,105r:0.01513653572674197)Node18:0.02833253022051609)Node16:0.007920142727420065,(719:0.02987702683997457,136:0.008041352973368533)Node21:0.04860052528159048)Node15:0.01598535562640375)Node11:0.01658093028561011)Node9:0.02665163637590678)Node5:0.02296003610334613); 321s + for i in *.bf 321s + '[' -f HKY852blocks.bf ']' 321s + hyphy HKY852blocks.bf 321s 321s ----- RESULTS ----- 321s Log Likelihood = -6801.91478504601; 321s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050228009453516,((((((ZMU60511:0.01039826080337449,ZMU60510:0.02379428148811296)Node8:0.08352366615180683,OSRAC2:0.1884847245559114)Node7:0.05837875194717072,(OSRAC1:0.0153668321708961,SVSOAC1:0.073396191831252)Node12:0.07297315003806909)Node6:0,((OSRAC3:0.07322564241503433,ZMU60507:0.06502753008098559)Node16:0.07979210906815236,ZMU60509:0.1288362448294179)Node15:0.001261914825281759)Node5:0.08267712557772787,(MZEACT1G:0.1142443479153361,OSRAC7:0.03419168970085958)Node20:0)Node4:0.1058666163937841,ZMU60508:0.01698024030831909)Node3:0.05976261542082731); 321s Tree actinTree2=(ZMU60513:0.01013562879080013,ZMU60514:0.02362726617077405,((((((ZMU60511:0.03959062941804365,ZMU60510:0.02870922201664623)Node8:0.04599411208572688,OSRAC2:0.1281475802179091)Node7:0.02274402447243551,(OSRAC1:0.04039556899966606,SVSOAC1:0.0553269187525176)Node12:0.09056605267429804)Node6:0.02100638146678956,((OSRAC3:0.1082307234132382,ZMU60507:0.07346564105739237)Node16:0.05601707802939447,ZMU60509:0.1117447288064283)Node15:0.02915977855876288)Node5:0.04980522506482434,(MZEACT1G:0.1070210259287632,OSRAC7:0.09561871041114016)Node20:0.02267613038232481)Node4:0.04830877453489211,ZMU60508:0.02346278451232213)Node3:0.05651941960868183); 321s + for i in *.bf 321s + '[' -f HKY852blocks2models.bf ']' 321s + hyphy HKY852blocks2models.bf 321s 321s ----- RESULTS ----- 321s Log Likelihood = -6049.33422499979; 321s Tree actinTree1=(ZMU60513:0.01367751588325816,ZMU60514:0.0666292917940192,((((((ZMU60511:0.1015161625625045,ZMU60510:0.08935228264205308)Node8:0.2111002549734343,OSRAC2:0.3683773207825736)Node7:0.06399101018353297,(OSRAC1:0.0433737678574602,SVSOAC1:0.2446681733460865)Node12:0.4079937067368911)Node6:0.1003268191522063,((OSRAC3:0.1862479438996988,ZMU60507:0.3287155061849231)Node16:0.1590194032164103,ZMU60509:0.4443394799128847)Node15:0.04671878405935084)Node5:0.1895109940647801,(MZEACT1G:0.3243894169931306,OSRAC7:0.2477955462670988)Node20:0.009377819907086995)Node4:0.266303811248945,ZMU60508:0.0103366366133024)Node3:0.2231162890006362); 321s Tree actinTree2=(ZMU60513:0.004497905560380018,ZMU60514:0.004484163859147836,((((((ZMU60511:0.004483151986878508,ZMU60510:0.005994052869381887)Node8:0.004874726331462179,OSRAC2:0.04747048996278908)Node7:0.003177765597701319,(OSRAC1:0.01209871667231744,SVSOAC1:0.007446146129308574)Node12:0.02729374045450093)Node6:0,((OSRAC3:0.04645202806565162,ZMU60507:0.009172995490983134)Node16:0.0104540110947039,ZMU60509:0.02448207962020756)Node15:0)Node5:0.01926666527562818,(MZEACT1G:0.03380886497532196,OSRAC7:0.03062907638449151)Node20:0.006211610537061563)Node4:0.007798915700619878,ZMU60508:0.004488028436437612)Node3:0.01512042010921891); 321s + for i in *.bf 321s + '[' -f HKY85relrate.bf ']' 321s + hyphy HKY85relrate.bf 321s 321s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371754591916; 321s Tree threeTaxaTree=(a:0.08470616865457746,b:0.07476331023320715,c:0.1740134200097299); 321s 321s 321s 1). Outgroup at taxon #1 321s a). Transition rate test. P-Value = 0.0209823363495063 321s Log Likelihood = -924.035884024616; 321s Tree threeTaxaTree=(a:0.08099120528023607,b:0.1064970049780444,c:0.1431287319939507); 321s 321s b). Transversion rate test. P-Value = 0.03655161545592389 321s Log Likelihood = -923.557345912349; 321s Tree threeTaxaTree=(a:0.08437179548099751,b:0.09106657080572136,c:0.1577519163243654); 321s 321s c). Both rates test. P-Value = 0.006324016976249847 321s Log Likelihood = -926.43515526719; 321s Tree threeTaxaTree=(a:0.08054162708885505,b:0.1248196470958234,c:0.1248196470958234); 321s 321s 321s 2). Outgroup at taxon #2 321s a). Transition rate test. P-Value = 0.02758045337486259 321s Log Likelihood = -923.798806027181; 321s Tree threeTaxaTree=(a:0.115836226409784,b:0.07098641258525744,c:0.144323146299356); 321s 321s b). Transversion rate test. P-Value = 0.1106463144845125 321s Log Likelihood = -922.644237437584; 321s Tree threeTaxaTree=(a:0.09760331129081504,b:0.0746365411846704,c:0.160896805968749); 321s 321s c). Both rates test. P-Value = 0.02199506592692957 321s Log Likelihood = -925.188691718794; 321s Tree threeTaxaTree=(a:0.1299134981841075,b:0.07078648366843789,c:0.1299134981841075); 321s 321s 321s 3). Outgroup at taxon #3 321s a). Transition rate test. P-Value = 0.9291997178533651 321s Log Likelihood = -921.375701909985; 321s Tree threeTaxaTree=(a:0.08354356494921542,b:0.07588178135451827,c:0.1740455423637466); 321s 321s b). Transversion rate test. P-Value = 0.5919916734342252 321s Log Likelihood = -921.515376904862; 321s Tree threeTaxaTree=(a:0.08115137193829434,b:0.07834954138626811,c:0.1740030844904938); 321s 321s c). Both rates test. P-Value = 0.8615442243838619 321s Log Likelihood = -921.520783482074; 321s Tree threeTaxaTree=(a:0.07974264124836725,b:0.07974264124836725,c:0.1740977408732409); 321s + for i in *.bf 321s + '[' -f HKY85relratio.bf ']' 321s + hyphy HKY85relratio.bf 321s 321s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78441247022; 321s Tree fourTaxaTree1=((1:0.1137753008592099,2:0.1109235750237855)Node1:0.1041248431659134,3:0.3523533314703389,4:0.3311996009458911); 321s Tree fourTaxaTree2=((1:0.08603826836975249,2:0.09351277816499561)Node1:0.08022848264340561,3:0.3859538982882255,4:0.3896405741637229); 321s 321s 321s 1). Relative ratio constraint on transitions; the P-value is:0.5738549378258683 321s Log Likelihood = -2541.23688975778; 321s Global Parameters: 321s R=0.8579070856020584; 321s 321s Tree fourTaxaTree1=((1:0.1086624551354322,2:0.09420709509598561)Node1:0.1115975389929941,3:0.3553174712398195,4:0.355135703639406); 321s Tree fourTaxaTree2=((1:0.09039857343854162,2:0.1091735450071624)Node1:0.07301057481440436,3:0.3839750461659144,4:0.3655234937433918); 321s 321s 321s 2). Relative ratio constraint on transversions; the P-value is:0.573849272064854 321s Log Likelihood = -2541.23690642844; 321s Global Parameters: 321s R=0.8583725768330295; 321s 321s Tree fourTaxaTree1=((1:0.1086704903842286,2:0.09419057767104047)Node1:0.1116418050885959,3:0.3553177756942,4:0.3549099034351177); 321s Tree fourTaxaTree2=((1:0.09039921100809488,2:0.1091887386703434)Node1:0.07309291670481963,3:0.3840653617042983,4:0.365540576649903); 321s 321s 321s 3). Relative ratio constraint on both rates; the P-value is:0.6565845863755081 321s Log Likelihood = -2543.19089807535; 321s Global Parameters: 321s R=0.9964156806638874; 321s 321s Tree fourTaxaTree1=((1:0.1004711133829953,2:0.1006979006674752)Node1:0.09261344826471235,3:0.3713980205637036,4:0.3581865151549528); 321s Tree fourTaxaTree2=((1:0.1002942149191716,2:0.1006796974321148)Node1:0.09289649081430244,3:0.3698025715499813,4:0.3576167915293305); 321s + for i in *.bf 321s + '[' -f HKY85shared.bf ']' 321s + hyphy HKY85shared.bf 321s Log Likelihood = -1165.70261216452; 321s Global Parameters: 321s R=2.985270111313039; 321s 321s Tree givenTree=(256:0.01208887834810965,(822:0.02962497685536022,159:0.00465400435667928)Node2:0.003521675182559771,((113:0.02180335276810885,9939:0.07937939791606255)Node6:0.004910492767676866,(6760:0.07155691643256673,((317:0.0379762645434964,6767:0.07151084045648526)Node12:0.01177117132944822,((135:0.02024393405104827,(529:0.03402215758796904,105r:0.01304776452222023)Node18:0.02631597095129413)Node16:0.005812235226919725,(719:0.02975107090861311,136:0.008128038064317632)Node21:0.04879740775540603)Node15:0.01556125089690762)Node11:0.01396730114030851)Node9:0.02326100835423129)Node5:0.02146650804015024); 321s + for i in *.bf 321s + '[' -f JC69.bf ']' 321s + hyphy JC69.bf 321s Log Likelihood = -1227.45124656194; 321s Tree givenTree=(256:0.0121031471469513,(822:0.02895919171534359,159:0.00466041997712167)Node2:0.003646944276310411,((113:0.02417187561317707,9939:0.07264010622973317)Node6:0.005841276370040769,(6760:0.06387903934602145,((317:0.04026899103627595,6767:0.06821500288806152)Node12:0.01443705918822943,((135:0.02431082223329727,(529:0.03327971740340237,105r:0.01296537960773594)Node18:0.0198783860976395)Node16:0.003613204946433143,(719:0.02785313695935753,136:0.009997027773531036)Node21:0.0511697865887011)Node15:0.01670127397604663)Node11:0.008455166764060393)Node9:0.02635808511771688)Node5:0.02074711317948095); 321s + for i in *.bf 321s + '[' -f K2P.bf ']' 321s + hyphy K2P.bf 321s Log Likelihood = -1198.26189385582; 321s Tree givenTree=(256:0.01177284359430885,(822:0.02926420039259947,159:0.004290513682724304)Node2:0.0036660290553929,((113:0.0236681223431271,9939:0.07261944359828695)Node6:0.003382357489197553,(6760:0.06224213105690853,((317:0.04074378033351071,6767:0.06830506242368696)Node12:0.01244537975380141,((135:0.02260274233272896,(529:0.03395246633578614,105r:0.01240375204968598)Node18:0.02142035405628374)Node16:0.004488785191239185,(719:0.02880975664693539,136:0.008845132842745461)Node21:0.05084376890115109)Node15:0.01733791703499467)Node11:0.01111378481027467)Node9:0.02819644519749408)Node5:0.02370264701278101); 321s + for i in *.bf 321s + '[' -f K2Pshared.bf ']' 321s + hyphy K2Pshared.bf 321s Log Likelihood = -1210.49404711972; 321s Global Parameters: 321s R=2.625794187774841; 321s 321s Tree givenTree=(256:0.01222499926579241,(822:0.0289788449154394,159:0.004781045780464576)Node2:0.003546874563857231,((113:0.02375931711147818,9939:0.07497889579492729)Node6:0.005891745344022515,(6760:0.06492705231608026,((317:0.03971607289988453,6767:0.06952805951567544)Node12:0.01423545272499157,((135:0.02390591837327521,(529:0.03397605182616147,105r:0.01262638012894715)Node18:0.02072334197561441)Node16:0.003968659541575091,(719:0.02814000813907024,136:0.00950386534577447)Node21:0.05082452969793991)Node15:0.01659353389863478)Node11:0.008793165749949931)Node9:0.02627457878177817)Node5:0.02011131839492598); 321s + for i in *.bf 321s + '[' -f MatrixIndexing.bf ']' 321s + hyphy MatrixIndexing.bf 321s 321s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 321s { 321s {0.2249454157950695, 0.4565556709320647, 0.5608522143589454, 0.8403724189476046, 0.6776080256508682, 0.4228789083247257} 321s {0.07572063642454348, 0.5962087119920665, 0.06636497775706579, 0.7977301945904572, 0.1935816712662535, 0.1136276719890599} 321s {0.6530425442971853, 0.9849115565849728, 0.5327067914262197, 0.4273955196671643, 0.5529375077581353, 0.06632936468029613} 321s {0.9510413345301154, 0.8433158597544106, 0.3124136401602099, 0.2413267912905027, 0.8392240837773364, 0.1735684543786497} 321s {0.4796345772872759, 0.1777276504267304, 0.3041175134256756, 0.7320474536931253, 0.4317526541258564, 0.9810534522358918} 321s } 321s 321s 2). Accessing a second-row third-column element and a random element. 321s 321s matrix[1][2]=0.06636497775706579 321s matrix[0][0]=0.2249454157950695 321s 321s 3). Accessing the fourth row. 321s 321s matrix[3][-1]= 321s { 321s {0.9510413345301154, 0.8433158597544106, 0.3124136401602099, 0.2413267912905027, 0.8392240837773364, 0.1735684543786497} 321s } 321s 321s 4). Accessing the first column. 321s 321s matrix[-1][0]= 321s { 321s {0.2249454157950695} 321s {0.07572063642454348} 321s {0.6530425442971853} 321s {0.9510413345301154} 321s {0.4796345772872759} 321s } 321s 321s 5). Populating a matrix template (below the diagonal). 321s 321s { 321s {0, 0, 0, 0, 0, 0} 321s {1, 0, 0, 0, 0, 0} 321s {1, 1, 0, 0, 0, 0} 321s {1, 1, 1, 0, 0, 0} 321s {1, 1, 1, 1, 0, 0} 321s } 321s 321s 6). Extracting (by row) matrix elements using the template. 321s 321s { 321s {0.07572063642454348, 0.6530425442971853, 0.9849115565849728, 0.9510413345301154, 0.8433158597544106, 0.3124136401602099, 0.4796345772872759, 0.1777276504267304, 0.3041175134256756, 0.7320474536931253} 321s } 321s 321s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 321s 321s matrix[{{1,1}}][{{3,2}}]= 321s { 321s {0.5962087119920665, 0.06636497775706579} 321s {0.9849115565849728, 0.5327067914262197} 321s {0.8433158597544106, 0.3124136401602099} 321s } 321s 321s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 321s 321s 321s { 321s {0.05060044008721671, 1.208443080660228, 1.314555206351332, 1.706225802527848, 1.459152636426468, 1.178826571105912} 321s {0.005733614780537901, 0.3554648282552389, 1.004404310272696, 1.636373463361329, 1.037473863450236, 1.012911247841653} 321s {0.4264645646621413, 0.970050774294634, 0.2837765256316179, 1.182666930231565, 1.305739887485778, 1.004399584618892} 321s {0.9044796199848228, 0.7111816393133207, 0.09760228255815311, 0.05823862019456986, 1.70429706279191, 1.030126008355393} 321s {0.2300493277295439, 0.0315871177262061, 0.09248746197221595, 0.5358934744585884, 0.1864103543447214, 1.962465876143961} 321s } 321s + for i in *.bf 321s + '[' -f MolecularClockF81.bf ']' 321s + hyphy MolecularClockF81.bf 322s 322s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124511854; 322s Tree theTree=(HVRNASS:0.02575001008577315,(RICRSS3:0.05627633315435268,((ZMSUCS1:0.071628218780981,(OSRSS1A:0.06060085904635536,(TASUCSYN1:0.02788050927962739,HVSSYNMR:0.02037103880006533)Internal1:0.05181504482629665)Node9:0.02013887521448224)Node7:0.1581214776815921,(MZESUS1:0.07667096356519239,ORRSS2:0.05436191928651032)Internal2:0.02506258303361215)Node6:0.0325492773734722)Node4:0.05901172520634045,TAAJ153:0.01372502138666495); 322s 322s 322s 1). Global Molecular Clock; the P-value is:0 322s Log Likelihood = -11927.6152775943; 322s Tree theTree=(HVRNASS:0.02157619045049623,(RICRSS3:0.1233417578932495,((ZMSUCS1:0.05657749787738824,(OSRSS1A:0.04750827480488878,(TASUCSYN1:0.01823836395149706,HVSSYNMR:0.01823836395149706)Internal1:0.02926991085339173)Node9:0.009069223072499463)Node7:0.05763969174849241,(MZESUS1:0.07013415361931936,ORRSS2:0.07013415361931936)Internal2:0.04408303600656129)Node6:0.009124568267368809)Node4:0.02715740214301151,TAAJ153:0.150499160036261); 322s 322s 322s 2). Molecular Clock starting at Internal1; the P-value is:0.1603812828119151 322s Log Likelihood = -11476.6977648854; 322s Tree theTree=(HVRNASS:0.02573844069742178,(RICRSS3:0.05631378682849189,((ZMSUCS1:0.07167038470787654,(OSRSS1A:0.06052200593892769,(TASUCSYN1:0.02412007133394174,HVSSYNMR:0.02412007133394174)Internal1:0.05180642483283451)Node9:0.02018832980879992)Node7:0.1580854000053244,(MZESUS1:0.07661279233954571,ORRSS2:0.05440972378044218)Internal2:0.02509732954531452)Node6:0.03251680753174561)Node4:0.05896716736965901,TAAJ153:0.01372945701059637); 322s 322s 322s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610219040405436 322s Log Likelihood = -11479.8412511518; 322s Tree theTree=(HVRNASS:0.02577426452184211,(RICRSS3:0.05653201637012232,((ZMSUCS1:0.07147876162201949,(OSRSS1A:0.06061733114627832,(TASUCSYN1:0.02412106887802992,HVSSYNMR:0.02412106887802992)Internal1:0.05166406762645684)Node9:0.02036487450651501)Node7:0.1580530405557081,(MZESUS1:0.0655359557494011,ORRSS2:0.0655359557494011)Internal2:0.02502384917030599)Node6:0.03235653778424119)Node4:0.05874167702059412,TAAJ153:0.0137001497515709); 322s + for i in *.bf 322s + '[' -f MolecularClockHKY85.bf ']' 322s + hyphy MolecularClockHKY85.bf 322s 322s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013420929; 322s Tree theTree=(HVRNASS:0.02587691899701215,(RICRSS3:0.05728330251161244,((ZMSUCS1:0.07269281496632593,(OSRSS1A:0.06094910646693515,(TASUCSYN1:0.02742974534174483,HVSSYNMR:0.02081801093463207)Node11:0.0528433435450073)Node9:0.02051548147480317)Node7:0.1589977182526351,(MZESUS1:0.0776238641538555,ORRSS2:0.05413968941080022)Node14:0.02601380956936772)Node6:0.03166782542649943)Node4:0.06040066922900952,TAAJ153:0.0138425738263658); 322s 322s 322s 1). Global Molecular Clock on transition rates; the P-value is:0 322s Log Likelihood = -11434.7015977528; 322s Tree theTree=(HVRNASS:0.0232009337703661,(RICRSS3:0.08335067889210075,((ZMSUCS1:0.0636722586619649,(OSRSS1A:0.05485628832512192,(TASUCSYN1:0.02325704396643562,HVSSYNMR:0.01890693687395116)Node11:0.04017289034136998)Node9:0.01328246085665211)Node7:0.1273883751879551,(MZESUS1:0.07240481719756202,ORRSS2:0.06226830765337666)Node14:0.0346182330471228)Node6:0.02068741869057213)Node4:0.03899077526780685,TAAJ153:0.08892019771048071); 322s 322s 322s 2). Global Molecular Clock on transversion rates; the P-value is:0 322s Log Likelihood = -11497.3782530813; 322s Tree theTree=(HVRNASS:0.02484418386258834,(RICRSS3:0.09398405719266521,((ZMSUCS1:0.06900827735845484,(OSRSS1A:0.05468866718414658,(TASUCSYN1:0.02276938785842402,HVSSYNMR:0.02034241479851344)Node11:0.04372112695184426)Node9:0.01673697604472169)Node7:0.09970300016590598,(MZESUS1:0.07446703140675773,ORRSS2:0.06134467826270223)Node14:0.03385757262735029)Node6:0.02079988765081456)Node4:0.05007075534055581,TAAJ153:0.07305296281046447); 322s 322s 322s 3). Global Molecular Clock on both rates; the P-value is:0 322s Log Likelihood = -11703.6261703774; 322s Tree theTree=(HVRNASS:0.022098831164952,(RICRSS3:0.1239713484114862,((ZMSUCS1:0.05799306359698909,(OSRSS1A:0.04854097640332263,(TASUCSYN1:0.01832817401217513,HVSSYNMR:0.01832817401217513)Node11:0.0302128023911475)Node9:0.009452087193666464)Node7:0.05732323182613498,(MZESUS1:0.07024684650821196,ORRSS2:0.07024684650821196)Node14:0.04506944891491211)Node6:0.008655052988362128)Node4:0.02801791998320697,TAAJ153:0.1519892683946932); 322s + for i in *.bf 322s + '[' -f Non-Rev.bf ']' 322s + hyphy Non-Rev.bf 322s Log Likelihood = -1152.77697677871; 322s Global Parameters: 322s GC=0.2871686920771574; 322s CG=0.1913235339824907; 322s GA=2.008234896843339; 322s CT=1.282066210869608; 322s GT=0.0903880302516875; 322s CA=0.9365170402616817; 322s AT=0.453519639599629; 322s AG=1.672702678139513; 322s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2612978769779289; 322s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.087961896879406; 322s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.8260929516656327; 322s 322s Tree givenTree=(256:0.0135047891920408,(822:0.02843354064753972,159:0.006171282680485959)Node2:0.003439208606168918,((113:0.02185280678036277,9939:0.07937256953583827)Node6:0.004973108465107143,(6760:0.07327260275204259,((317:0.04010219481676604,6767:0.06981043262082666)Node12:0.01159678637381856,((135:0.02157766994507406,(529:0.03495681382164914,105r:0.01412783759149833)Node18:0.02379499786582731)Node16:0.00527911271393415,(719:0.02872374790224739,136:0.009490714255149949)Node21:0.04925512564903264)Node15:0.01636347123377185)Node11:0.01279802647008929)Node9:0.02191639212619522)Node5:0.02024589844800782); 322s + for i in *.bf 322s + '[' -f PBootstrapHetRates.bf ']' 322s + hyphy PBootstrapHetRates.bf 322s 322s ----ORIGINAL DATA---- 322s Log Likelihood = -1127.31557548004; 322s Global Parameters: 322s alpha=0.3190382676118035; 322s kappa=0.3234807955743362; 322s 322s Tree givenTree=(256:0.01259121414147856,(822:0.03174906182138278,159:0.004696746937470214)Node2:0.00378405286073732,((113:0.02291226963405653,9939:0.09714381362971219)Node6:0.001957336350850507,(6760:0.08722089673819462,((317:0.04574858436547819,6767:0.08109947886295431)Node12:0.007397508642620092,((135:0.01862859879600477,(529:0.03694189401760728,105r:0.01500637095368908)Node18:0.03036654281500907)Node16:0.007153344940829484,(719:0.03342588619170248,136:0.007167816934875686)Node21:0.05748873916870237)Node15:0.01789059297455927)Node11:0.01883873557531643)Node9:0.02369093518099946)Node5:0.02502054605982561); 322s 322s Using the seed: 322s 1739668139 322s Category variable name: TRUE 322s Site Rate 322s 0 0.00000 322s 1 0.00000 322s 2 0.00000 322s 3 0.00000 322s 4 0.00000 322s 5 0.00000 322s 6 0.00000 322s 7 0.00001 322s 8 0.00001 322s 9 0.00002 322s 10 0.00003 322s 11 0.00003 322s 12 0.00009 322s 13 0.00015 322s 14 0.00019 322s 15 0.00020 322s 16 0.00021 322s 17 0.00028 322s 18 0.00038 322s 19 0.00040 322s 20 0.00045 322s 21 0.00046 322s 22 0.00047 322s 23 0.00047 322s 24 0.00050 322s 25 0.00054 322s 26 0.00055 322s 27 0.00058 322s 28 0.00084 322s 29 0.00091 322s 30 0.00108 322s 31 0.00123 322s 32 0.00129 322s 33 0.00175 322s 34 0.00182 322s 35 0.00191 322s 36 0.00202 322s 37 0.00232 322s 38 0.00261 322s 39 0.00342 322s 40 0.00349 322s 41 0.00435 322s 42 0.00471 322s 43 0.00526 322s 44 0.00556 322s 45 0.00684 322s 46 0.00734 322s 47 0.00777 322s 48 0.00881 322s 49 0.00885 322s 50 0.00986 322s 51 0.01102 322s 52 0.01173 322s 53 0.01201 322s 54 0.01205 322s 55 0.01220 322s 56 0.01392 322s 57 0.01567 322s 58 0.01599 322s 59 0.01618 322s 60 0.01962 322s 61 0.02037 322s 62 0.02152 322s 63 0.02561 322s 64 0.02651 322s 65 0.02726 322s 66 0.02973 322s 67 0.03457 322s 68 0.03601 322s 69 0.03660 322s 70 0.03866 322s 71 0.04111 322s 72 0.04177 322s 73 0.04315 322s 74 0.04553 322s 75 0.04787 322s 76 0.04871 322s 77 0.05075 322s 78 0.05101 322s 79 0.05204 322s 80 0.05345 322s 81 0.05608 322s 82 0.05640 322s 83 0.06219 322s 84 0.06498 322s 85 0.06577 322s 86 0.06652 322s 87 0.06677 322s 88 0.06736 322s 89 0.06794 322s 90 0.07207 322s + for i in *.bf 322s + '[' -f REV.bf ']' 322s + hyphy REV.bf 322s 91 0.07262 322s 92 0.08049 322s 93 0.08105 322s 94 0.08106 322s 95 0.08534 322s 96 0.08625 322s 97 0.08653 322s 98 0.08993 322s 99 0.09516 322s 100 0.09591 322s 101 0.09798 322s 102 0.10816 322s 103 0.10882 322s 104 0.11045 322s 105 0.11167 322s 106 0.11441 322s 107 0.11863 322s 108 0.11893 322s 109 0.12080 322s 110 0.12153 322s 111 0.12310 322s 112 0.12370 322s 113 0.12395 322s 114 0.12447 322s 115 0.12942 322s 116 0.12950 322s 117 0.13336 322s 118 0.13418 322s 119 0.13449 322s 120 0.13925 322s 121 0.14264 322s 122 0.14267 322s 123 0.14743 322s 124 0.15197 322s 125 0.15458 322s 126 0.15495 322s 127 0.16755 322s 128 0.17158 322s 129 0.18024 322s 130 0.18236 322s 131 0.18687 322s 132 0.18695 322s 133 0.18882 322s 134 0.18896 322s 135 0.19019 322s 136 0.19066 322s 137 0.19314 322s 138 0.19648 322s 139 0.20553 322s 140 0.21147 322s 141 0.21447 322s 142 0.21747 322s 143 0.22244 322s 144 0.23148 322s 145 0.23503 322s 146 0.23651 322s 147 0.23689 322s 148 0.24700 322s 149 0.25420 322s 150 0.25460 322s 151 0.26733 322s 152 0.27886 322s 153 0.28237 322s 154 0.30470 322s 155 0.31192 322s 156 0.32677 322s 157 0.33233 322s 158 0.33870 322s 159 0.34171 322s 160 0.34486 322s 161 0.35865 322s 162 0.36863 322s 163 0.37369 322s 164 0.37411 322s 165 0.38658 322s 166 0.38985 322s 167 0.40034 322s 168 0.40154 322s 169 0.40591 322s 170 0.41895 322s 171 0.43204 322s 172 0.43767 322s 173 0.43965 322s 174 0.46069 322s 175 0.46114 322s 176 0.46514 322s 177 0.47841 322s 178 0.49098 322s 179 0.49878 322s 180 0.50108 322s 181 0.50359 322s 182 0.53245 322s 183 0.54865 322s 184 0.55500 322s 185 0.58432 322s 186 0.58847 322s 187 0.59462 322s 188 0.61265 322s 189 0.61696 322s 190 0.63452 322s 191 0.65730 322s 192 0.68368 322s 193 0.68783 322s 194 0.69100 322s 195 0.70315 322s 196 0.71717 322s 197 0.75154 322s 198 0.77337 322s 199 0.77419 322s 200 0.79317 322s 201 0.79559 322s 202 0.82339 322s 203 0.83839 322s 204 0.84118 322s 205 0.84609 322s 206 0.84846 322s 207 0.85448 322s 208 0.86067 322s 209 0.87946 322s 210 0.95665 322s 211 0.97586 322s 212 1.00743 322s 213 1.03808 322s 214 1.06580 322s 215 1.07824 322s 216 1.09608 322s 217 1.15172 322s 218 1.20009 322s 219 1.22864 322s 220 1.23641 322s 221 1.26806 322s 222 1.27176 322s 223 1.27818 322s 224 1.28063 322s 225 1.30823 322s 226 1.33204 322s 227 1.33235 322s 228 1.46223 322s 229 1.46591 322s 230 1.50114 322s 231 1.54945 322s 232 1.67705 322s 233 1.69717 322s 234 1.70610 322s 235 1.76088 322s 236 1.78021 322s 237 1.83986 322s 238 1.88409 322s 239 1.93265 322s 240 1.98107 322s 241 2.13448 322s 242 2.23616 322s 243 2.26270 322s 244 2.39457 322s 245 2.46944 322s 246 2.48304 322s 247 2.48895 322s 248 2.59564 322s 249 2.72507 322s 250 2.78841 322s 251 2.85827 322s 252 3.00747 322s 253 3.00992 322s 254 3.25039 322s 255 3.43783 322s 256 3.56404 322s 257 3.62485 322s 258 3.99436 322s 259 4.14691 322s 260 4.18603 322s 261 4.20977 322s 262 4.29962 322s 263 4.32643 322s 264 4.78322 322s 265 5.07839 322s 266 5.45734 322s 267 5.61368 322s 268 5.65107 322s 269 5.74003 322s 270 6.18780 322s 271 6.57890 322s 272 7.27265 322s 322s Mean = 0.7739607391145543 322s Var = 1.733198955587441 (1/alpha) = 3.134420229540523 322s + for i in *.bf 322s + '[' -f REVshared.bf ']' 322s + hyphy REVshared.bf 322s Log Likelihood = -1099.5665425022; 322s Tree givenTree=(256:0.01860538216191678,(822:0.02270294264857962,159:0.01094295281510875)Node2:0.003780125294847123,((113:0.01828957717646393,9939:0.07803362153128988)Node6:0.007454163233756575,(6760:0.07117756915902107,((317:0.03719474218835103,6767:0.07205711590917928)Node12:0.01019711246835016,((135:0.02037016374631629,(529:0.03423644449076697,105r:0.01129635937372845)Node18:0.02853411014706152)Node16:0.006570771740898335,(719:0.02829658762867322,136:0.009598218473527429)Node21:0.04403605915576612)Node15:0.01656544084943881)Node11:0.01314632213647495)Node9:0.02914838884912191)Node5:0.01372591364348294); 322s + for i in *.bf 322s + '[' -f ReplicateConstraint1.bf ']' 322s + hyphy ReplicateConstraint1.bf 322s Log Likelihood = -1156.62524729896; 322s Global Parameters: 322s AT=0.3650291814137866; 322s GT=0.463431711641809; 322s CG=0.2484259702169752; 322s AG=1.861304103801272; 322s CT=1.206843764137238; 322s 322s Tree givenTree=(256:0.0120792910865987,(822:0.0297441538075769,159:0.004673959608648702)Node2:0.003486656686416395,((113:0.02208311421118298,9939:0.07982164495335727)Node6:0.004712311623176048,(6760:0.07209574827296067,((317:0.03911302391471642,6767:0.07110009225428129)Node12:0.01084101532484846,((135:0.02052279172147824,(529:0.03437857506357853,105r:0.01466290152650919)Node18:0.02466781408621951)Node16:0.005563692832140551,(719:0.02875625138623298,136:0.009460715568383965)Node21:0.04911135329636342)Node15:0.01583954348240539)Node11:0.01426103492691909)Node9:0.02295700197186488)Node5:0.02146330567418091); 322s 1).Unconstrained HKY85 322s 322s Log Likelihood = -1152.88; 322s 322s Independent Parameters List 322s 322s Parameter 1 : hivTree.317.trvs 322s Parameter 2 : hivTree.317.trst 322s Parameter 3 : hivTree.6767.trvs 322s Parameter 4 : hivTree.6767.trst 322s Parameter 5 : hivTree.Node2.trvs 322s Parameter 6 : hivTree.Node2.trst 322s Parameter 7 : hivTree.135.trvs 322s Parameter 8 : hivTree.135.trst 322s Parameter 9 : hivTree.529.trvs 322s Parameter 10 : hivTree.529.trst 322s Parameter 11 : hivTree.105r.trvs 322s Parameter 12 : hivTree.105r.trst 322s Parameter 13 : hivTree.Node8.trvs 322s Parameter 14 : hivTree.Node8.trst 322s Parameter 15 : hivTree.iNode1.trvs 322s Parameter 16 : hivTree.iNode1.trst 322s Parameter 17 : hivTree.719.trvs 322s Parameter 18 : hivTree.719.trst 322s Parameter 19 : hivTree.136.trvs 322s Parameter 20 : hivTree.136.trst 322s Parameter 21 : hivTree.Node11.trvs 322s Parameter 22 : hivTree.Node11.trst 322s Parameter 23 : hivTree.Node5.trvs 322s Parameter 24 : hivTree.Node5.trst 322s Parameter 25 : hivTree.Node1.trvs 322s Parameter 26 : hivTree.Node1.trst 322s Parameter 27 : hivTree.6760.trvs 322s Parameter 28 : hivTree.6760.trst 322s Parameter 29 : hivTree.113.trvs 322s Parameter 30 : hivTree.113.trst 322s Parameter 31 : hivTree.9939.trvs 322s Parameter 32 : hivTree.9939.trst 322s Parameter 33 : hivTree.Node16.trvs 322s Parameter 34 : hivTree.Node16.trst 322s Parameter 35 : hivTree.256.trvs 322s Parameter 36 : hivTree.256.trst 322s Parameter 37 : hivTree.822.trvs 322s Parameter 38 : hivTree.822.trst 322s Parameter 39 : hivTree.159.trvs 322s Parameter 40 : hivTree.159.trst 322s Parameter 41 : hivTree.Node21.trvs 322s Parameter 42 : hivTree.Node21.trst 322s Parameter 43 : hivTree.iNode2.trvs 322s Parameter 44 : hivTree.iNode2.trst 322s Parameter 45 : hivTree.Node15.trvs 322s Parameter 46 : hivTree.Node15.trst 322s 322s 2).HKY85 constrained to F81 322s 322s Log Likelihood = -1187.55; 322s 322s Independent Parameters List 322s 322s Parameter 1 : hivTree.317.trvs 322s Parameter 2 : hivTree.6767.trvs 322s Parameter 3 : hivTree.Node2.trvs 322s Parameter 4 : hivTree.135.trvs 322s Parameter 5 : hivTree.529.trvs 322s Parameter 6 : hivTree.105r.trvs 322s Parameter 7 : hivTree.Node8.trvs 322s Parameter 8 : hivTree.iNode1.trvs 322s Parameter 9 : hivTree.719.trvs 322s Parameter 10 : hivTree.136.trvs 322s Parameter 11 : hivTree.Node11.trvs 322s Parameter 12 : hivTree.Node5.trvs 322s Parameter 13 : hivTree.Node1.trvs 322s Parameter 14 : hivTree.6760.trvs 322s Parameter 15 : hivTree.113.trvs 322s Parameter 16 : hivTree.9939.trvs 322s Parameter 17 : hivTree.Node16.trvs 322s Parameter 18 : hivTree.256.trvs 322s Parameter 19 : hivTree.822.trvs 322s Parameter 20 : hivTree.159.trvs 322s Parameter 21 : hivTree.Node21.trvs 322s Parameter 22 : hivTree.iNode2.trvs 322s Parameter 23 : hivTree.Node15.trvs 322s 322s Constrained Parameters List 322s 322s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 322s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 322s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 322s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 322s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 322s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 322s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 322s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 322s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 322s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 322s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 322s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 322s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 322s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 322s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 322s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 322s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 322s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 322s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 322s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 322s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 322s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 322s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 322s 322s 3).HKY85 constrained to F81 on internal branches 322s 322s Log Likelihood = -1167.99; 322s 322s Independent Parameters List 322s 322s Parameter 1 : hivTree.Node2.trvs 322s Parameter 2 : hivTree.Node8.trvs 322s Parameter 3 : hivTree.iNode1.trvs 322s Parameter 4 : hivTree.Node11.trvs 322s Parameter 5 : hivTree.Node5.trvs 322s Parameter 6 : hivTree.Node1.trvs 322s Parameter 7 : hivTree.Node16.trvs 322s Parameter 8 : hivTree.Node21.trvs 322s Parameter 9 : hivTree.iNode2.trvs 322s Parameter 10 : hivTree.Node15.trvs 322s Parameter 11 : hivTree.317.trst 322s Parameter 12 : hivTree.317.trvs 322s Parameter 13 : hivTree.6767.trvs 322s Parameter 14 : hivTree.6767.trst 322s Parameter 15 : hivTree.135.trst 322s Parameter 16 : hivTree.135.trvs 322s Parameter 17 : hivTree.529.trvs 322s Parameter 18 : hivTree.529.trst 322s Parameter 19 : hivTree.105r.trst 322s Parameter 20 : hivTree.105r.trvs 322s Parameter 21 : hivTree.719.trvs 322s Parameter 22 : hivTree.719.trst 322s Parameter 23 : hivTree.136.trvs 322s Parameter 24 : hivTree.136.trst 322s Parameter 25 : hivTree.6760.trvs 322s Parameter 26 : hivTree.6760.trst 322s Parameter 27 : hivTree.113.trvs 322s Parameter 28 : hivTree.113.trst 322s Parameter 29 : hivTree.9939.trst 322s Parameter 30 : hivTree.9939.trvs 322s Parameter 31 : hivTree.256.trvs 322s Parameter 32 : hivTree.256.trst 322s Parameter 33 : hivTree.822.trvs 322s Parameter 34 : hivTree.822.trst 322s Parameter 35 : hivTree.159.trst 322s Parameter 36 : hivTree.159.trvs 322s 322s Constrained Parameters List 322s 322s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 322s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 322s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 322s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 322s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 322s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 322s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 322s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 322s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 322s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs+ for i in *.bf 322s + '[' -f ReplicateConstraint2.bf ']' 322s + hyphy ReplicateConstraint2.bf 322s 322s 322s 4).HKY85 with shared ratio. 322s 322s Log Likelihood = -1165.7; 322s 322s Independent Parameters List 322s 322s Parameter 1 : R 322s Parameter 2 : hivTree.317.trst 322s Parameter 3 : hivTree.6767.trst 322s Parameter 4 : hivTree.Node2.trst 322s Parameter 5 : hivTree.135.trst 322s Parameter 6 : hivTree.529.trst 322s Parameter 7 : hivTree.105r.trst 322s Parameter 8 : hivTree.Node8.trst 322s Parameter 9 : hivTree.iNode1.trst 322s Parameter 10 : hivTree.719.trst 322s Parameter 11 : hivTree.136.trst 322s Parameter 12 : hivTree.Node11.trst 322s Parameter 13 : hivTree.Node5.trst 322s Parameter 14 : hivTree.Node1.trst 322s Parameter 15 : hivTree.6760.trst 322s Parameter 16 : hivTree.113.trst 322s Parameter 17 : hivTree.9939.trst 322s Parameter 18 : hivTree.Node16.trst 322s Parameter 19 : hivTree.256.trst 322s Parameter 20 : hivTree.822.trst 322s Parameter 21 : hivTree.159.trst 322s Parameter 22 : hivTree.Node21.trst 322s Parameter 23 : hivTree.iNode2.trst 322s Parameter 24 : hivTree.Node15.trst 322s 322s Constrained Parameters List 322s 322s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 322s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 322s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 322s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 322s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 322s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 322s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 322s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 322s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 322s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 322s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 322s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 322s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 322s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 322s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 322s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 322s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 322s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 322s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 322s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 322s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 322s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 322s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst1).Unconstrained HKY85 322s 322s Log Likelihood = -1152.88; 322s 322s Independent Parameters List 322s 322s Parameter 1 : hivTree.317.trvs 322s Parameter 2 : hivTree.317.trst 322s Parameter 3 : hivTree.6767.trvs 322s Parameter 4 : hivTree.6767.trst 322s Parameter 5 : hivTree.Node2.trvs 322s Parameter 6 : hivTree.Node2.trst 322s Parameter 7 : hivTree.135.trvs 322s Parameter 8 : hivTree.135.trst 322s Parameter 9 : hivTree.529.trvs 322s Parameter 10 : hivTree.529.trst 322s Parameter 11 : hivTree.105r.trvs 322s Parameter 12 : hivTree.105r.trst 322s Parameter 13 : hivTree.Node8.trvs 322s Parameter 14 : hivTree.Node8.trst 322s Parameter 15 : hivTree.iNode1.trvs 322s Parameter 16 : hivTree.iNode1.trst 322s Parameter 17 : hivTree.719.trvs 322s Parameter 18 : hivTree.719.trst 322s Parameter 19 : hivTree.136.trvs 322s Parameter 20 : hivTree.136.trst 322s Parameter 21 : hivTree.Node11.trvs 322s Parameter 22 : hivTree.Node11.trst 322s Parameter 23 : hivTree.Node5.trvs 322s Parameter 24 : hivTree.Node5.trst 322s Parameter 25 : hivTree.Node1.trvs 322s Parameter 26 : hivTree.Node1.trst 322s Parameter 27 : hivTree.6760.trvs 322s Parameter 28 : hivTree.6760.trst 322s Parameter 29 : hivTree.113.trvs 322s Parameter 30 : hivTree.113.trst 322s Parameter 31 : hivTree.9939.trvs 322s Parameter 32 : hivTree.9939.trst 322s Parameter 33 : hivTree.Node16.trvs 322s Parameter 34 : hivTree.Node16.trst 322s Parameter 35 : hivTree.256.trvs 322s Parameter 36 : hivTree.256.trst 322s Parameter 37 : hivTree.822.trvs 322s Parameter 38 : hivTree.822.trst 322s Parameter 39 : hivTree.159.trvs 322s Parameter 40 : hivTree.159.trst 322s Parameter 41 : hivTree.Node21.trvs 322s Parameter 42 : hivTree.Node21.trst 322s Parameter 43 : hivTree.iNode2.trvs 322s Parameter 44 : hivTree.iNode2.trst 322s Parameter 45 : hivTree.Node15.trvs 322s Parameter 46 : hivTree.Node15.trst 322s 322s 2).HKY85 constrained to F81 on the "iNode1" subtree 322s 322s Log Likelihood = -1157.82; 322s 322s Independent Parameters List 322s 322s Parameter 1 : hivTree.135.trvs 322s Parameter 2 : hivTree.529.trvs 322s Parameter 3 : hivTree.105r.trvs 322s Parameter 4 : hivTree.Node8.trvs 322s Parameter 5 : hivTree.317.trvs 322s Parameter 6 : hivTree.317.trst 322s Parameter 7 : hivTree.6767.trst 322s Parameter 8 : hivTree.6767.trvs 322s Parameter 9 : hivTree.Node2.trst 322s Parameter 10 : hivTree.Node2.trvs 322s Parameter 11 : hivTree.iNode1.trvs 322s Parameter 12 : hivTree.iNode1.trst 322s Parameter 13 : hivTree.719.trvs 322s Parameter 14 : hivTree.719.trst 322s Parameter 15 : hivTree.136.trvs 322s Parameter 16 : hivTree.136.trst 322s Parameter 17 : hivTree.Node11.trvs 322s Parameter 18 : hivTree.Node11.trst 322s Parameter 19 : hivTree.Node5.trvs 322s Parameter 20 : hivTree.Node5.trst 322s Parameter 21 : hivTree.Node1.trvs 322s Parameter 22 : hivTree.Node1.trst 322s Parameter 23 : hivTree.6760.trvs 322s Parameter 24 : hivTree.6760.trst 322s Parameter 25 : hivTree.113.trvs 322s Parameter 26 : hivTree.113.trst 322s Parameter 27 : hivTree.9939.trvs 322s Parameter 28 : hivTree.9939.trst 322s Parameter 29 : hivTree.Node16.trvs 322s Parameter 30 : hivTree.Node16.trst 322s Parameter 31 : hivTree.256.trvs 322s Parameter 32 : hivTree.256.trst 322s Parameter 33 : hivTree.822.trvs 322s Parameter 34 : hivTree.822.trst 322s Parameter 35 : hivTree.159.trvs 322s Parameter 36 : hivTree.159.trst 322s Parameter 37 : hivTree.Node21.trvs 322s Parameter 38 : hivTree.Node21.trst 322s Parameter 39 : hivTree.iNode2.trvs 322s Parameter 40 : hivTree.iNode2.trst 322s Parameter 41 : hivTree.Node15.trvs 322s Parameter 42 : hivTree.Node15.trst 322s 322s Constrained Parameters List 322s 322s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 322s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 322s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 322s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 322s 322s 3).HKY85 constrained to F81 on the "iNode1" branch 322s 322s Log Likelihood = -1152.88; 322s 322s Independent Parameters List 322s 322s Parameter 1 : hivTree.317.trvs 322s Parameter 2 : hivTree.317.trst 322s Parameter 3 : hivTree.6767.trvs 322s Parameter 4 : hivTree.6767.trst 322s Parameter 5 : hivTree.Node2.trvs 322s Parameter 6 : hivTree.Node2.trst 322s Parameter 7 : hivTree.135.trvs 322s Parameter 8 : hivTree.135.trst 322s Parameter 9 : hivTree.529.trvs 322s Parameter 10 : hivTree.529.trst 322s Parameter 11 : hivTree.105r.trvs 322s Parameter 12 : hivTree.105r.trst 322s Parameter 13 : hivTree.Node8.trvs 322s Parameter 14 : hivTree.Node8.trst 322s Parameter 15 : hivTree.iNode1.trvs 322s Parameter 16 : hivTree.iNode1.trst 322s Parameter 17 : hivTree.719.trvs 322s Parameter 18 : hivTree.719.trst 322s Parameter 19 : hivTree.136.trvs 322s Parameter 20 : hivTree.136.trst 322s Parameter 21 : hivTree.Node11.trvs 322s Parameter 22 : hivTree.Node11.trst 322s Parameter 23 : hivTree.Node5.trvs 322s Parameter 24 : hivTree.Node5.trst 322s Parameter 25 : hivTree.Node1.trvs 322s Parameter 26 : hivTree.Node1.trst 322s Parameter 27 : hivTree.6760.trvs 322s Parameter 28 : hivTree.6760.trst 322s Parameter 29 : hivTree.113.trvs 322s Parameter 30 : hivTree.113.trst 322s Parameter 31 : hivTree.9939.trvs 322s Parameter 32 : hivTree.9939.trst 322s Parameter 33 : hivTree.Node16.trvs 322s Parameter 34 : hivTree.Node16.trst 322s Parameter 35 : hivTree.256.trvs 322s Parameter 36 : hivTree.256.trst 322s Parameter 37 : hivTree.822.trvs 322s Parameter 38 : hivTree.822.trst 322s Parameter 39 : hivTree.159.trvs 322s Parameter 40 : hivTree.159.trst 322s Parameter 41 : hivTree.Node21.trvs 322s Parameter 42 : hivTree.Node21.trst 322s Parameter 43 : hivTree.iNode2.trvs 322s Parameter 44 : hivTree.iNode2.trst 322s Parameter 45 : hivTree.Node15.trvs 322s Parameter 46 : hivTree.Node15.trst 322s 322s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 322s 322s Log Likelihood = -1152.88; 322s 322s Independent Parameters List 322s 322s Parameter 1 : hivTree.317.trvs 322s Parameter 2 : hivTree.317.trst 322s Parameter 3 : hivTree.6767.trvs 322s Parameter 4 : hivTree.6767.trst 322s Parameter 5 : hivTree.Node2.trvs 322s Parameter 6 : hivTree.Node2.trst 322s Parameter 7 : hivTree.135.trvs 322s Parameter 8 : hivTree.135.trst 322s Parameter 9 : hivTree.529.trvs 322s Parameter 10 : hivTree.529.trst 322s Parameter 11 : hivTree.105r.trvs 322s Parameter 12 : hivTree.105r.trst 322s Parameter 13 : hivTree.Node8.trvs 322s Parameter 14 : hivTree.Node8.trst 322s Parameter 15 : hivTree.iNode1.trvs 322s Parameter 16 : hivTree.iNode1.trst 322s Parameter 17 : hivTree.719.trvs 322s Parameter 18 : hivTree.719.trst 322s Parameter 19 : hivTree.136.trvs 322s Parameter 20 : hivTree.136.trst 322s Parameter 21 : hivTree.Node11.trvs 322s Parameter 22 : hivTree.Node11.trst 322s Parameter 23 : hivTree.Node5.trvs 322s Parameter 24 : hivTree.Node5.trst 322s Parameter 25 : hivTree.Node1.trvs 322s Parameter 26 : hivTree.Node1.trst 322s Parameter 27 : hivTree.6760.trvs 322s Parameter 28 : hivTree.6760.trst 322s Parameter 29 : hivTree.113.trvs 322s Parameter 30 : hivTree.113.trst 322s Parameter 31 : hivTree.9939.trvs 322s Parameter 32 : hivTree.9939.trst 322s Parameter 33 : hivTree.Node16.trvs 322s Parameter 34 : hivTree.Node16.trst 322s Parameter 35 : hivTree.256.trvs 322s Parameter 36 : hivTree.256.trst 322s Parameter 37 : hivTree.822.trvs 322s Parameter 38 : hivTree.822.trst 322s Parameter 39 : hivTree.159.trvs 322s Parameter 40 : hivTree.159.trst 322s Parameter 41 : hivTree.Node21.trvs 322s Parameter 42 : hivTree.Node21.trst 322s Parameter 43 : hivTree.iNode2.trvs 322s Parameter 44 : hivTree.iNode2.trst 322s Parameter 45 : hivTree.Node15.trvs 323s Parameter 46 : hivTree.Node15.trst 323s 323s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 323s 323s Log Likelihood = -1152.88; 323s 323s Independent Parameters List 323s 323s Parameter 1 : hivTree.317.trvs 323s Parameter 2 : hivTree.317.trst 323s Parameter 3 : hivTree.6767.trvs 323s Parameter 4 : hivTree.6767.trst 323s Parameter 5 : hivTree.Node2.trvs 323s Parameter 6 : hivTree.Node2.trst 323s Parameter 7 : hivTree.135.trvs 323s Parameter 8 : hivTree.135.trst 323s Parameter 9 : hivTree.529.trvs 323s Parameter 10 : hivTree.529.trst 323s Parameter 11 : hivTree.105r.trvs 323s Parameter 12 : hivTree.105r.trst 323s Parameter 13 : hivTree.Node8.trvs 323s Parameter 14 : hivTree.Node8.trst 323s Parameter 15 : hivTree.iNode1.trvs 323s Parameter 16 : hivTree.iNode1.trst 323s Parameter 17 : hivTree.719.trvs 323s Parameter 18 : hivTree.719.trst 323s Parameter 19 : hivTree.136.trvs 323s Parameter 20 : hivTree.136.trst 323s Parameter 21 : hivTree.Node11.trvs 323s Parameter 22 : hivTree.Node11.trst 323s Parameter 23 : hivTree.Node5.trvs 323s Parameter 24 : hivTree.Node5.trst 323s Parameter 25 : hivTree.Node1.trvs 323s Parameter 26 : hivTree.Node1.trst 323s Parameter 27 : hivTree.6760.trvs 323s Parameter 28 : hivTree.6760.trst 323s Parameter 29 : hivTree.113.trvs 323s Parameter 30 : hivTree.113.trst 323s Parameter 31 : hivTree.9939.trvs 323s Parameter 32 : hivTree.9939.trst 323s Parameter 33 : hivTree.Node16.trvs 323s Parameter 34 : hivTree.Node16.trst 323s Parameter 35 : hivTree.256.trvs 323s Parameter 36 : hivTree.256.trst 323s Parameter 37 : hivTree.822.trvs 323s Parameter 38 : hivTree.822.trst 323s Parameter 39 : hivTree.159.trvs 323s Parameter 40 : hivTree.159.trst 323s Parameter 41 : hivTree.Node21.trvs 323s Parameter 42 : hivTree.Node21.trst 323s Parameter 43 : hivTree.iNode2.trvs 323s Parameter 44 : hivTree.iNode2.trst 323s Parameter 45 : hivTree.Node15.trvs 323s Parameter 46 : hivTree.Node15.trst 323s 323s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 323s 323s Log Likelihood = -1157.82; 323s 323s Independent Parameters List 323s 323s Parameter 1 : hivTree.135.trst 323s Parameter 2 : hivTree.529.trst 323s Parameter 3 : hivTree.105r.trst 323s Parameter 4 : hivTree.Node8.trst 323s Parameter 5 : hivTree.317.trvs 323s Parameter 6 : hivTree.317.trst 323s Parameter 7 : hivTree.6767.trst 323s Parameter 8 : hivTree.6767.trvs 323s Parameter 9 : hivTree.Node2.trst 323s Parameter 10 : hivTree.Node2.trvs 323s Parameter 11 : hivTree.iNode1.trvs 323s Parameter 12 : hivTree.iNode1.trst 323s Parameter 13 : hivTree.719.trvs 323s Parameter 14 : hivTree.719.trst 323s Parameter 15 : hivTree.136.trvs 323s Parameter 16 : hivTree.136.trst 323s Parameter 17 : hivTree.Node11.trvs 323s Parameter 18 : hivTree.Node11.trst 323s Parameter 19 : hivTree.Node5.trvs 323s Parameter 20 : hivTree.Node5.trst 323s Parameter 21 : hivTree.Node1.trvs 323s Parameter 22 : hivTree.Node1.trst 323s Parameter 23 : hivTree.6760.trvs 323s Parameter 24 : hivTree.6760.trst 323s Parameter 25 : hivTree.113.trvs 323s Parameter 26 : hivTree.113.trst 323s Parameter 27 : hivTree.9939.trvs 323s Parameter 28 : hivTree.9939.trst 323s Parameter 29 : hivTree.Node16.trvs 323s Parameter 30 : hivTree.Node16.trst 323s Parameter 31 : hivTree.256.trvs 323s Parameter 32 : hivTree.256.trst 323s Parameter 33 : hivTree.822.trvs 323s Parameter 34 : hivTree.822.trst 323s Parameter 35 : hivTree.159.trvs 323s Parameter 36 : hivTree.159.trst 323s Parameter 37 : hivTree.Node21.trvs 323s Parameter 38 : hivTree.Node21.trst 323s Parameter 39 : hivTree.iNode2.trvs 323s Parameter 40 : hivTree.iNode2.trst 323s Parameter 41 : hivTree.Node15.trvs 323s Parameter 42 : hivTree.Node15.trst 323s 323s Constrained Parameters List 323s 323s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 323s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 323s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 323s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 323s + '[' -f aa.bf ']' 323s + hyphy aa.bf 323s Log Likelihood = -1134.73159786164; 323s Tree theTree=(((Langur:0.07428656825898035,Baboon:0.0383372426720565)Node2:0.02338350071386285,Human:0.05948335126407791)Node1:0.02006356755930697,Rat:0.2458393538929597,(Cow:0.2550385870833224,Horse:0.5625920217708038)Node7:0.07059881528679296); 323s + for i in *.bf 323s + '[' -f definitions2.bf ']' 323s + hyphy definitions2.bf 323s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 323s 323s Sample by MEAN: 323s 323s Sample mean = 0.5 (sample variance = 0.2450374540764348) 323s 323s Rate[0]= 0.06847689 (weight=0.2500000) 323s Rate[1]= 0.23837593 (weight=0.2500000) 323s Rate[2]= 0.50000000 (weight=0.2500000) 323s Rate[3]= 1.19314718 (weight=0.2500000) 323s ------------------------------------------------ 323s 323s Sample by MEDIAN: 323s 323s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 323s 323s Rate[0]= 0.06676570 (weight=0.2500000) 323s Rate[1]= 0.23500181 (weight=0.2500000) 323s Rate[2]= 0.49041463 (weight=0.2500000) 323s Rate[3]= 1.03972077 (weight=0.2500000) 323s ------------------------------------------------ 323s 323s Sample by SCALED_MEDIAN: 323s 323s Sample mean = 0.5 (sample variance = 0.2154404122636025) 323s 323s Rate[0]= 0.07289218 (weight=0.2500000) 323s Rate[1]= 0.25656580 (weight=0.2500000) 323s Rate[2]= 0.53541552 (weight=0.2500000) 323s Rate[3]= 1.13512650 (weight=0.2500000) 323s ------------------------------------------------ 323s 323s Sample by MEAN (numerical averaging): 323s 323s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 323s 323s Rate[0]= 0.06846096 (weight=0.2500000) 323s Rate[1]= 0.23834015 (weight=0.2500000) 323s Rate[2]= 0.49996411 (weight=0.2500000) 323s Rate[3]= 1.19314889 (weight=0.2500000) 323s ------------------------------------------------ 323s 323s Sample by MEAN (numerical CDF and averaging): 323s 323s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 323s 323s Rate[0]= 0.06849282 (weight=0.2500000) 323s Rate[1]= 0.23835613 (weight=0.2500000) 323s Rate[2]= 0.49994751 (weight=0.2500000) 323s Rate[3]= 1.19311765 (weight=0.2500000) 323s ------------------------------------------------ 323s 2). Equiprobable rates sampled from Exponential with lambda = 2 323s 323s Sample by MEDIAN (3 rate classes): 323s 323s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 323s 323s Rate[0]= 0.09116078 (weight=0.3333333) 323s Rate[1]= 0.34657359 (weight=0.3333333) 323s Rate[2]= 0.89587973 (weight=0.3333333) 323s ------------------------------------------------ 323s 323s Sample by MEDIAN (9 rate classes): 323s 323s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 323s 323s Rate[0]= 0.02857921 (weight=0.1111111) 323s Rate[1]= 0.09116078 (weight=0.1111111) 323s Rate[2]= 0.16271120 (weight=0.1111111) 323s Rate[3]= 0.24623824 (weight=0.1111111) 323s Rate[4]= 0.34657359 (weight=0.1111111) 323s Rate[5]= 0.47223080 (weight=0.1111111) 323s Rate[6]= 0.64046692 (weight=0.1111111) 323s Rate[7]= 0.89587973 (weight=0.1111111) 323s Rate[8]= 1.44518588 (weight=0.1111111) 323s ------------------------------------------------ 323s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 323s 323s Sample by MEAN (10 rate classes): 323s 323s Sample mean = 1 (sample variance = 0.1057310289486733) 323s 323s Rate[0]= 0.52447499 (weight=0.1000000) 323s Rate[1]= 0.67866972 (weight=0.1000000) 323s Rate[2]= 0.77209919 (weight=0.1000000) 323s Rate[3]= 0.85214884 (weight=0.1000000) 323s Rate[4]= 0.92850815 (weight=0.1000000) 323s Rate[5]= 1.00664500 (weight=0.1000000) 323s Rate[6]= 1.09192933 (weight=0.1000000) 323s Rate[7]= 1.19267960 (weight=0.1000000) 323s Rate[8]= 1.32858029 (weight=0.1000000) 323s Rate[9]= 1.62426489 (weight=0.1000000) 323s ------------------------------------------------ 323s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 323s 323s Sample by MEAN (10 rate classes): 323s 323s Sample mean = 2 (sample variance = 0.04259071282256012) 323s 323s Rate[0]= 1.66431246 (weight=0.1000000) 323s Rate[1]= 1.79212822 (weight=0.1000000) 323s Rate[2]= 1.86123411 (weight=0.1000000) 323s Rate[3]= 1.91722052 (weight=0.1000000) 323s Rate[4]= 1.96832799 (weight=0.1000000) 323s Rate[5]= 2.01862937 (weight=0.1000000) 323s Rate[6]= 2.07152664 (weight=0.1000000) 323s Rate[7]= 2.13166629 (weight=0.1000000) 323s Rate[8]= 2.20930216 (weight=0.1000000) 323s Rate[9]= 2.36565224 (weight=0.1000000) 323s ------------------------------------------------ 323s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 323s 323s Sample by MEAN (8 rate classes): 323s 323s Sample mean = 0.5 (sample variance = 0.09375000225643569) 323s 323s Rate[0]= 0.06250000 (weight=0.1250000) 323s Rate[1]= 0.18750000 (weight=0.1250000) 323s Rate[2]= 0.31250001 (weight=0.1250000) 323s Rate[3]= 0.43750001 (weight=0.1250000) 323s Rate[4]= 0.56249993 (weight=0.1250000) 323s Rate[5]= 0.68750001 (weight=0.1250000) 323s Rate[6]= 0.81250002 (weight=0.1250000) 323s Rate[7]= 0.93750002 (weight=0.1250000) 323s ------------------------------------------------ 323s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 323s 323s Sample by MEAN (8 rate classes): 323s 323s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 323s 323s Rate[0]= 2.17658588 (weight=0.1250000) 323s Rate[1]= 2.55230783 (weight=0.1250000) 323s Rate[2]= 2.75432532 (weight=0.1250000) 323s Rate[3]= 2.92101185 (weight=0.1250000) 323s Rate[4]= 3.07898815 (weight=0.1250000) 323s Rate[5]= 3.24567468 (weight=0.1250000) 323s Rate[6]= 3.44769217 (weight=0.1250000) 323s Rate[7]= 3.82341415 (weight=0.1250000) 323s ------------------------------------------------ 323s + for i in *.bf 323s + '[' -f definitions3.bf ']' 323s + hyphy definitions3.bf 323s 323s 323s Sample mean = 1 (sample variance = 0.9920002887656187) 323s 323s Rate[0]= 0.05175536 (weight=0.1000000) 323s Rate[1]= 0.16309623 (weight=0.1000000) 323s Rate[2]= 0.28842380 (weight=0.1000000) 323s Rate[3]= 0.43177086 (weight=0.1000000) 323s Rate[4]= 0.59921784 (weight=0.1000000) 323s Rate[5]= 0.80057298 (weight=0.1000000) 323s Rate[6]= 1.05324451 (weight=0.1000000) 323s Rate[7]= 1.39304259 (weight=0.1000000) 323s Rate[8]= 1.91629073 (weight=0.1000000) 323s Rate[9]= 3.30258509 (weight=0.1000000) 323s ------------------------------------------------ 323s + for i in *.bf 323s + '[' -f displayFunction.bf ']' 323s + hyphy displayFunction.bf 323s + for i in *.bf 323s + '[' -f profile_test.bf ']' 323s + hyphy profile_test.bf 323s 323s Total run time (seconds) : 0.000000 323s Total number of steps : 1500005 323s 323s 1 : s=0; 323s Call count: 1 323s Time (seconds): 1.8e-11 323s 2 : m={5,1}; 323s Call count: 1 323s Time (seconds): 2.6e-11 323s 3 : k=0; 323s Call count: 1 323s Time (seconds): 2e-12 323s 4 : Branch under condition 'k<250000' 323s to 323s s=s+k; 323s else 323s #profilePAUSE, ; 323s Call count: 250001 323s Time (seconds): 3.084100000000992e-08 323s 5 : s=s+k; 323s Call count: 250000 323s Time (seconds): 3.390800000001306e-08 323s 6 : t=Random(0,5); 323s Call count: 250000 323s Time (seconds): 3.453900000001367e-08 323s 7 : m[t]=m[t]+1; 323s Call count: 250000 323s Time (seconds): 8.218300000006033e-08 323s 8 : k=k+1; 323s Call count: 250000 323s Time (seconds): 3.380600000001352e-08 323s 9 : Go to step 4 323s Call count: 250000 323s Time (seconds): 1.088899999999846e-08 323s 10 : #profilePAUSE, ; 323s Call count: 1 323s Time (seconds): 1e-12 323s + for i in *.bf 323s + '[' -f shared.bf ']' 323s + hyphy shared.bf 323s + rm -f '*messages.log*' '*errors.log*' 323s autopkgtest [00:16:12]: test run-unit-tests: -----------------------] 324s run-unit-tests PASS 324s autopkgtest [00:16:13]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 324s autopkgtest [00:16:13]: @@@@@@@@@@@@@@@@@@@@ summary 324s run-unit-tests PASS 496s nova [W] Using flock in prodstack6-arm64 496s Creating nova instance adt-plucky-arm64-hyphy-20250216-001049-juju-7f2275-prod-proposed-migration-environment-2-e7302dbe-2406-42d9-b667-3ce5fa2f63a2 from image adt/ubuntu-plucky-arm64-server-20250215.img (UUID 8f82fa69-4462-4e93-a46b-73be9ea2c381)... 496s nova [W] Timed out waiting for 1b41481d-36fc-4558-9b0e-ebaeb2138a86 to get deleted.