0s autopkgtest [06:31:45]: starting date and time: 2024-03-24 06:31:45+0000 0s autopkgtest [06:31:45]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [06:31:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zkvpa8pu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl,src:orthanc-python --apt-upgrade hyphy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2 orthanc-python/4.1+ds-2build3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-18.secgroup --name adt-noble-ppc64el-hyphy-20240324-063145-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 287s autopkgtest [06:36:32]: testbed dpkg architecture: ppc64el 287s autopkgtest [06:36:32]: testbed apt version: 2.7.12 287s autopkgtest [06:36:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 288s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 289s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 289s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 289s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4009 kB] 291s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 291s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [698 kB] 291s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 291s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 291s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 291s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4267 kB] 292s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 292s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 292s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 295s Fetched 9723 kB in 4s (2202 kB/s) 295s Reading package lists... 298s Reading package lists... 298s Building dependency tree... 298s Reading state information... 298s Calculating upgrade... 299s The following packages will be REMOVED: 299s libssl3 299s The following NEW packages will be installed: 299s libssl3t64 299s The following packages have been kept back: 299s curl 299s The following packages will be upgraded: 299s openssl 299s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 299s Need to get 3151 kB of archives. 299s After this operation, 73.7 kB of additional disk space will be used. 299s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 299s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 300s Fetched 3151 kB in 1s (3663 kB/s) 300s (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 ... 70156 files and directories currently installed.) 300s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 300s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 300s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 300s wget depends on libssl3 (>= 3.0.0). 300s tnftp depends on libssl3 (>= 3.0.0). 300s tcpdump depends on libssl3 (>= 3.0.0). 300s systemd-resolved depends on libssl3 (>= 3.0.0). 300s systemd depends on libssl3 (>= 3.0.0). 300s sudo depends on libssl3 (>= 3.0.0). 300s rsync depends on libssl3 (>= 3.0.0). 300s python3-cryptography depends on libssl3 (>= 3.0.0). 300s openssh-server depends on libssl3 (>= 3.0.10). 300s openssh-client depends on libssl3 (>= 3.0.10). 300s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 300s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 300s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 300s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 300s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 300s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 300s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 300s libnvme1 depends on libssl3 (>= 3.0.0). 300s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 300s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 300s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 300s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 300s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 300s kmod depends on libssl3 (>= 3.0.0). 300s dhcpcd-base depends on libssl3 (>= 3.0.0). 300s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 300s 300s (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 ... 70156 files and directories currently installed.) 300s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 300s Selecting previously unselected package libssl3t64:ppc64el. 300s (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 ... 70145 files and directories currently installed.) 300s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 300s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 300s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 300s Setting up openssl (3.0.13-0ubuntu2) ... 300s Processing triggers for man-db (2.12.0-3) ... 301s Processing triggers for libc-bin (2.39-0ubuntu6) ... 301s Reading package lists... 301s Building dependency tree... 301s Reading state information... 301s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 302s sh: Attempting to set up Debian/Ubuntu apt sources automatically 302s sh: Distribution appears to be Ubuntu 303s Reading package lists... 303s Building dependency tree... 303s Reading state information... 303s eatmydata is already the newest version (131-1). 303s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 303s Reading package lists... 303s Building dependency tree... 303s Reading state information... 304s dbus is already the newest version (1.14.10-4ubuntu1). 304s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 304s Reading package lists... 304s Building dependency tree... 304s Reading state information... 304s rng-tools-debian is already the newest version (2.4). 304s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 304s Reading package lists... 304s Building dependency tree... 304s Reading state information... 304s The following packages will be REMOVED: 304s cloud-init* python3-configobj* python3-debconf* 305s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 305s After this operation, 3256 kB disk space will be freed. 305s (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 ... 70158 files and directories currently installed.) 305s Removing cloud-init (24.1.2-0ubuntu1) ... 305s Removing python3-configobj (5.0.8-3) ... 305s Removing python3-debconf (1.5.86) ... 305s Processing triggers for man-db (2.12.0-3) ... 306s (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 ... 69769 files and directories currently installed.) 306s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 307s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 307s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 307s invoke-rc.d: policy-rc.d denied execution of try-restart. 307s Reading package lists... 307s Building dependency tree... 307s Reading state information... 307s linux-generic is already the newest version (6.8.0-11.11+1). 307s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 308s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 308s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 310s Reading package lists... 310s Reading package lists... 310s Building dependency tree... 310s Reading state information... 311s Calculating upgrade... 311s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 311s Reading package lists... 311s Building dependency tree... 311s Reading state information... 311s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 311s autopkgtest [06:36:56]: rebooting testbed after setup commands that affected boot 486s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 493s autopkgtest [06:39:58]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 496s autopkgtest [06:40:01]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 500s Get:1 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (dsc) [2423 B] 500s Get:2 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (tar) [2613 kB] 500s Get:3 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (diff) [17.0 kB] 500s gpgv: Signature made Sat Jan 13 16:06:18 2024 UTC 500s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 500s gpgv: issuer "emollier@debian.org" 500s gpgv: Can't check signature: No public key 500s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.59+dfsg-1.dsc: no acceptable signature found 501s autopkgtest [06:40:06]: testing package hyphy version 2.5.59+dfsg-1 501s autopkgtest [06:40:06]: build not needed 502s autopkgtest [06:40:07]: test run-unit-tests: preparing testbed 509s Reading package lists... 509s Building dependency tree... 509s Reading state information... 509s Starting pkgProblemResolver with broken count: 0 509s Starting 2 pkgProblemResolver with broken count: 0 509s Done 509s The following additional packages will be installed: 509s hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 libdrm-amdgpu1 509s libevent-pthreads-2.1-7 libfabric1 libgomp1 libhsa-runtime64-1 libhsakmt1 509s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libopenmpi3 libpciaccess0 509s libpmix2 librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 509s Suggested packages: 509s opencl-icd 509s The following NEW packages will be installed: 509s autopkgtest-satdep hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 509s libamdhip64-5 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libgomp1 509s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 509s libmunge2 libopenmpi3 libpciaccess0 libpmix2 librdmacm1t64 libucx0 509s libxnvctrl0 ocl-icd-libopencl1 509s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 509s Need to get 57.9 MB/57.9 MB of archives. 509s After this operation, 265 MB of additional disk space will be used. 509s Get:1 /tmp/autopkgtest.t8lht3/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 509s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el hyphy-common all 2.5.59+dfsg-1 [624 kB] 510s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 510s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-9 [7844 B] 510s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el librdmacm1t64 ppc64el 50.0-2 [80.9 kB] 510s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfabric1 ppc64el 1.17.0-3build1 [694 kB] 511s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] 511s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmunge2 ppc64el 0.5.15-3ubuntu1 [17.6 kB] 511s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] 511s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] 511s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] 511s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] 511s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpmix2 ppc64el 5.0.1-4 [750 kB] 511s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libllvm17 ppc64el 1:17.0.6-5build1 [27.3 MB] 515s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3 [15.3 MB] 516s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] 516s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsakmt1 ppc64el 5.7.0-1 [76.5 kB] 516s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-1 [330 kB] 516s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamdhip64-5 ppc64el 5.2.3-12 [5004 kB] 516s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libucx0 ppc64el 1.16.0+ds-4 [1203 kB] 516s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el libopenmpi3 ppc64el 4.1.6-5ubuntu1 [3404 kB] 516s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el hyphy-mpi ppc64el 2.5.59+dfsg-1 [1354 kB] 516s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el hyphy-pt ppc64el 2.5.59+dfsg-1 [1312 kB] 517s Fetched 57.9 MB in 7s (8115 kB/s) 517s Selecting previously unselected package hyphy-common. 517s (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 ... 69714 files and directories currently installed.) 517s Preparing to unpack .../00-hyphy-common_2.5.59+dfsg-1_all.deb ... 517s Unpacking hyphy-common (2.5.59+dfsg-1) ... 517s Selecting previously unselected package libgomp1:ppc64el. 517s Preparing to unpack .../01-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 517s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 517s Selecting previously unselected package libevent-pthreads-2.1-7:ppc64el. 517s Preparing to unpack .../02-libevent-pthreads-2.1-7_2.1.12-stable-9_ppc64el.deb ... 517s Unpacking libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 517s Selecting previously unselected package librdmacm1t64:ppc64el. 517s Preparing to unpack .../03-librdmacm1t64_50.0-2_ppc64el.deb ... 517s Unpacking librdmacm1t64:ppc64el (50.0-2) ... 517s Selecting previously unselected package libfabric1:ppc64el. 517s Preparing to unpack .../04-libfabric1_1.17.0-3build1_ppc64el.deb ... 517s Unpacking libfabric1:ppc64el (1.17.0-3build1) ... 517s Selecting previously unselected package libhwloc15:ppc64el. 517s Preparing to unpack .../05-libhwloc15_2.10.0-1_ppc64el.deb ... 517s Unpacking libhwloc15:ppc64el (2.10.0-1) ... 517s Selecting previously unselected package libmunge2:ppc64el. 517s Preparing to unpack .../06-libmunge2_0.5.15-3ubuntu1_ppc64el.deb ... 517s Unpacking libmunge2:ppc64el (0.5.15-3ubuntu1) ... 517s Selecting previously unselected package libpciaccess0:ppc64el. 517s Preparing to unpack .../07-libpciaccess0_0.17-3_ppc64el.deb ... 517s Unpacking libpciaccess0:ppc64el (0.17-3) ... 517s Selecting previously unselected package libxnvctrl0:ppc64el. 517s Preparing to unpack .../08-libxnvctrl0_510.47.03-0ubuntu1_ppc64el.deb ... 517s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 517s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 517s Preparing to unpack .../09-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... 517s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 517s Selecting previously unselected package libhwloc-plugins:ppc64el. 517s Preparing to unpack .../10-libhwloc-plugins_2.10.0-1_ppc64el.deb ... 517s Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... 517s Selecting previously unselected package libpmix2:ppc64el. 517s Preparing to unpack .../11-libpmix2_5.0.1-4_ppc64el.deb ... 517s Unpacking libpmix2:ppc64el (5.0.1-4) ... 517s Selecting previously unselected package libllvm17:ppc64el. 517s Preparing to unpack .../12-libllvm17_1%3a17.0.6-5build1_ppc64el.deb ... 517s Unpacking libllvm17:ppc64el (1:17.0.6-5build1) ... 518s Selecting previously unselected package libamd-comgr2:ppc64el. 518s Preparing to unpack .../13-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_ppc64el.deb ... 518s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 519s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 519s Preparing to unpack .../14-libdrm-amdgpu1_2.4.120-2_ppc64el.deb ... 519s Unpacking libdrm-amdgpu1:ppc64el (2.4.120-2) ... 519s Selecting previously unselected package libhsakmt1:ppc64el. 519s Preparing to unpack .../15-libhsakmt1_5.7.0-1_ppc64el.deb ... 519s Unpacking libhsakmt1:ppc64el (5.7.0-1) ... 519s Selecting previously unselected package libhsa-runtime64-1. 519s Preparing to unpack .../16-libhsa-runtime64-1_5.7.1-1_ppc64el.deb ... 519s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 519s Selecting previously unselected package libamdhip64-5. 519s Preparing to unpack .../17-libamdhip64-5_5.2.3-12_ppc64el.deb ... 519s Unpacking libamdhip64-5 (5.2.3-12) ... 519s Selecting previously unselected package libucx0:ppc64el. 519s Preparing to unpack .../18-libucx0_1.16.0+ds-4_ppc64el.deb ... 519s Unpacking libucx0:ppc64el (1.16.0+ds-4) ... 519s Selecting previously unselected package libopenmpi3:ppc64el. 519s Preparing to unpack .../19-libopenmpi3_4.1.6-5ubuntu1_ppc64el.deb ... 519s Unpacking libopenmpi3:ppc64el (4.1.6-5ubuntu1) ... 519s Selecting previously unselected package hyphy-mpi. 519s Preparing to unpack .../20-hyphy-mpi_2.5.59+dfsg-1_ppc64el.deb ... 519s Unpacking hyphy-mpi (2.5.59+dfsg-1) ... 519s Selecting previously unselected package hyphy-pt. 519s Preparing to unpack .../21-hyphy-pt_2.5.59+dfsg-1_ppc64el.deb ... 519s Unpacking hyphy-pt (2.5.59+dfsg-1) ... 519s Selecting previously unselected package autopkgtest-satdep. 519s Preparing to unpack .../22-1-autopkgtest-satdep.deb ... 519s Unpacking autopkgtest-satdep (0) ... 519s Setting up libpciaccess0:ppc64el (0.17-3) ... 519s Setting up hyphy-common (2.5.59+dfsg-1) ... 519s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 519s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 519s Setting up libmunge2:ppc64el (0.5.15-3ubuntu1) ... 519s Setting up libhwloc15:ppc64el (2.10.0-1) ... 519s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 519s Setting up librdmacm1t64:ppc64el (50.0-2) ... 519s Setting up libllvm17:ppc64el (1:17.0.6-5build1) ... 519s Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 519s Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... 519s Setting up libfabric1:ppc64el (1.17.0-3build1) ... 519s Setting up hyphy-pt (2.5.59+dfsg-1) ... 519s Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... 519s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 519s Setting up libhsakmt1:ppc64el (5.7.0-1) ... 519s Setting up libpmix2:ppc64el (5.0.1-4) ... 519s Setting up libhsa-runtime64-1 (5.7.1-1) ... 519s Setting up libamdhip64-5 (5.2.3-12) ... 519s Setting up libucx0:ppc64el (1.16.0+ds-4) ... 519s Setting up libopenmpi3:ppc64el (4.1.6-5ubuntu1) ... 519s Setting up hyphy-mpi (2.5.59+dfsg-1) ... 519s Setting up autopkgtest-satdep (0) ... 519s Processing triggers for man-db (2.12.0-3) ... 520s Processing triggers for libc-bin (2.39-0ubuntu6) ... 523s (Reading database ... 70616 files and directories currently installed.) 523s Removing autopkgtest-satdep (0) ... 524s autopkgtest [06:40:29]: test run-unit-tests: [----------------------- 524s + for i in *.bf 524s + '[' -f ExonIntron.bf ']' 524s + hyphy ExonIntron.bf 525s Log Likelihood = -1113.3452348024; 525s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134922462160502,(ZMUBIS27F:0,(ZMU29160:0.054394345696772,ZMU29161:0.03970987859324619)Node8:0.01201455568871097)Node6:0)Node4:0.02459325729877982,BLYMUB1:0.01185774570687971); 525s Tree exon2Tree=(BLYMUB2:0.03542380289141799,(RICRMA630:0.02935130548911293,(ZMUBIS27F:0.07549022996233165,(ZMU29160:0.09103103261942465,ZMU29161:0.02593591330706529)Node8:0.0115726990288497)Node6:0.04929251050218417)Node4:0.02930501220434101,BLYMUB1:0.02204551205158142); 525s Tree intronTree=(BLYMUB2:0.03120129062242439,(RICRMA630:0.04155594446163559,(ZMUBIS27F:0.02044498247849313,(ZMU29160:0.02069034622416463,ZMU29161:0.01019754642743267)Node8:0.0206897122963175)Node6:0)Node4:0,BLYMUB1:0.01036548361237174); 525s + for i in *.bf 525s + '[' -f F81.bf ']' 525s + hyphy F81.bf 525s Log Likelihood = -1187.54702793712; 525s Tree givenTree=(256:0.01194350373384025,(822:0.0294483178715643,159:0.004470566159462158)Node2:0.003648416568238714,((113:0.0224474710969397,9939:0.0763290701719256)Node6:0.005077660588396596,(6760:0.06903115384056212,((317:0.0375181805221699,6767:0.07086144938272695)Node12:0.01229344518656625,((135:0.02045619176225368,(529:0.03338017126117491,105r:0.01322045023334663)Node18:0.02586876845877579)Node16:0.005414279316364114,(719:0.02965903782232076,136:0.008234229505830207)Node21:0.04882999615832644)Node15:0.01525962732194813)Node11:0.01379933463843443)Node9:0.02422268519451894)Node5:0.02148378736797665); 525s + for i in *.bf 525s + '[' -f F81relrate.bf ']' 525s + hyphy F81relrate.bf 525s + for i in *.bf 525s + '[' -f F81relratio.bf ']' 525s 525s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001001418486; 525s Tree threeTaxaTree=(a:0.08501458081697648,b:0.0733761297957005,c:0.1653894109016959); 525s 525s 525s 1). With the outgroup at taxon #1, the P-value is:0.002155106158058917 525s Log Likelihood = -948.707253867892; 525s Tree threeTaxaTree=(a:0.08228741153904655,b:0.119450759858316,c:0.119450759858316); 525s 525s 525s 2). With the outgroup at taxon #2, the P-value is:0.008353404399322084 525s Log Likelihood = -947.479050125766; 525s Tree threeTaxaTree=(a:0.1250762630043411,b:0.07125949122322148,c:0.1250762630043411); 525s 525s 525s 3). With the outgroup at taxon #3, the P-value is:0.6669137053248184 525s Log Likelihood = -944.093618166699; 525s Tree threeTaxaTree=(a:0.07922729811878117,b:0.07922729811878117,c:0.165333983818582); 525s 525s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059583111; 525s Tree fourTaxaTree1=((1:0.1129103974967786,2:0.1073438667590712)Node1:0.09978716101100081,3:0.3469444073497459,4:0.321901988109122); 525s Tree fourTaxaTree2=((1:0.08585822407067131,2:0.09338071137963387)Node1:0.07364164481371639,3:0.3933120496818053,4:0.3801922686510784); 525s 525s 525s 1). Relative ratio constraint; the P-value is:0.6933531589969584 525s Log Likelihood = -2575.74610909071; 525s Global Parameters: 525s R=1.007290914989641; 525s 525s Tree fourTaxaTree1=((1:0.09948363759362119,2:0.09943036934765574)Node1:0.0869682813941792,3:0.3687236032519883,4:0.3489177318846092); 525s Tree fourTaxaTree2=((1:0.1000737336848971,2:0.100020149473568)Node1:0.08748414153115294,3:0.3709107202724674,4:0.3509873686082183); 525s + hyphy F81relratio.bf 525s + for i in *.bf 525s + '[' -f HKY85.bf ']' 525s + hyphy HKY85.bf 525s Log Likelihood = -1152.88077773909; 525s Tree givenTree=(256:0.01162070182604088,(822:0.02979926451443584,159:0.004015046911942904)Node2:0.003749827223630768,((113:0.02130520770118562,9939:0.07785954801431182)Node6:0.004320565418539774,(6760:0.07315576754142032,((317:0.03809412646592474,6767:0.07101550063779899)Node12:0.006276164739972901,((135:0.01788112592444625,(529:0.03257791789990102,105r:0.01513878382158365)Node18:0.02833956064538017)Node16:0.007921503868834619,(719:0.02987628482584961,136:0.00804153730286988)Node21:0.04859310335914813)Node15:0.01599223438105079)Node11:0.01658044691131713)Node9:0.02665634421821494)Node5:0.02296564552436482); 525s + for i in *.bf 525s + '[' -f HKY852blocks.bf ']' 525s + hyphy HKY852blocks.bf 525s 525s ----- RESULTS ----- 525s Log Likelihood = -6801.91478425276; 525s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050202321568921,((((((ZMU60511:0.01039488408135273,ZMU60510:0.02379070780713856)Node8:0.08348786107702381,OSRAC2:0.1885079102240996)Node7:0.05839366558942005,(OSRAC1:0.01536275994074223,SVSOAC1:0.07341325799891436)Node12:0.07295373451860043)Node6:0,((OSRAC3:0.07321302548671947,ZMU60507:0.06503975186773671)Node16:0.07977604215561537,ZMU60509:0.1288921885884091)Node15:0.001251872635464636)Node5:0.08269589050191273,(MZEACT1G:0.1142676217413272,OSRAC7:0.0341931097703487)Node20:0)Node4:0.1058973733340671,ZMU60508:0.01696789302960674)Node3:0.05975686204336134); 525s Tree actinTree2=(ZMU60513:0.01013471033128259,ZMU60514:0.02361992336180286,((((((ZMU60511:0.03958621037682149,ZMU60510:0.02871409626377734)Node8:0.0459917013426994,OSRAC2:0.1281527526633053)Node7:0.02274333471502154,(OSRAC1:0.04038736776829079,SVSOAC1:0.05533230239637962)Node12:0.09055757439546061)Node6:0.02100604348917753,((OSRAC3:0.108221164542607,ZMU60507:0.07346472812084469)Node16:0.05601779804320004,ZMU60509:0.1117227194511854)Node15:0.0291599894270592)Node5:0.04981252790522362,(MZEACT1G:0.1070039276414496,OSRAC7:0.09559155674444123)Node20:0.02268055914719592)Node4:0.04831150224458001,ZMU60508:0.02346330777492431)Node3:0.05651673682762296); 525s + for i in *.bf 525s + '[' -f HKY852blocks2models.bf ']' 525s + hyphy HKY852blocks2models.bf 525s 525s ----- RESULTS ----- 525s Log Likelihood = -6049.33413410755; 525s Tree actinTree1=(ZMU60513:0.01368111326830167,ZMU60514:0.06662165180548506,((((((ZMU60511:0.1014489610315025,ZMU60510:0.08940384587953119)Node8:0.2112347538259576,OSRAC2:0.3684206026894413)Node7:0.06392754822453442,(OSRAC1:0.04321367172357589,SVSOAC1:0.2447959878714145)Node12:0.4083947499795273)Node6:0.1002631510870106,((OSRAC3:0.1861737502599249,ZMU60507:0.3288459731518424)Node16:0.1590820363686745,ZMU60509:0.4442394027840464)Node15:0.04671167693415579)Node5:0.1895852966375731,(MZEACT1G:0.324493305604111,OSRAC7:0.247713489120728)Node20:0.009395678586464595)Node4:0.2662546000798074,ZMU60508:0.01033677340734289)Node3:0.223056294686429); 525s Tree actinTree2=(ZMU60513:0.004497206954537016,ZMU60514:0.004482860703023138,((((((ZMU60511:0.004483118612014198,ZMU60510:0.005992290361288377)Node8:0.004873742452637385,OSRAC2:0.04746326688188292)Node7:0.003177747582480156,(OSRAC1:0.01210015672457146,SVSOAC1:0.007446821280902099)Node12:0.02730445498714606)Node6:0,((OSRAC3:0.04645835124091833,ZMU60507:0.009174262025148719)Node16:0.0104545219968459,ZMU60509:0.02448226894659258)Node15:0)Node5:0.0192740564450552,(MZEACT1G:0.0338123940904346,OSRAC7:0.03062749757373966)Node20:0.006212161690449578)Node4:0.007802281177312584,ZMU60508:0.004488900142641823)Node3:0.01512222983434826); 525s + for i in *.bf 525s + '[' -f HKY85relrate.bf ']' 525s + hyphy HKY85relrate.bf 525s 525s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371751632424; 525s Tree threeTaxaTree=(a:0.08473003175317764,b:0.07473137597643539,c:0.174064542689109); 525s 525s 525s 1). Outgroup at taxon #1 525s a). Transition rate test. P-Value = 0.02098226516725465 525s Log Likelihood = -924.035884021378; 525s Tree threeTaxaTree=(a:0.08099123330674669,b:0.1064970277501439,c:0.1431287422547734); 525s 525s b). Transversion rate test. P-Value = 0.03655174813200768 525s Log Likelihood = -923.55733986013; 525s Tree threeTaxaTree=(a:0.084385863180111,b:0.09108496720824998,c:0.1577932370277693); 525s 525s c). Both rates test. P-Value = 0.00632399828374719 525s Log Likelihood = -926.435155263498; 525s Tree threeTaxaTree=(a:0.08054167256686441,b:0.1248197388549912,c:0.1248197388549912); 525s 525s 525s 2). Outgroup at taxon #2 525s a). Transition rate test. P-Value = 0.02758028958440228 525s Log Likelihood = -923.798808189923; 525s Tree threeTaxaTree=(a:0.1157945362947561,b:0.0710231672763683,c:0.1442792954111021); 525s 525s b). Transversion rate test. P-Value = 0.1106456954857765 525s Log Likelihood = -922.644238896077; 525s Tree threeTaxaTree=(a:0.09762132520456517,b:0.07463527366174004,c:0.1608971533992973); 525s 525s c). Both rates test. P-Value = 0.02199500082285188 525s Log Likelihood = -925.188691719246; 525s Tree threeTaxaTree=(a:0.1299135255623827,b:0.07078650465677661,c:0.1299135255623827); 525s 525s 525s 3). Outgroup at taxon #3 525s a). Transition rate test. P-Value = 0.9291732773304646 525s Log Likelihood = -921.37570190709; 525s Tree threeTaxaTree=(a:0.08354358737958395,b:0.07588180027038632,c:0.1740455829900139); 525s 525s b). Transversion rate test. P-Value = 0.5919879178907992 525s Log Likelihood = -921.515376857668; 525s Tree threeTaxaTree=(a:0.08115157531975309,b:0.07834973653854679,c:0.1740031943295483); 525s 525s c). Both rates test. P-Value = 0.8615417030144421 525s Log Likelihood = -921.520783449156; 525s Tree threeTaxaTree=(a:0.07974273880137919,b:0.07974273880137919,c:0.1740977261800018); 525s 525s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78442604578; 525s Tree fourTaxaTree1=((1:0.113791381333629,2:0.1109812084398387)Node1:0.1041142737713125,3:0.3523124007351069,4:0.3312024761326549); 525s Tree fourTaxaTree2=((1:0.08607518432405536,2:0.09347854528016543)Node1:0.08034238812430958,3:0.3860171002678663,4:0.3896629274258822); 525s 525s 525s 1). Relative ratio constraint on transitions; the P-value is:0.5738619496010586 525s Log Likelihood = -2541.23688270234; 525s Global Parameters: 525s R=0.857859886787587; 525s 525s Tree fourTaxaTree1=((1:0.1086802469370478,2:0.09422126334199116)Node1:0.1116166730257614,3:0.3552433767353616,4:0.3552103925067623); 525s Tree fourTaxaTree2=((1:0.09038010622587356,2:0.1091768128240128)Node1:0.07302607950862043,3:0.3839597771249044,4:0.3656457444895455); 525s 525s 525s 2). Relative ratio constraint on transversions; the P-value is:0.5738586713323656 525s Log Likelihood = -2541.23689234809; 525s Global Parameters: 525s R=0.8583181346135639; 525s 525s Tree fourTaxaTree1=((1:0.108676326355565,2:0.09420490762588636)Node1:0.1115472480453758,3:0.3552507058813295,4:0.3551641378526289); 525s Tree fourTaxaTree2=((1:0.0903829267380851,2:0.1092126253201284)Node1:0.07300223899624374,3:0.383998103571856,4:0.3657564835059527); 525s 525s 525s 3). Relative ratio constraint on both rates; the P-value is:+ for i in *.bf 525s + '[' -f HKY85relratio.bf ']' 525s + hyphy HKY85relratio.bf 525s + for i in *.bf 525s 0.656593458642062 525s Log Likelihood = -2543.19086899059; 525s Global Parameters: 525s R=0.99658305319929; 525s 525s Tree fourTaxaTree1=((1:0.1004912977418655,2:0.1007192360110612)Node1:0.09258175841483439,3:0.3715174282866335,4:0.3582233653223759); 525s Tree fourTaxaTree2=((1:0.1003311983863386,2:0.1007179506033033)Node1:0.09288090482056402,3:0.369982009902517,4:0.357712490363656); 525s + '[' -f HKY85shared.bf ']' 525s + hyphy HKY85shared.bf 525s Log Likelihood = -1165.7030112399; 525s Global Parameters: 525s R=2.970525480369322; 525s 525s Tree givenTree=(256:0.01208775874240385,(822:0.02960969242842239,159:0.004651935922381986)Node2:0.003524627730247529,((113:0.02180311146506052,9939:0.07941957840856706)Node6:0.004908085031679929,(6760:0.07148879723071785,((317:0.03799252272507093,6767:0.07150930940338038)Node12:0.0117834581966,((135:0.02022927930934443,(529:0.03405040853159545,105r:0.01304700993554644)Node18:0.02630176943824726)Node16:0.005817018630508959,(719:0.02973913912309081,136:0.008132531372814212)Node21:0.04877233488388807)Node15:0.01555696820124204)Node11:0.01396229563682027)Node9:0.02325905690683486)Node5:0.02146761133354992); 525s + for i in *.bf 525s + '[' -f JC69.bf ']' 525s + hyphy JC69.bf 525s Log Likelihood = -1230.82014326801; 525s Tree givenTree=(256:0.01105783470408406,(822:0.0337163664527533,159:0)Node2:0.007429579934259283,((113:0.02424611426527905,9939:0.0725802651184263)Node6:0.005767383812149995,(6760:0.0638269405763779,((317:0.04028429666635566,6767:0.06818598123703087)Node12:0.01439273294250011,((135:0.02427386729192116,(529:0.03328088534022183,105r:0.01296513381563256)Node18:0.01987484261181434)Node16:0.003608131256170868,(719:0.02788390238543526,136:0.009958341228777826)Node21:0.05117020263783743)Node15:0.01669617026509551)Node11:0.008546699816280461)Node9:0.02628932634763947)Node5:0.02193532028282088); 525s + for i in *.bf 525s + '[' -f K2P.bf ']' 525s + hyphy K2P.bf 525s Log Likelihood = -1198.26189040159; 525s Tree givenTree=(256:0.01177097015287166,(822:0.0292650899352115,159:0.004288833282599508)Node2:0.003666744641530305,((113:0.02366847939011765,9939:0.07263930397311814)Node6:0.003381404331131326,(6760:0.06223848869678048,((317:0.04074705026017417,6767:0.06832244811213056)Node12:0.01244114821505695,((135:0.02259184656605941,(529:0.03395411437149459,105r:0.01240069418950374)Node18:0.02142029867404293)Node16:0.004488091670671351,(719:0.02880312688567206,136:0.00884059779211563)Node21:0.05082995288653029)Node15:0.01734727694991429)Node11:0.01111518474926427)Node9:0.02820676022923729)Node5:0.0237003714776299); 525s + for i in *.bf 525s + '[' -f K2Pshared.bf ']' 525s + hyphy K2Pshared.bf 526s Log Likelihood = -1210.49419565614; 526s Global Parameters: 526s R=2.61677690422922; 526s 526s Tree givenTree=(256:0.01222052600796084,(822:0.02897524902103144,159:0.0047767594921817)Node2:0.003546476214582444,((113:0.0237609213031269,9939:0.07494541521469669)Node6:0.005887499660027141,(6760:0.0649116523386828,((317:0.03971077642678172,6767:0.06949275831976666)Node12:0.01422847207035552,((135:0.02389757841610578,(529:0.03395152381109477,105r:0.01263083620870724)Node18:0.02071510112051736)Node16:0.003965724802892091,(719:0.02813630817803825,136:0.009504474950289998)Node21:0.05080950687447722)Node15:0.01659145578218263)Node11:0.008799324573365243)Node9:0.02626396108843616)Node5:0.02011706663646625); 526s + for i in *.bf 526s + '[' -f MatrixIndexing.bf ']' 526s + hyphy MatrixIndexing.bf 526s 526s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 526s { 526s {0.6943381670150762, 0.9613136646713395, 0.1176425386494125, 0.07397487738029446, 0.06781848801016306, 0.5989256267433347} 526s {0.1360333117507476, 0.6969314677866482, 0.3124612097890259, 0.2766227427117114, 0.8419344208300892, 0.3520154050439632} 526s {0.6832667974949038, 0.5518836920503256, 0.4964087336548624, 0.1180029716617435, 0.2048970291402417, 0.3698900941223582} 526s {0.194323426856269, 0.5372487370710002, 0.2695823792064521, 0.6047272036328742, 0.2323034736868701, 0.9338387253074532} 526s {0.6155396037771226, 0.0452265231975416, 0.9489772014666761, 0.918610378382404, 0.9069058750539333, 0.2611916971535402} 526s } 526s 526s 2). Accessing a second-row third-column element and a random element. 526s 526s matrix[1][2]=0.3124612097890259 526s matrix[0][1]=0.9613136646713395 526s 526s 3). Accessing the fourth row. 526s 526s matrix[3][-1]= 526s { 526s {0.194323426856269, 0.5372487370710002, 0.2695823792064521, 0.6047272036328742, 0.2323034736868701, 0.9338387253074532} 526s } 526s 526s 4). Accessing the first column. 526s 526s matrix[-1][0]= 526s { 526s {0.6943381670150762} 526s {0.1360333117507476} 526s {0.6832667974949038} 526s {0.194323426856269} 526s {0.6155396037771226} 526s } 526s 526s 5). Populating a matrix template (below the diagonal). 526s 526s { 526s {0, 0, 0, 0, 0, 0} 526s {1, 0, 0, 0, 0, 0} 526s {1, 1, 0, 0, 0, 0} 526s {1, 1, 1, 0, 0, 0} 526s {1, 1, 1, 1, 0, 0} 526s } 526s 526s 6). Extracting (by row) matrix elements using the template. 526s 526s { 526s {0.1360333117507476, 0.6832667974949038, 0.5518836920503256, 0.194323426856269, 0.5372487370710002, 0.2695823792064521, 0.6155396037771226, 0.0452265231975416, 0.9489772014666761, 0.918610378382404} 526s } 526s 526s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 526s 526s matrix[{{1,1}}][{{3,2}}]= 526s { 526s {0.6969314677866482, 0.3124612097890259} 526s {0.5518836920503256, 0.4964087336548624} 526s {0.5372487370710002, 0.2695823792064521} 526s } 526s 526s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 526s 526s 526s { 526s {0.4821054901738559, 1.924123961883841, 1.013839766899878, 1.00547228248343, 1.004599347315985, 1.358711906369896} 526s {0.01850506190587608, 0.4857134707912518, 1.097632007622822, 1.07652014178535, 1.708853568978498, 1.123914845388265} 526s {0.4668535165589419, 0.3045756095510986, 0.2464216308488242, 1.013924701321002, 1.041982792550497, 1.136818681729847} 526s {0.03776159422516372, 0.2886362054843847, 0.07267465917861135, 0.3656949908136358, 1.053964903886986, 1.872054764883849} 526s {0.378889003818097, 0.002045438400537768, 0.9005577289035244, 0.8438450272718635, 0.8224782662073404, 1.068221102661947} 526s } 526s + for i in *.bf 526s + '[' -f MolecularClockF81.bf ']' 526s + hyphy MolecularClockF81.bf 526s 526s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124421372; 526s Tree theTree=(HVRNASS:0.02574320256855454,(RICRSS3:0.05627851742798395,((ZMSUCS1:0.07161066928468893,(OSRSS1A:0.06059739725441392,(TASUCSYN1:0.02788097017899352,HVSSYNMR:0.02036991396821741)Internal1:0.05182308387639757)Node9:0.02015236147588837)Node7:0.1581547052281858,(MZESUS1:0.07665727571837029,ORRSS2:0.05437303153305795)Internal2:0.02506493312141303)Node6:0.03254782967988285)Node4:0.0590049435511152,TAAJ153:0.01372840481177689); 526s 526s 526s 1). Global Molecular Clock; the P-value is:0 526s Log Likelihood = -11927.6152937466; 526s Tree theTree=(HVRNASS:0.02157256088103099,(RICRSS3:0.1233391480781409,((ZMSUCS1:0.05658067598526034,(OSRSS1A:0.04751102722821727,(TASUCSYN1:0.01824592528706053,HVSSYNMR:0.01824592528706053)Internal1:0.02926510194115674)Node9:0.009069648757043065)Node7:0.05762932420162047,(MZESUS1:0.070145046522887,ORRSS2:0.070145046522887)Internal2:0.04406495366399382)Node6:0.009129147891260068)Node4:0.02715542687212286,TAAJ153:0.1504945749502637); 526s 526s 526s 2). Molecular Clock starting at Internal1; the P-value is:0.160379891009284 526s Log Likelihood = -11476.6977623965; 526s Tree theTree=(HVRNASS:0.02574689688442725,(RICRSS3:0.05630777906695299,((ZMSUCS1:0.07168624934650621,(OSRSS1A:0.06050389429618578,(TASUCSYN1:0.0241267525513656,HVSSYNMR:0.0241267525513656)Internal1:0.05180641472291372)Node9:0.02018289971100367)Node7:0.1580631123432984,(MZESUS1:0.0766028941295268,ORRSS2:0.05440238831432395)Internal2:0.02509210348024966)Node6:0.03252032609824578)Node4:0.0589636429523885,TAAJ153:0.01372136324106363); 526s 526s 526s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610191699969754 526s Log Likelihood = -11479.841259083; 526s Tree theTree=(HVRNASS:0.02577199241771832,(RICRSS3:0.05650887182451454,((ZMSUCS1:0.0714810651525935,(OSRSS1A:0.06062414664017753,(TASUCSYN1:0.02412281661282775,HVSSYNMR:0.02412281661282775)Internal1:0.05166917557584396)Node9:0.02036314585801411)Node7:0.1580479241645817,(MZESUS1:0.06553054667663613,ORRSS2:0.06553054667663613)Internal2:0.02502100766961171)Node6:0.03235796154953852)Node4:0.05873963987451332,TAAJ153:0.01369897485123984); 526s + for i in *.bf 526s + '[' -f MolecularClockHKY85.bf ']' 526s + hyphy MolecularClockHKY85.bf 526s 526s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013283038; 526s Tree theTree=(HVRNASS:0.02587743457443942,(RICRSS3:0.05729290966256458,((ZMSUCS1:0.07272534704665261,(OSRSS1A:0.06094885889423878,(TASUCSYN1:0.0274215052323902,HVSSYNMR:0.02081976368952715)Node11:0.05283851203645621)Node9:0.02050493694741961)Node7:0.1590019762384745,(MZESUS1:0.07762137158169617,ORRSS2:0.05413759348131894)Node14:0.02601795305008483)Node6:0.03166526586491966)Node4:0.06041305598989313,TAAJ153:0.01384598063765552); 526s 526s 526s 1). Global Molecular Clock on transition rates; the P-value is:0 526s Log Likelihood = -11434.7016033505; 526s Tree theTree=(HVRNASS:0.02319732345917447,(RICRSS3:0.08334082646277663,((ZMSUCS1:0.06367263689382201,(OSRSS1A:0.05485168593181718,(TASUCSYN1:0.02325513670224505,HVSSYNMR:0.01890603068464118)Node11:0.04016830271520158)Node9:0.01328536077718002)Node7:0.1273995968145573,(MZESUS1:0.07240242164513809,ORRSS2:0.06226501706007253)Node14:0.03460944097224466)Node6:0.02068820539812524)Node4:0.0389942521914492,TAAJ153:0.08890802688190375); 526s 526s 526s 2). Global Molecular Clock on transversion rates; the P-value is:0 526s Log Likelihood = -11497.3782660734; 526s Tree theTree=(HVRNASS:0.02484219884725461,(RICRSS3:0.0939784387095552,((ZMSUCS1:0.06898900865845495,(OSRSS1A:0.05467493181591331,(TASUCSYN1:0.02277422526430717,HVSSYNMR:0.02034279491478003)Node11:0.04373585743228762)Node9:0.01674146819493375)Node7:0.09973184816820219,(MZESUS1:0.07446982849634663,ORRSS2:0.06135118932081673)Node14:0.0338731330125675)Node6:0.02080002379937089)Node4:0.05008126778397642,TAAJ153:0.07306031345081865); 526s 526s 526s 3). Global Molecular Clock on both rates; the P-value is:0 526s Log Likelihood = -11703.6261633936; 526s Tree theTree=(HVRNASS:0.02209790524913105,(RICRSS3:0.1239838041625247,((ZMSUCS1:0.0580005191388791,(OSRSS1A:0.04854685895429329,(TASUCSYN1:0.01832952130566496,HVSSYNMR:0.01832952130566496)Node11:0.03021733764862832)Node9:0.009453660184585806)Node7:0.05732732377110523,(MZESUS1:0.07025388165506863,ORRSS2:0.07025388165506863)Node14:0.04507396125491571)Node6:0.008655961252540395)Node4:0.02800717113897166,TAAJ153:0.1519909753014964); 526s + for i in *.bf 526s + '[' -f Non-Rev.bf ']' 526s + hyphy Non-Rev.bf 526s Log Likelihood = -1152.78946406138; 526s Global Parameters: 526s GC=0.2667970727982397; 526s CG=0.1875554967277978; 526s GA=1.906089646433191; 526s CT=1.253873069192627; 526s GT=0.08497028984049242; 526s CA=0.9158397008997602; 526s AT=0.427916851911592; 526s AG=1.574270855478508; 526s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2515087514931346; 526s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.029734532161373; 526s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.8025832629524018; 526s 526s Tree givenTree=(256:0.01348467632020813,(822:0.02843366377441912,159:0.006109563897345608)Node2:0.003449508365948894,((113:0.02187115940820621,9939:0.07939695278804303)Node6:0.00498779785121619,(6760:0.07328803047961323,((317:0.04011284466746813,6767:0.06988625101569867)Node12:0.01160511108636972,((135:0.02156866759267965,(529:0.03499044586799199,105r:0.0142228633834453)Node18:0.02378932712297713)Node16:0.005236446475533178,(719:0.02864349773238617,136:0.00958016563097224)Node21:0.04931198942790867)Node15:0.01636750481678838)Node11:0.01271687842003792)Node9:0.02191655258283604)Node5:0.02022192271202969); 526s + for i in *.bf 526s + '[' -f PBootstrapHetRates.bf ']' 526s + hyphy PBootstrapHetRates.bf 527s 527s ----ORIGINAL DATA---- 527s Log Likelihood = -1127.31557906324; 527s Global Parameters: 527s alpha=0.3190248733457374; 527s kappa=0.3235517732929273; 527s 527s Tree givenTree=(256:0.012589830987996,(822:0.03175949780219962,159:0.00469347552655627)Node2:0.003782846707131159,((113:0.02292921028898077,9939:0.09719730242331615)Node6:0.001949131349452405,(6760:0.0871704992501887,((317:0.04571908016793932,6767:0.08110700587160141)Node12:0.007402728084840686,((135:0.01865010090284569,(529:0.03695329188471939,105r:0.01500500192167933)Node18:0.03034405155116922)Node16:0.007153931171057414,(719:0.03341020937608474,136:0.00716452472299578)Node21:0.05749354930129584)Node15:0.01788634937734265)Node11:0.01886065339054629)Node9:0.02368432633707689)Node5:0.02502472265536359); 527s 527s Using the seed: 527s 1711264009 527s Category variable name: TRUE 527s Site Rate 527s 0 0.00000 527s 1 0.00000 527s 2 0.00000 527s 3 0.00000 527s 4 0.00000 527s 5 0.00000 527s 6 0.00001 527s 7 0.00007 527s 8 0.00009 527s 9 0.00010 527s 10 0.00019 527s 11 0.00020 527s 12 0.00020 527s 13 0.00024 527s 14 0.00031 527s 15 0.00035 527s 16 0.00040 527s 17 0.00043 527s 18 0.00044 527s 19 0.00052 527s 20 0.00054 527s 21 0.00061 527s 22 0.00118 527s 23 0.00118 527s 24 0.00133 527s 25 0.00158 527s 26 0.00179 527s 27 0.00189 527s 28 0.00190 527s 29 0.00207 527s 30 0.00208 527s 31 0.00226 527s 32 0.00368 527s 33 0.00369 527s 34 0.00390 527s 35 0.00455 527s 36 0.00506 527s 37 0.00509 527s 38 0.00521 527s 39 0.00595 527s 40 0.00639 527s 41 0.00654 527s 42 0.00660 527s 43 0.00686 527s 44 0.00797 527s 45 0.00876 527s 46 0.00878 527s 47 0.00968 527s 48 0.01060 527s 49 0.01080 527s 50 0.01150 527s 51 0.01340 527s 52 0.01357 527s 53 0.01395 527s 54 0.01513 527s 55 0.01559 527s 56 0.01704 527s 57 0.01935 527s 58 0.02226 527s 59 0.02235 527s 60 0.02382 527s 61 0.02396 527s 62 0.02501 527s 63 0.02627 527s 64 0.02732 527s 65 0.02813 527s 66 0.02913 527s 67 0.02954 527s 68 0.02980 527s 69 0.03075 527s 70 0.03202 527s 71 0.03315 527s 72 0.03358 527s 73 0.03590 527s 74 0.03633 527s 75 0.03742 527s 76 0.03752 527s 77 0.03839 527s 78 0.04010 527s 79 0.04016 527s 80 0.04022 527s 81 0.04070 527s 82 0.04273 527s 83 0.04996 527s 84 0.05064 527s 85 0.05205 527s 86 0.05359 527s 87 0.05408 527s 88 0.06146 527s 89 0.06172 527s 90 0.06401 527s 91 0.06620 527s 92 0.06768 527s 93 0.07235 527s 94 0.08086 527s 95 0.08197 527s 96 0.08341 527s 97 0.08357 527s 98 0.08470 527s 99 0.08477 527s 100 0.08617 527s 101 0.08796 527s 102 0.08825 527s 103 0.09385 527s 104 0.10018 527s 105 0.10061 527s 106 0.10217 527s 107 0.10271 527s 108 0.10276 527s 109 0.10335 527s 110 0.10352 527s 111 0.10704 527s 112 0.10751 527s 113 0.11001 527s 114 0.11782 527s 115 0.12002 527s 116 0.12528 527s 117 0.12760 527s 118 0.12984 527s 119 0.13817 527s 120 0.13858 527s 121 0.14123 527s 122 0.14599 527s 123 0.14724 527s 124 0.15323 527s 125 0.16025 527s 126 0.16401 527s 127 0.16622 527s 128 0.16676 527s 129 0.16803 527s 130 0.17832 527s 131 0.18740 527s 132 0.19282 527s 133 0.20492 527s 134 0.20620 527s 135 0.22274 527s 136 0.22378 527s 137 0.22526 527s 138 0.22828 527s 139 0.23144 527s 140 0.23899 527s 141 0.26299 527s 142 0.26330 527s 143 0.26332 527s 144 0.26426 527s 145 0.27189 527s 146 0.31610 527s 147 0.31678 527s 148 0.32667 527s 149 0.34498 527s 150 0.34799 527s 151 0.36369 527s 152 0.38362 527s 153 0.38472 527s 154 0.40447 527s 155 0.43736 527s 156 0.45359 527s 157 0.46300 527s 158 0.48237 527s 159 0.49279 527s 160 0.51252 527s 161 0.51376 527s 162 0.53001 527s 163 0.54322 527s 164 0.56662 527s 165 0.57468 527s 166 0.57572 527s 167 0.60124 527s 168 0.60639 527s 169 0.61970 527s 170 0.62874 527s 171 0.62944 527s 172 0.63083 527s 173 0.65242 527s 174 0.65627 527s 175 0.67606 527s 176 0.68027 527s 177 0.70087 527s 178 0.70715 527s 179 0.75266 527s 180 0.77354 527s 181 0.77895 527s 182 0.78708 527s 183 0.79615 527s 184 0.80449 527s 185 0.84433 527s 186 0.85140 527s 187 0.85658 527s 188 0.86722 527s 189 0.87611 527s 190 0.90672 527s 191 0.91540 527s 192 0.91840 527s 193 0.93225 527s 194 0.93344 527s 195 0.95539 527s 196 0.95551 527s 197 1.01694 527s 198 1.02208 527s 199 1.04742 527s 200 1.05355 527s 201 1.08602 527s 202 1.10599 527s 203 1.10769 527s 204 1.10947 527s 205 1.14623 527s 206 1.17348 527s 207 1.19691 527s 208 1.22322 527s 209 1.26191 527s 210 1.26281 527s 211 1.26901 527s 212 1.29113 527s 213 1.29458 527s 214 1.33437 527s 215 1.33960 527s 216 1.34473 527s 217 1.39891 527s 218 1.40209 527s 219 1.40888 527s 220 1.41232 527s 221 1.45284 527s 222 1.46981 527s 223 1.47925 527s 224 1.58468 527s 225 1.58538 527s 226 1.65526 527s 227 1.71170 527s 228 1.72988 527s 229 1.86912 527s 230 1.88213 527s 231 2.10756 527s 232 2.11561 527s 233 2.11700 527s 234 2.11809 527s 235 2.14887 527s 236 2.18733 527s 237 2.20227 527s 238 2.23850 527s 239 2.25037 527s 240 2.27896 527s 241 2.28709 527s 242 2.29780 527s 243 2.32858 527s 244 2.38193 527s 245 2.39469 527s 246 2.49060 527s 247 2.52106 527s 248 2.52633 527s 249 2.59798 527s 250 2.61094 527s 251 2.71813 527s 252 2.89332 527s 253 2.91151 527s 254 2.91973 527s 255 3.34148 527s 256 3.66314 527s 257 3.74369 527s 258 3.74944 527s 259 3.76979 527s 260 3.96220 527s 261 4.04880 527s 262 4.27312 527s 263 4.75726 527s 264 5.43627 527s 265 5.56519 527s 266 6.51178 527s 267 7.34051 527s 268 7.87636 527s 269 8.76445 527s 270 8.95102 527s 271 9.52215 527s 272 11.37356 527s 527s Mean = 0.9239819201789559 527s Var = 2.684707439850206 (1/alpha) = 3.134551828240264 527s + for i in *.bf 527s + '[' -f REV.bf ']' 527s + hyphy REV.bf 527s Log Likelihood = -1100.00325191866; 527s Tree givenTree=(256:0.02246871715179021,(822:0.0186782583067158,159:0.01469055620687253)Node2:0.00378003874004391,((113:0.01829385684306101,9939:0.07804101277214386)Node6:0.007456156099842235,(6760:0.07113584789038471,((317:0.03719085081332714,6767:0.07206936832575188)Node12:0.01019125494234549,((135:0.02036489448782649,(529:0.03424009935519055,105r:0.01130058848081756)Node18:0.02851169018796876)Node16:0.006571254431245538,(719:0.02830812923415984,136:0.009595580145079382)Node21:0.04404095947014051)Node15:0.01655093339125076)Node11:0.01315864827904064)Node9:0.02915628788240542)Node5:0.00998042866583106); 527s + for i in *.bf 527s + '[' -f REVshared.bf ']' 527s + hyphy REVshared.bf 527s Log Likelihood = -1156.6254044555; 527s Global Parameters: 527s AT=0.3620866660397165; 527s GT=0.4597052642244015; 527s CG=0.2460538300724483; 527s AG=1.843832202866545; 527s CT=1.197638573724416; 527s 527s Tree givenTree=(256:0.01208257782001154,(822:0.02973749125990288,159:0.004672402948851907)Node2:0.003488309758806649,((113:0.02208109703794506,9939:0.07975698542765576)Node6:0.004708075668466313,(6760:0.07205502735911434,((317:0.03911304241188958,6767:0.07107177298532763)Node12:0.01083741204707386,((135:0.02050382102488421,(529:0.03438701642971406,105r:0.01467791478754357)Node18:0.02467635589712433)Node16:0.005560773143169295,(719:0.02873587757279733,136:0.009469214730691691)Node21:0.04910008433217519)Node15:0.01584221370372315)Node11:0.01426582961653043)Node9:0.02296726578976446)Node5:0.02144993076283973); 527s + for i in *.bf 527s + '[' -f ReplicateConstraint1.bf ']' 527s + hyphy ReplicateConstraint1.bf 527s 1).Unconstrained HKY85 527s 527s Log Likelihood = -1152.88; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.317.trvs 527s Parameter 2 : hivTree.317.trst 527s Parameter 3 : hivTree.6767.trvs 527s Parameter 4 : hivTree.6767.trst 527s Parameter 5 : hivTree.Node2.trvs 527s Parameter 6 : hivTree.Node2.trst 527s Parameter 7 : hivTree.135.trvs 527s Parameter 8 : hivTree.135.trst 527s Parameter 9 : hivTree.529.trvs 527s Parameter 10 : hivTree.529.trst 527s Parameter 11 : hivTree.105r.trvs 527s Parameter 12 : hivTree.105r.trst 527s Parameter 13 : hivTree.Node8.trvs 527s Parameter 14 : hivTree.Node8.trst 527s Parameter 15 : hivTree.iNode1.trvs 527s Parameter 16 : hivTree.iNode1.trst 527s Parameter 17 : hivTree.719.trvs 527s Parameter 18 : hivTree.719.trst 527s Parameter 19 : hivTree.136.trvs 527s Parameter 20 : hivTree.136.trst 527s Parameter 21 : hivTree.Node11.trvs 527s Parameter 22 : hivTree.Node11.trst 527s Parameter 23 : hivTree.Node5.trvs 527s Parameter 24 : hivTree.Node5.trst 527s Parameter 25 : hivTree.Node1.trvs 527s Parameter 26 : hivTree.Node1.trst 527s Parameter 27 : hivTree.6760.trvs 527s Parameter 28 : hivTree.6760.trst 527s Parameter 29 : hivTree.113.trvs 527s Parameter 30 : hivTree.113.trst 527s Parameter 31 : hivTree.9939.trvs 527s Parameter 32 : hivTree.9939.trst 527s Parameter 33 : hivTree.Node16.trvs 527s Parameter 34 : hivTree.Node16.trst 527s Parameter 35 : hivTree.256.trvs 527s Parameter 36 : hivTree.256.trst 527s Parameter 37 : hivTree.822.trvs 527s Parameter 38 : hivTree.822.trst 527s Parameter 39 : hivTree.159.trvs 527s Parameter 40 : hivTree.159.trst 527s Parameter 41 : hivTree.Node21.trvs 527s Parameter 42 : hivTree.Node21.trst 527s Parameter 43 : hivTree.iNode2.trvs 527s Parameter 44 : hivTree.iNode2.trst 527s Parameter 45 : hivTree.Node15.trvs 527s Parameter 46 : hivTree.Node15.trst 527s 527s 2).HKY85 constrained to F81 527s 527s Log Likelihood = -1187.55; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.317.trvs 527s Parameter 2 : hivTree.6767.trvs 527s Parameter 3 : hivTree.Node2.trvs 527s Parameter 4 : hivTree.135.trvs 527s Parameter 5 : hivTree.529.trvs 527s Parameter 6 : hivTree.105r.trvs 527s Parameter 7 : hivTree.Node8.trvs 527s Parameter 8 : hivTree.iNode1.trvs 527s Parameter 9 : hivTree.719.trvs 527s Parameter 10 : hivTree.136.trvs 527s Parameter 11 : hivTree.Node11.trvs 527s Parameter 12 : hivTree.Node5.trvs 527s Parameter 13 : hivTree.Node1.trvs 527s Parameter 14 : hivTree.6760.trvs 527s Parameter 15 : hivTree.113.trvs 527s Parameter 16 : hivTree.9939.trvs 527s Parameter 17 : hivTree.Node16.trvs 527s Parameter 18 : hivTree.256.trvs 527s Parameter 19 : hivTree.822.trvs 527s Parameter 20 : hivTree.159.trvs 527s Parameter 21 : hivTree.Node21.trvs 527s Parameter 22 : hivTree.iNode2.trvs 527s Parameter 23 : hivTree.Node15.trvs 527s 527s Constrained Parameters List 527s 527s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 527s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 527s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 527s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 527s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 527s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 527s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 527s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 527s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 527s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 527s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 527s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 527s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 527s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 527s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 527s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 527s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 527s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 527s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 527s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 527s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 527s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 527s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 527s 527s 3).HKY85 constrained to F81 on internal branches 527s 527s Log Likelihood = -1167.99; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.Node2.trvs 527s Parameter 2 : hivTree.Node8.trvs 527s Parameter 3 : hivTree.iNode1.trvs 527s Parameter 4 : hivTree.Node11.trvs 527s Parameter 5 : hivTree.Node5.trvs 527s Parameter 6 : hivTree.Node1.trvs 527s Parameter 7 : hivTree.Node16.trvs 527s Parameter 8 : hivTree.Node21.trvs 527s Parameter 9 : hivTree.iNode2.trvs 527s Parameter 10 : hivTree.Node15.trvs 527s Parameter 11 : hivTree.317.trst 527s Parameter 12 : hivTree.317.trvs 527s Parameter 13 : hivTree.6767.trvs 527s Parameter 14 : hivTree.6767.trst 527s Parameter 15 : hivTree.135.trst 527s Parameter 16 : hivTree.135.trvs 527s Parameter 17 : hivTree.529.trvs 527s Parameter 18 : hivTree.529.trst 527s Parameter 19 : hivTree.105r.trst 527s Parameter 20 : hivTree.105r.trvs 527s Parameter 21 : hivTree.719.trvs 527s Parameter 22 : hivTree.719.trst 527s Parameter 23 : hivTree.136.trvs 527s Parameter 24 : hivTree.136.trst 527s Parameter 25 : hivTree.6760.trvs 527s Parameter 26 : hivTree.6760.trst 527s Parameter 27 : hivTree.113.trvs 527s Parameter 28 : hivTree.113.trst 527s Parameter 29 : hivTree.9939.trst 527s Parameter 30 : hivTree.9939.trvs 527s Parameter 31 : hivTree.256.trvs 527s Parameter 32 : hivTree.256.trst 527s Parameter 33 : hivTree.822.trvs 527s Parameter 34 : hivTree.822.trst 527s Parameter 35 : hivTree.159.trst 527s Parameter 36 : hivTree.159.trvs 527s 527s Constrained Parameters List 527s 527s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 527s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 527s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 527s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 527s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 527s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 527s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 527s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 527s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 527s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 527s 527s 4).HKY85 with shared ratio. 527s 527s Log Likelihood = -1165.7; 527s 527s Independent Parameters List 527s 527s Parameter 1 : R 527s Parameter 2 : hivTree.317.trst 527s Parameter 3 : hivTree.6767.trst 527s Parameter 4 : hivTree.Node2.trst 527s Parameter 5 : hivTree.135.trst 527s Parameter 6 : hivTree.529.trst 527s Parameter 7 : hivTree.105r.trst 527s Parameter 8 : hivTree.Node8.trst 527s Parameter 9 : hivTree.iNode1.trst 527s Parameter 10 : hivTree.719.trst 527s Parameter 11 : hivTree.136.trst 527s Parameter 12 : hivTree.Node11.trst 527s Parameter 13 : hivTree.Node5.trst 527s Parameter 14 : hivTree.Node1.trst 527s Parameter 15 : hivTree.6760.trst 527s Parameter 16 : hivTree.113.trst 527s Parameter 17 : hivTree.9939.trst 527s Parameter 18 : hivTree.Node16.trst 527s Parameter 19 : hivTree.256.trst 527s Parameter 20 : hivTree.822.trst 527s Parameter 21 : hivTree.159.trst 527s Parameter 22 : hivTree.Node21.trst 527s Parameter 23 : hivTree.iNode2.trst 527s Parameter 24 : hivTree.Node15.trst 527s 527s Constrained Parameters List 527s 527s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 527s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 527s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 527s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 527s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 527s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 527s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 527s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 527s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 527s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 527s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 527s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 527s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 527s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 527s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 527s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 527s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 527s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 527s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 527s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 527s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 527s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 527s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 527s + '[' -f ReplicateConstraint2.bf ']' 527s + hyphy ReplicateConstraint2.bf 527s 1).Unconstrained HKY85 527s 527s Log Likelihood = -1152.88; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.317.trvs 527s Parameter 2 : hivTree.317.trst 527s Parameter 3 : hivTree.6767.trvs 527s Parameter 4 : hivTree.6767.trst 527s Parameter 5 : hivTree.Node2.trvs 527s Parameter 6 : hivTree.Node2.trst 527s Parameter 7 : hivTree.135.trvs 527s Parameter 8 : hivTree.135.trst 527s Parameter 9 : hivTree.529.trvs 527s Parameter 10 : hivTree.529.trst 527s Parameter 11 : hivTree.105r.trvs 527s Parameter 12 : hivTree.105r.trst 527s Parameter 13 : hivTree.Node8.trvs 527s Parameter 14 : hivTree.Node8.trst 527s Parameter 15 : hivTree.iNode1.trvs 527s Parameter 16 : hivTree.iNode1.trst 527s Parameter 17 : hivTree.719.trvs 527s Parameter 18 : hivTree.719.trst 527s Parameter 19 : hivTree.136.trvs 527s Parameter 20 : hivTree.136.trst 527s Parameter 21 : hivTree.Node11.trvs 527s Parameter 22 : hivTree.Node11.trst 527s Parameter 23 : hivTree.Node5.trvs 527s Parameter 24 : hivTree.Node5.trst 527s Parameter 25 : hivTree.Node1.trvs 527s Parameter 26 : hivTree.Node1.trst 527s Parameter 27 : hivTree.6760.trvs 527s Parameter 28 : hivTree.6760.trst 527s Parameter 29 : hivTree.113.trvs 527s Parameter 30 : hivTree.113.trst 527s Parameter 31 : hivTree.9939.trvs 527s Parameter 32 : hivTree.9939.trst 527s Parameter 33 : hivTree.Node16.trvs 527s Parameter 34 : hivTree.Node16.trst 527s Parameter 35 : hivTree.256.trvs 527s Parameter 36 : hivTree.256.trst 527s Parameter 37 : hivTree.822.trvs 527s Parameter 38 : hivTree.822.trst 527s Parameter 39 : hivTree.159.trvs 527s Parameter 40 : hivTree.159.trst 527s Parameter 41 : hivTree.Node21.trvs 527s Parameter 42 : hivTree.Node21.trst 527s Parameter 43 : hivTree.iNode2.trvs 527s Parameter 44 : hivTree.iNode2.trst 527s Parameter 45 : hivTree.Node15.trvs 527s Parameter 46 : hivTree.Node15.trst 527s 527s 2).HKY85 constrained to F81 on the "iNode1" subtree 527s 527s Log Likelihood = -1157.82; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.135.trvs 527s Parameter 2 : hivTree.529.trvs 527s Parameter 3 : hivTree.105r.trvs 527s Parameter 4 : hivTree.Node8.trvs 527s Parameter 5 : hivTree.317.trvs 527s Parameter 6 : hivTree.317.trst 527s Parameter 7 : hivTree.6767.trst 527s Parameter 8 : hivTree.6767.trvs 527s Parameter 9 : hivTree.Node2.trst 527s Parameter 10 : hivTree.Node2.trvs 527s Parameter 11 : hivTree.iNode1.trvs 527s Parameter 12 : hivTree.iNode1.trst 527s Parameter 13 : hivTree.719.trvs 527s Parameter 14 : hivTree.719.trst 527s Parameter 15 : hivTree.136.trvs 527s Parameter 16 : hivTree.136.trst 527s Parameter 17 : hivTree.Node11.trvs 527s Parameter 18 : hivTree.Node11.trst 527s Parameter 19 : hivTree.Node5.trvs 527s Parameter 20 : hivTree.Node5.trst 527s Parameter 21 : hivTree.Node1.trvs 527s Parameter 22 : hivTree.Node1.trst 527s Parameter 23 : hivTree.6760.trvs 527s Parameter 24 : hivTree.6760.trst 527s Parameter 25 : hivTree.113.trvs 527s Parameter 26 : hivTree.113.trst 527s Parameter 27 : hivTree.9939.trvs 527s Parameter 28 : hivTree.9939.trst 527s Parameter 29 : hivTree.Node16.trvs 527s Parameter 30 : hivTree.Node16.trst 527s Parameter 31 : hivTree.256.trvs 527s Parameter 32 : hivTree.256.trst 527s Parameter 33 : hivTree.822.trvs 527s Parameter 34 : hivTree.822.trst 527s Parameter 35 : hivTree.159.trvs 527s Parameter 36 : hivTree.159.trst 527s Parameter 37 : hivTree.Node21.trvs 527s Parameter 38 : hivTree.Node21.trst 527s Parameter 39 : hivTree.iNode2.trvs 527s Parameter 40 : hivTree.iNode2.trst 527s Parameter 41 : hivTree.Node15.trvs 527s Parameter 42 : hivTree.Node15.trst 527s 527s Constrained Parameters List 527s 527s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 527s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 527s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 527s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 527s 527s 3).HKY85 constrained to F81 on the "iNode1" branch 527s 527s Log Likelihood = -1152.88; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.317.trvs 527s Parameter 2 : hivTree.317.trst 527s Parameter 3 : hivTree.6767.trvs 527s Parameter 4 : hivTree.6767.trst 527s Parameter 5 : hivTree.Node2.trvs 527s Parameter 6 : hivTree.Node2.trst 527s Parameter 7 : hivTree.135.trvs 527s Parameter 8 : hivTree.135.trst 527s Parameter 9 : hivTree.529.trvs 527s Parameter 10 : hivTree.529.trst 527s Parameter 11 : hivTree.105r.trvs 527s Parameter 12 : hivTree.105r.trst 527s Parameter 13 : hivTree.Node8.trvs 527s Parameter 14 : hivTree.Node8.trst 527s Parameter 15 : hivTree.iNode1.trvs 527s Parameter 16 : hivTree.iNode1.trst 527s Parameter 17 : hivTree.719.trvs 527s Parameter 18 : hivTree.719.trst 527s Parameter 19 : hivTree.136.trvs 527s Parameter 20 : hivTree.136.trst 527s Parameter 21 : hivTree.Node11.trvs 527s Parameter 22 : hivTree.Node11.trst 527s Parameter 23 : hivTree.Node5.trvs 527s Parameter 24 : hivTree.Node5.trst 527s Parameter 25 : hivTree.Node1.trvs 527s Parameter 26 : hivTree.Node1.trst 527s Parameter 27 : hivTree.6760.trvs 527s Parameter 28 : hivTree.6760.trst 527s Parameter 29 : hivTree.113.trvs 527s Parameter 30 : hivTree.113.trst 527s Parameter 31 : hivTree.9939.trvs 527s Parameter 32 : hivTree.9939.trst 527s Parameter 33 : hivTree.Node16.trvs 527s Parameter 34 : hivTree.Node16.trst 527s Parameter 35 : hivTree.256.trvs 527s Parameter 36 : hivTree.256.trst 527s Parameter 37 : hivTree.822.trvs 527s Parameter 38 : hivTree.822.trst 527s Parameter 39 : hivTree.159.trvs 527s Parameter 40 : hivTree.159.trst 527s Parameter 41 : hivTree.Node21.trvs 527s Parameter 42 : hivTree.Node21.trst 527s Parameter 43 : hivTree.iNode2.trvs 527s Parameter 44 : hivTree.iNode2.trst 527s Parameter 45 : hivTree.Node15.trvs 527s Parameter 46 : hivTree.Node15.trst 527s 527s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 527s 527s Log Likelihood = -1152.88; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.317.trvs 527s Parameter 2 : hivTree.317.trst 527s Parameter 3 : hivTree.6767.trvs 527s Parameter 4 : hivTree.6767.trst 527s Parameter 5 : hivTree.Node2.trvs 527s Parameter 6 : hivTree.Node2.trst 527s Parameter 7 : hivTree.135.trvs 527s Parameter 8 : hivTree.135.trst 527s Parameter 9 : hivTree.529.trvs 527s Parameter 10 : hivTree.529.trst 527s Parameter 11 : hivTree.105r.trvs 527s Parameter 12 : hivTree.105r.trst 527s Parameter 13 : hivTree.Node8.trvs 527s Parameter 14 : hivTree.Node8.trst 527s Parameter 15 : hivTree.iNode1.trvs 527s Parameter 16 : hivTree.iNode1.trst 527s Parameter 17 : hivTree.719.trvs 527s Parameter 18 : hivTree.719.trst 527s Parameter 19 : hivTree.136.trvs 527s Parameter 20 : hivTree.136.trst 527s Parameter 21 : hivTree.Node11.trvs 527s Parameter 22 : hivTree.Node11.trst 527s Parameter 23 : hivTree.Node5.trvs 527s Parameter 24 : hivTree.Node5.trst 527s Parameter 25 : hivTree.Node1.trvs 527s Parameter 26 : hivTree.Node1.trst 527s Parameter 27 : hivTree.6760.trvs 527s Parameter 28 : hivTree.6760.trst 527s Parameter 29 : hivTree.113.trvs 527s Parameter 30 : hivTree.113.trst 527s Parameter 31 : hivTree.9939.trvs 527s Parameter 32 : hivTree.9939.trst 527s Parameter 33 : hivTree.Node16.trvs 527s Parameter 34 : hivTree.Node16.trst 527s Parameter 35 : hivTree.256.trvs 527s Parameter 36 : hivTree.256.trst 527s Parameter 37 : hivTree.822.trvs 527s Parameter 38 : hivTree.822.trst 527s Parameter 39 : hivTree.159.trvs 527s Parameter 40 : hivTree.159.trst 527s Parameter 41 : hivTree.Node21.trvs 527s Parameter 42 : hivTree.Node21.trst 527s Parameter 43 : hivTree.iNode2.trvs 527s Parameter 44 : hivTree.iNode2.trst 527s Parameter 45 : hivTree.Node15.trvs 527s Parameter 46 : hivTree.Node15.trst 527s 527s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 527s 527s Log Likelihood = -1152.88; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.317.trvs 527s Parameter 2 : hivTree.317.trst 527s Parameter 3 : hivTree.6767.trvs 527s Parameter 4 : hivTree.6767.trst 527s Parameter 5 : hivTree.Node2.trvs 527s Parameter 6 : hivTree.Node2.trst 527s Parameter 7 : hivTree.135.trvs 527s Parameter 8 : hivTree.135.trst 527s Parameter 9 : hivTree.529.trvs 527s Parameter 10 : hivTree.529.trst 527s Parameter 11 : hivTree.105r.trvs 527s Parameter 12 : hivTree.105r.trst 527s Parameter 13 : hivTree.Node8.trvs 527s Parameter 14 : hivTree.Node8.trst 527s Parameter 15 : hivTree.iNode1.trvs 527s Parameter 16 : hivTree.iNode1.trst 527s Parameter 17 : hivTree.719.trvs 527s Parameter 18 : hivTree.719.trst 527s Parameter 19 : hivTree.136.trvs 527s Parameter 20 : hivTree.136.trst 527s Parameter 21 : hivTree.Node11.trvs 527s Parameter 22 : hivTree.Node11.trst 527s Parameter 23 : hivTree.Node5.trvs 527s Parameter 24 : hivTree.Node5.trst 527s Parameter 25 : hivTree.Node1.trvs 527s Parameter 26 : hivTree.Node1.trst 527s Parameter 27 : hivTree.6760.trvs 527s Parameter 28 : hivTree.6760.trst 527s Parameter 29 : hivTree.113.trvs 527s Parameter 30 : hivTree.113.trst 527s Parameter 31 : hivTree.9939.trvs 527s Parameter 32 : hivTree.9939.trst 527s Parameter 33 : hivTree.Node16.trvs 527s Parameter 34 : hivTree.Node16.trst 527s Parameter 35 : hivTree.256.trvs 527s Parameter 36 : hivTree.256.trst 527s Parameter 37 : hivTree.822.trvs 527s Parameter 38 : hivTree.822.trst 527s Parameter 39 : hivTree.159.trvs 527s Parameter 40 : hivTree.159.trst 527s Parameter 41 : hivTree.Node21.trvs 527s Parameter 42 : hivTree.Node21.trst 527s Parameter 43 : hivTree.iNode2.trvs 527s Parameter 44 : hivTree.iNode2.trst 527s Parameter 45 : hivTree.Node15.trvs 527s Parameter 46 : hivTree.Node15.trst 527s 527s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 527s 527s Log Likelihood = -1157.82; 527s 527s Independent Parameters List 527s 527s Parameter 1 : hivTree.135.trst 527s Parameter 2 : hivTree.529.trst 527s Parameter 3 : hivTree.105r.trst 527s Parameter 4 : hivTree.Node8.trst 527s Parameter 5 : hivTree.317.trvs 527s Parameter 6 : hivTree.317.trst 527s Parameter 7 : hivTree.6767.trst 527s Parameter 8 : hivTree.6767.trvs 527s Parameter 9 : hivTree.Node2.trst 527s Parameter 10 : hivTree.Node2.trvs 527s Parameter 11 : hivTree.iNode1.trvs 527s Parameter 12 : hivTree.iNode1.trst 527s Parameter 13 : hivTree.719.trvs 527s Parameter 14 : hivTree.719.trst 527s Parameter 15 : hivTree.136.trvs 527s Parameter 16 : hivTree.136.trst 527s Parameter 17 : hivTree.Node11.trvs 527s Parameter 18 : hivTree.Node11.trst 527s Parameter 19 : hivTree.Node5.trvs 527s Parameter 20 : hivTree.Node5.trst 527s Parameter 21 : hivTree.Node1.trvs 527s Parameter 22 : hivTree.Node1.trst 527s Parameter 23 : hivTree.6760.trvs 527s Parameter 24 : hivTree.6760.trst 527s Parameter 25 : hivTree.113.trvs 527s Parameter 26 : hivTree.113.trst 527s Parameter 27 : hivTree.9939.trvs 527s Parameter 28 : hivTree.9939.trst 527s Parameter 29 : hivTree.Node16.trvs 527s Parameter 30 : hivTree.Node16.trst 527s Parameter 31 : hivTree.256.trvs 527s Parameter 32 : hivTree.256.trst 527s Parameter 33 : hivTree.822.trvs 527s Parameter 34 : hivTree.822.trst 527s Parameter 35 : hivTree.159.trvs 527s Parameter 36 : hivTree.159.trst 527s Parameter 37 : hivTree.Node21.trvs 527s Parameter 38 : hivTree.Node21.trst 527s Parameter 39 : hivTree.iNode2.trvs 527s Parameter 40 : hivTree.iNode2.trst 527s Parameter 41 : hivTree.Node15.trvs 527s Parameter 42 : hivTree.Node15.trst 527s 527s Constrained Parameters List 527s 527s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 527s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 527s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 527s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 527s + '[' -f aa.bf ']' 527s + hyphy aa.bf 527s Log Likelihood = -1134.73158903811; 527s Tree theTree=(((Langur:0.07430929885972404,Baboon:0.03832849634012803)Node2:0.0233919252843166,Human:0.05949976654865775)Node1:0.0200665584749996,Rat:0.2458809231757731,(Cow:0.2552868234106432,Horse:0.5627637317168085)Node7:0.07060308955953205); 527s + for i in *.bf 527s + '[' -f definitions2.bf ']' 527s + hyphy definitions2.bf 527s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 527s 527s Sample by MEAN: 527s 527s Sample mean = 0.5 (sample variance = 0.2450374540764348) 527s 527s Rate[0]= 0.06847689 (weight=0.2500000) 527s Rate[1]= 0.23837593 (weight=0.2500000) 527s Rate[2]= 0.50000000 (weight=0.2500000) 527s Rate[3]= 1.19314718 (weight=0.2500000) 527s ------------------------------------------------ 527s 527s Sample by MEDIAN: 527s 527s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 527s 527s Rate[0]= 0.06676570 (weight=0.2500000) 527s Rate[1]= 0.23500181 (weight=0.2500000) 527s Rate[2]= 0.49041463 (weight=0.2500000) 527s Rate[3]= 1.03972077 (weight=0.2500000) 527s ------------------------------------------------ 527s 527s Sample by SCALED_MEDIAN: 527s 527s Sample mean = 0.5 (sample variance = 0.2154404122636025) 527s 527s Rate[0]= 0.07289218 (weight=0.2500000) 527s Rate[1]= 0.25656580 (weight=0.2500000) 527s Rate[2]= 0.53541552 (weight=0.2500000) 527s Rate[3]= 1.13512650 (weight=0.2500000) 527s ------------------------------------------------ 527s 527s Sample by MEAN (numerical averaging): 527s 527s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 527s 527s Rate[0]= 0.06846096 (weight=0.2500000) 527s Rate[1]= 0.23834015 (weight=0.2500000) 527s Rate[2]= 0.49996411 (weight=0.2500000) 527s Rate[3]= 1.19314889 (weight=0.2500000) 527s ------------------------------------------------ 527s 527s Sample by MEAN (numerical CDF and averaging): 527s 527s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 527s 527s Rate[0]= 0.06849282 (weight=0.2500000) 527s Rate[1]= 0.23835613 (weight=0.2500000) 527s Rate[2]= 0.49994751 (weight=0.2500000) 527s Rate[3]= 1.19311765 (weight=0.2500000) 527s ------------------------------------------------ 527s 2). Equiprobable rates sampled from Exponential with lambda = 2 527s 527s Sample by MEDIAN (3 rate classes): 527s 527s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 527s 527s Rate[0]= 0.09116078 (weight=0.3333333) 527s Rate[1]= 0.34657359 (weight=0.3333333) 527s Rate[2]= 0.89587973 (weight=0.3333333) 527s ------------------------------------------------ 527s 527s Sample by MEDIAN (9 rate classes): 527s 527s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 527s 527s Rate[0]= 0.02857921 (weight=0.1111111) 527s Rate[1]= 0.09116078 (weight=0.1111111) 527s Rate[2]= 0.16271120 (weight=0.1111111) 527s Rate[3]= 0.24623824 (weight=0.1111111) 527s Rate[4]= 0.34657359 (weight=0.1111111) 527s Rate[5]= 0.47223080 (weight=0.1111111) 527s Rate[6]= 0.64046692 (weight=0.1111111) 527s Rate[7]= 0.89587973 (weight=0.1111111) 527s Rate[8]= 1.44518588 (weight=0.1111111) 527s ------------------------------------------------ 527s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 527s 527s Sample by MEAN (10 rate classes): 527s 527s Sample mean = 1 (sample variance = 0.1057310289486733) 527s 527s Rate[0]= 0.52447499 (weight=0.1000000) 527s Rate[1]= 0.67866972 (weight=0.1000000) 527s Rate[2]= 0.77209919 (weight=0.1000000) 527s Rate[3]= 0.85214884 (weight=0.1000000) 527s Rate[4]= 0.92850815 (weight=0.1000000) 527s Rate[5]= 1.00664500 (weight=0.1000000) 527s Rate[6]= 1.09192933 (weight=0.1000000) 527s Rate[7]= 1.19267960 (weight=0.1000000) 527s Rate[8]= 1.32858029 (weight=0.1000000) 527s Rate[9]= 1.62426489 (weight=0.1000000) 527s ------------------------------------------------ 527s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 527s 527s Sample by MEAN (10 rate classes): 527s 527s Sample mean = 2 (sample variance = 0.04259071282256012) 527s 527s Rate[0]= 1.66431246 (weight=0.1000000) 527s Rate[1]= 1.79212822 (weight=0.1000000) 527s Rate[2]= 1.86123411 (weight=0.1000000) 527s Rate[3]= 1.91722052 (weight=0.1000000) 527s Rate[4]= 1.96832799 (weight=0.1000000) 527s Rate[5]= 2.01862937 (weight=0.1000000) 527s Rate[6]= 2.07152664 (weight=0.1000000) 527s Rate[7]= 2.13166629 (weight=0.1000000) 527s Rate[8]= 2.20930216 (weight=0.1000000) 527s Rate[9]= 2.36565224 (weight=0.1000000) 527s ------------------------------------------------ 527s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 527s 527s Sample by MEAN (8 rate classes): 527s 527s Sample mean = 0.5 (sample variance = 0.09375000225643569) 527s 527s Rate[0]= 0.06250000 (weight=0.1250000) 527s Rate[1]= 0.18750000 (weight=0.1250000) 527s Rate[2]= 0.31250001 (weight=0.1250000) 527s Rate[3]= 0.43750001 (weight=0.1250000) 527s Rate[4]= 0.56249993 (weight=0.1250000) 527s Rate[5]= 0.68750001 (weight=0.1250000) 527s Rate[6]= 0.81250002 (weight=0.1250000) 527s Rate[7]= 0.93750002 (weight=0.1250000) 527s ------------------------------------------------ 527s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 527s 527s Sample by MEAN (8 rate classes): 527s 527s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 527s 527s Rate[0]= 2.17658588 (weight=0.1250000) 527s Rate[1]= 2.55230783 (weight=0.1250000) 527s Rate[2]= 2.75432532 (weight=0.1250000) 527s Rate[3]= 2.92101185 (weight=0.1250000) 527s Rate[4]= 3.07898815 (weight=0.1250000) 527s Rate[5]= 3.24567468 (weight=0.1250000) 527s Rate[6]= 3.44769217 (weight=0.1250000) 527s Rate[7]= 3.82341415 (weight=0.1250000) 527s ------------------------------------------------ 527s 527s 527s Sample mean = 1 (sample variance = 0.9920002887656187) 527s 527s Rate[0]= 0.05175536 (weight=0.1000000) 527s Rate[1]= 0.16309623 (weight=0.1000000) 527s Rate[2]= 0.28842380 (weight=0.1000000) 527s Rate[3]= 0.43177086 (weight=0.1000000) 527s Rate[4]= 0.59921784 (weight=0.1000000) 527s Rate[5]= 0.80057298 (weight=0.1000000) 527s Rate[6]= 1.05324451 (weight=0.1000000) 527s Rate[7]= 1.39304259 (weight=0.1000000) 527s Rate[8]= 1.91629073 (weight=0.1000000) 527s Rate[9]= 3.30258509 (weight=0.1000000) 527s ------------------------------------------------ 527s + for i in *.bf 527s + '[' -f definitions3.bf ']' 527s + hyphy definitions3.bf 527s + for i in *.bf 527s + '[' -f displayFunction.bf ']' 527s + hyphy displayFunction.bf 527s + for i in *.bf 527s + '[' -f profile_test.bf ']' 527s + hyphy profile_test.bf 528s 528s Total run time (seconds) : 0.000000 528s Total number of steps : 1500005 528s 528s 1 : s=0; 528s Call count: 1 528s Time (seconds): 1.7e-11 528s 2 : m={5,1};+ for i in *.bf 528s + '[' -f shared.bf ']' 528s 528s Call count: 1 528s Time (seconds): 1.8e-11 528s 3 : k=0; 528s Call count: 1 528s Time (seconds): 3e-12 528s 4 : Branch under condition 'k<250000' 528s to 528s s=s+k; 528s else 528s #profilePAUSE, ; 528s Call count: 250001 528s Time (seconds): 4.185600000002102e-08 528s 5 : s=s+k; 528s Call count: 250000 528s Time (seconds): 6.669300000004589e-08 528s 6 : t=Random(0,5); 528s Call count: 250000 528s Time (seconds): 4.760900000002654e-08 528s 7 : m[t]=m[t]+1; 528s Call count: 250000 528s Time (seconds): 1.469840000001256e-07 528s 8 : k=k+1; 528s Call count: 250000 528s Time (seconds): 6.650200000004552e-08 528s 9 : Go to step 4 528s Call count: 250000 528s Time (seconds): 1.388599999999625e-08 528s 10 : #profilePAUSE, ; 528s Call count: 1 528s Time (seconds): 1e-12 528s + hyphy shared.bf 528s + rm -f '*messages.log*' '*errors.log*' 528s autopkgtest [06:40:33]: test run-unit-tests: -----------------------] 529s run-unit-tests PASS 529s autopkgtest [06:40:34]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 529s autopkgtest [06:40:34]: @@@@@@@@@@@@@@@@@@@@ summary 529s run-unit-tests PASS 550s Creating nova instance adt-noble-ppc64el-hyphy-20240324-063145-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...