0s autopkgtest [14:51:32]: starting date and time: 2024-03-16 14:51:32+0000 0s autopkgtest [14:51:32]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [14:51:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hdmrfhni/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:hyphy,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openmpi,src:pmix --apt-upgrade hyphy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=hyphy/2.5.59+dfsg-1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openmpi/4.1.6-6ubuntu1 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-4.secgroup --name adt-noble-arm64-hyphy-20240316-145132-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 108s autopkgtest [14:53:20]: testbed dpkg architecture: arm64 108s autopkgtest [14:53:20]: testbed apt version: 2.7.12 108s autopkgtest [14:53:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 110s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 110s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 111s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 111s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3690 kB] 111s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 111s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 111s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 111s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 111s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 111s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4007 kB] 111s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 111s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.8 kB] 111s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 117s Fetched 9093 kB in 3s (2996 kB/s) 118s Reading package lists... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 124s Calculating upgrade... 125s The following packages have been kept back: 125s curl 125s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 127s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 127s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 131s Reading package lists... 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s Calculating upgrade... 134s The following packages have been kept back: 134s curl 134s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 139s autopkgtest [14:53:51]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 139s autopkgtest [14:53:51]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 143s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (dsc) [2417 B] 143s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (tar) [2613 kB] 143s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (diff) [17.2 kB] 144s gpgv: Signature made Sat Mar 16 06:59:46 2024 UTC 144s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 144s gpgv: issuer "steve.langasek@ubuntu.com" 144s gpgv: Can't check signature: No public key 144s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.59+dfsg-1build2.dsc: no acceptable signature found 144s autopkgtest [14:53:56]: testing package hyphy version 2.5.59+dfsg-1build2 145s autopkgtest [14:53:57]: build not needed 202s autopkgtest [14:54:54]: test run-unit-tests: preparing testbed 204s Reading package lists... 204s Building dependency tree... 204s Reading state information... 205s Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 206s Done 207s The following additional packages will be installed: 207s curl hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 libatomic1 207s libcurl3t64-gnutls libcurl4t64 libdrm-amdgpu1 libevent-pthreads-2.1-7 207s libfabric1 libgnutls30t64 libgomp1 libhogweed6t64 libhsa-runtime64-1 207s libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 libmunge2 libnettle8t64 207s libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 librdmacm1t64 libssl3t64 207s libucx0 libxnvctrl0 ocl-icd-libopencl1 207s Suggested packages: 207s gnutls-bin opencl-icd 207s The following packages will be REMOVED: 207s libcurl3-gnutls libcurl4 libgnutls30 libhogweed6 libnettle8 libpsl5 libssl3 207s The following NEW packages will be installed: 207s autopkgtest-satdep hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 207s libamdhip64-5 libatomic1 libcurl3t64-gnutls libcurl4t64 libdrm-amdgpu1 207s libevent-pthreads-2.1-7 libfabric1 libgnutls30t64 libgomp1 libhogweed6t64 207s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 207s libmunge2 libnettle8t64 libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 207s librdmacm1t64 libssl3t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 207s The following packages will be upgraded: 207s curl 207s 1 upgraded, 31 newly installed, 7 to remove and 0 not upgraded. 207s Need to get 57.0 MB/57.0 MB of archives. 207s After this operation, 233 MB of additional disk space will be used. 207s Get:1 /tmp/autopkgtest.GZD1aa/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 207s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnettle8t64 arm64 3.9.1-2.2 [192 kB] 208s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhogweed6t64 arm64 3.9.1-2.2 [199 kB] 208s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu2 [1042 kB] 208s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 208s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 208s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 208s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 208s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl3t64-gnutls arm64 8.5.0-2ubuntu7 [327 kB] 208s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 hyphy-common all 2.5.59+dfsg-1build2 [624 kB] 208s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 208s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 208s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 208s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 208s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 208s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 208s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 208s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 208s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 208s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 208s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 208s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libpmix2t64 arm64 5.0.1-4.1 [655 kB] 208s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 209s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 209s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 209s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 209s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 209s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 209s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 209s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmpi3t64 arm64 4.1.6-6ubuntu1 [2463 kB] 209s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 hyphy-mpi arm64 2.5.59+dfsg-1build2 [1199 kB] 209s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 hyphy-pt arm64 2.5.59+dfsg-1build2 [1162 kB] 210s Fetched 57.0 MB in 2s (27.6 MB/s) 210s dpkg: libhogweed6:arm64: dependency problems, but removing anyway as you requested: 210s librtmp1:arm64 depends on libhogweed6. 210s libjcat1:arm64 depends on libhogweed6. 210s libgnutls30:arm64 depends on libhogweed6 (>= 3.6). 210s 211s (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 ... 75850 files and directories currently installed.) 211s Removing libhogweed6:arm64 (3.9.1-2) ... 211s dpkg: libnettle8:arm64: dependency problems, but removing anyway as you requested: 211s librtmp1:arm64 depends on libnettle8. 211s libgnutls30:arm64 depends on libnettle8 (>= 3.9~). 211s libcurl3-gnutls:arm64 depends on libnettle8. 211s libarchive13:arm64 depends on libnettle8. 211s 211s Removing libnettle8:arm64 (3.9.1-2) ... 211s Selecting previously unselected package libnettle8t64:arm64. 211s (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 ... 75838 files and directories currently installed.) 211s Preparing to unpack .../libnettle8t64_3.9.1-2.2_arm64.deb ... 211s Unpacking libnettle8t64:arm64 (3.9.1-2.2) ... 211s Selecting previously unselected package libhogweed6t64:arm64. 211s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_arm64.deb ... 211s Unpacking libhogweed6t64:arm64 (3.9.1-2.2) ... 211s dpkg: libgnutls30:arm64: dependency problems, but removing anyway as you requested: 211s u-boot-tools depends on libgnutls30 (>= 3.7.3). 211s librtmp1:arm64 depends on libgnutls30 (>= 3.7.2). 211s libldap2:arm64 depends on libgnutls30 (>= 3.8.2). 211s libjcat1:arm64 depends on libgnutls30 (>= 3.7.3). 211s libcurl3-gnutls:arm64 depends on libgnutls30 (>= 3.8.2). 211s fwupd depends on libgnutls30 (>= 3.7.3). 211s dirmngr depends on libgnutls30 (>= 3.8.1). 211s apt depends on libgnutls30 (>= 3.8.1). 211s 211s (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 ... 75852 files and directories currently installed.) 211s Removing libgnutls30:arm64 (3.8.3-1ubuntu1) ... 211s Selecting previously unselected package libgnutls30t64:arm64. 211s (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 ... 75843 files and directories currently installed.) 211s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_arm64.deb ... 211s Unpacking libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ... 212s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 212s wget depends on libssl3 (>= 3.0.0). 212s u-boot-tools depends on libssl3 (>= 3.0.0). 212s tnftp depends on libssl3 (>= 3.0.0). 212s tcpdump depends on libssl3 (>= 3.0.0). 212s systemd-resolved depends on libssl3 (>= 3.0.0). 212s systemd depends on libssl3 (>= 3.0.0). 212s sudo depends on libssl3 (>= 3.0.0). 212s sbsigntool depends on libssl3 (>= 3.0.0). 212s rsync depends on libssl3 (>= 3.0.0). 212s python3-cryptography depends on libssl3 (>= 3.0.0). 212s openssl depends on libssl3 (>= 3.0.9). 212s openssh-server depends on libssl3 (>= 3.0.10). 212s openssh-client depends on libssl3 (>= 3.0.10). 212s mtd-utils depends on libssl3 (>= 3.0.0). 212s mokutil depends on libssl3 (>= 3.0.0). 212s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 212s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 212s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 212s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 212s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 212s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 212s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 212s libnvme1 depends on libssl3 (>= 3.0.0). 212s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 212s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 212s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 212s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 212s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 212s kmod depends on libssl3 (>= 3.0.0). 212s dhcpcd-base depends on libssl3 (>= 3.0.0). 212s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 212s 212s (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 ... 75871 files and directories currently installed.) 212s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 212s Selecting previously unselected package libssl3t64:arm64. 212s (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 ... 75860 files and directories currently installed.) 212s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 212s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 212s dpkg: libcurl4:arm64: dependency problems, but removing anyway as you requested: 212s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 212s 212s (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 ... 75873 files and directories currently installed.) 212s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 212s Selecting previously unselected package libcurl4t64:arm64. 212s (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 ... 75868 files and directories currently installed.) 212s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 212s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 213s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 213s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 213s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 213s wget depends on libpsl5 (>= 0.16.0). 213s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 213s 213s (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 ... 75874 files and directories currently installed.) 213s Removing libpsl5:arm64 (0.21.2-1build1) ... 213s Selecting previously unselected package libpsl5t64:arm64. 213s (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 ... 75869 files and directories currently installed.) 213s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 213s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 213s dpkg: libcurl3-gnutls:arm64: dependency problems, but removing anyway as you requested: 213s libfwupd2:arm64 depends on libcurl3-gnutls (>= 7.63.0). 213s fwupd depends on libcurl3-gnutls (>= 7.63.0). 213s 213s (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 ... 75875 files and directories currently installed.) 213s Removing libcurl3-gnutls:arm64 (8.5.0-2ubuntu2) ... 213s Selecting previously unselected package libcurl3t64-gnutls:arm64. 213s (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 ... 75868 files and directories currently installed.) 213s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu7_arm64.deb ... 213s Unpacking libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu7) ... 213s Selecting previously unselected package hyphy-common. 213s Preparing to unpack .../01-hyphy-common_2.5.59+dfsg-1build2_all.deb ... 213s Unpacking hyphy-common (2.5.59+dfsg-1build2) ... 214s Selecting previously unselected package libgomp1:arm64. 214s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 214s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 214s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 214s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 214s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 214s Selecting previously unselected package libatomic1:arm64. 214s Preparing to unpack .../04-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 214s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 214s Selecting previously unselected package librdmacm1t64:arm64. 214s Preparing to unpack .../05-librdmacm1t64_50.0-2_arm64.deb ... 214s Unpacking librdmacm1t64:arm64 (50.0-2) ... 214s Selecting previously unselected package libfabric1:arm64. 214s Preparing to unpack .../06-libfabric1_1.17.0-3_arm64.deb ... 214s Unpacking libfabric1:arm64 (1.17.0-3) ... 214s Selecting previously unselected package libhwloc15:arm64. 214s Preparing to unpack .../07-libhwloc15_2.10.0-1_arm64.deb ... 214s Unpacking libhwloc15:arm64 (2.10.0-1) ... 214s Selecting previously unselected package libmunge2:arm64. 214s Preparing to unpack .../08-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 214s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 214s Selecting previously unselected package libpciaccess0:arm64. 214s Preparing to unpack .../09-libpciaccess0_0.17-3_arm64.deb ... 214s Unpacking libpciaccess0:arm64 (0.17-3) ... 214s Selecting previously unselected package libxnvctrl0:arm64. 214s Preparing to unpack .../10-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 214s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 214s Selecting previously unselected package ocl-icd-libopencl1:arm64. 214s Preparing to unpack .../11-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 214s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 215s Selecting previously unselected package libhwloc-plugins:arm64. 215s Preparing to unpack .../12-libhwloc-plugins_2.10.0-1_arm64.deb ... 215s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 215s Selecting previously unselected package libpmix2t64:arm64. 215s Preparing to unpack .../13-libpmix2t64_5.0.1-4.1_arm64.deb ... 215s Unpacking libpmix2t64:arm64 (5.0.1-4.1) ... 215s Selecting previously unselected package libllvm17:arm64. 215s Preparing to unpack .../14-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 215s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 216s Selecting previously unselected package libamd-comgr2:arm64. 216s Preparing to unpack .../15-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 216s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 217s Selecting previously unselected package libdrm-amdgpu1:arm64. 217s Preparing to unpack .../16-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 217s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 217s Selecting previously unselected package libhsakmt1:arm64. 217s Preparing to unpack .../17-libhsakmt1_5.7.0-1_arm64.deb ... 217s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 217s Selecting previously unselected package libhsa-runtime64-1. 217s Preparing to unpack .../18-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 217s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 218s Selecting previously unselected package libamdhip64-5. 218s Preparing to unpack .../19-libamdhip64-5_5.2.3-12_arm64.deb ... 218s Unpacking libamdhip64-5 (5.2.3-12) ... 218s Selecting previously unselected package libucx0:arm64. 218s Preparing to unpack .../20-libucx0_1.16.0+ds-4_arm64.deb ... 218s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 218s Selecting previously unselected package libopenmpi3t64:arm64. 218s Preparing to unpack .../21-libopenmpi3t64_4.1.6-6ubuntu1_arm64.deb ... 218s Unpacking libopenmpi3t64:arm64 (4.1.6-6ubuntu1) ... 218s Selecting previously unselected package hyphy-mpi. 218s Preparing to unpack .../22-hyphy-mpi_2.5.59+dfsg-1build2_arm64.deb ... 218s Unpacking hyphy-mpi (2.5.59+dfsg-1build2) ... 218s Selecting previously unselected package hyphy-pt. 218s Preparing to unpack .../23-hyphy-pt_2.5.59+dfsg-1build2_arm64.deb ... 218s Unpacking hyphy-pt (2.5.59+dfsg-1build2) ... 219s Selecting previously unselected package autopkgtest-satdep. 219s Preparing to unpack .../24-1-autopkgtest-satdep.deb ... 219s Unpacking autopkgtest-satdep (0) ... 219s Setting up libpciaccess0:arm64 (0.17-3) ... 219s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 219s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 219s Setting up hyphy-common (2.5.59+dfsg-1build2) ... 219s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 219s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 219s Setting up libnettle8t64:arm64 (3.9.1-2.2) ... 219s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 219s Setting up libhwloc15:arm64 (2.10.0-1) ... 219s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 219s Setting up libhogweed6t64:arm64 (3.9.1-2.2) ... 219s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 219s Setting up librdmacm1t64:arm64 (50.0-2) ... 219s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 219s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 219s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 219s Setting up libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ... 219s Setting up libfabric1:arm64 (1.17.0-3) ... 219s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 219s Setting up libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu7) ... 219s Setting up hyphy-pt (2.5.59+dfsg-1build2) ... 219s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 219s Setting up libpmix2t64:arm64 (5.0.1-4.1) ... 219s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 219s Setting up curl (8.5.0-2ubuntu7) ... 219s Setting up libhsakmt1:arm64 (5.7.0-1) ... 219s Setting up libhsa-runtime64-1 (5.7.1-1) ... 219s Setting up libamdhip64-5 (5.2.3-12) ... 219s Setting up libucx0:arm64 (1.16.0+ds-4) ... 219s Setting up libopenmpi3t64:arm64 (4.1.6-6ubuntu1) ... 219s Setting up hyphy-mpi (2.5.59+dfsg-1build2) ... 219s Setting up autopkgtest-satdep (0) ... 219s Processing triggers for man-db (2.12.0-3) ... 220s Processing triggers for libc-bin (2.39-0ubuntu2) ... 227s (Reading database ... 76782 files and directories currently installed.) 227s Removing autopkgtest-satdep (0) ... 228s autopkgtest [14:55:20]: test run-unit-tests: [----------------------- 229s + for i in *.bf 229s + '[' -f ExonIntron.bf ']' 229s + hyphy ExonIntron.bf 230s Log Likelihood = -1113.34523093823; 230s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134922377013523,(ZMUBIS27F:0,(ZMU29160:0.05439434205555755,ZMU29161:0.0397099920707908)Node8:0.01201941603219406)Node6:0)Node4:0.024593255793118,BLYMUB1:0.01185775856148526); 230s Tree exon2Tree=(BLYMUB2:0.03542711161011008,(RICRMA630:0.02935212298046051,(ZMUBIS27F:0.0754561862717683,(ZMU29160:0.09103007688546581,ZMU29161:0.02595054789089673)Node8:0.01157422438148664)Node6:0.04928335134660832)Node4:0.0293070179401226,BLYMUB1:0.02204339668689216); 230s Tree intronTree=(BLYMUB2:0.03120148427034726,(RICRMA630:0.04155588440025249,(ZMUBIS27F:0.02044499908430787,(ZMU29160:0.02069042212081659,ZMU29161:0.01019776647832744)Node8:0.02068976996248074)Node6:0)Node4:0,BLYMUB1:0.01036597515885792); 230s + for i in *.bf 230s + '[' -f F81.bf ']' 230s + hyphy F81.bf 230s Log Likelihood = -1187.54702793755; 230s Tree givenTree=(256:0.01194350383198776,(822:0.02944830535067936,159:0.004470566641478981)Node2:0.003648416798768103,((113:0.02244746421090052,9939:0.07632907795011984)Node6:0.005077663434270926,(6760:0.06903113887339882,((317:0.03751818003606587,6767:0.07086144053643872)Node12:0.01229344910542729,((135:0.0204561966689408,(529:0.03338016202897984,105r:0.01322045242403323)Node18:0.02586876285451697)Node16:0.005414274244521212,(719:0.02965902532867767,136:0.00823423126564937)Node21:0.04882998609564283)Node15:0.01525962444960303)Node11:0.01379933321924546)Node9:0.02422268145877303)Node5:0.02148378325227054); 230s + for i in *.bf 230s + '[' -f F81relrate.bf ']' 230s + hyphy F81relrate.bf 230s 230s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.00100141847; 230s Tree threeTaxaTree=(a:0.08501458078571071,b:0.0733761302676995,c:0.1653894108755128); 230s 230s 230s 1). With the outgroup at taxon #1, the P-value is:0.002155106158012732 230s Log Likelihood = -948.707253867895; 230s Tree threeTaxaTree=(a:0.08228741139559752,b:0.1194507598364935,c:0.1194507598364935); 230s 230s 230s 2). With the outgroup at taxon #2, the P-value is:0.008353404406027276 230s Log Likelihood = -947.479050125031; 230s Tree threeTaxaTree=(a:0.1250762650865298,b:0.07125949231018089,c:0.1250762650865298); 230s 230s 230s 3). With the outgroup at taxon #3, the P-value is:0.6669137051109912 230s Log Likelihood = -944.093618166809; 230s Tree threeTaxaTree=(a:0.07922730021537434,b:0.07922730021537434,c:0.1653339858408152); 230s + for i in *.bf 230s + '[' -f F81relratio.bf ']' 230s + hyphy F81relratio.bf 230s 230s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.6305958295; 230s Tree fourTaxaTree1=((1:0.1129104492125219,2:0.1073439047614921)Node1:0.09978717865825038,3:0.3469443599499342,4:0.3219019510192432); 230s Tree fourTaxaTree2=((1:0.08585820917628031,2:0.09338078540397989)Node1:0.0736417066106991,3:0.3933121047170701,4:0.3801923094565385); 230s 230s 230s 1). Relative ratio constraint; the P-value is:0.6933531573039489 230s Log Likelihood = -2575.74610909373; 230s Global Parameters: 230s R=1.007290880092107; 230s 230s Tree fourTaxaTree1=((1:0.0994836464016693,2:0.09943037069217289)Node1:0.0869682969122717,3:0.3687236014963378,4:0.3489177341828117); 230s Tree fourTaxaTree2=((1:0.1000737390781421,2:0.100020147360868)Node1:0.08748415411040895,3:0.3709107056562232,4:0.3509873587601161); 230s + for i in *.bf 230s + '[' -f HKY85.bf ']' 230s + hyphy HKY85.bf 230s Log Likelihood = -1152.88077759984; 230s Tree givenTree=(256:0.01162288667782179,(822:0.02979925771976042,159:0.004015138877223606)Node2:0.003749807242919053,((113:0.02130516453029382,9939:0.0778595684461199)Node6:0.004320575954985553,(6760:0.07315569451374035,((317:0.03809378462441171,6767:0.07101548352042635)Node12:0.006276166945365902,((135:0.01788116181775997,(529:0.0325778241649983,105r:0.01514141560707552)Node18:0.02833952512606345)Node16:0.007921523942608337,(719:0.02987633065012513,136:0.008041687755300973)Node21:0.0485931478377624)Node15:0.01599220240534575)Node11:0.01658008402363219)Node9:0.0266563505744944)Node5:0.02296365216628453); 230s + for i in *.bf 230s + '[' -f HKY852blocks.bf ']' 230s + hyphy HKY852blocks.bf 231s 231s ----- RESULTS ----- 231s Log Likelihood = -6801.91483914271; 231s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050213079878777,((((((ZMU60511:0.0103964390210716,ZMU60510:0.02378493210091168)Node8:0.08350026384022306,OSRAC2:0.1885441289425745)Node7:0.05846032966993056,(OSRAC1:0.01535047106336434,SVSOAC1:0.07341796996529404)Node12:0.07285957830769609)Node6:0,((OSRAC3:0.07326281403030475,ZMU60507:0.06501886193980418)Node16:0.07966506413955368,ZMU60509:0.12889876402029)Node15:0.001337061339439503)Node5:0.08259949396484567,(MZEACT1G:0.1142070205924238,OSRAC7:0.03425239723740178)Node20:0)Node4:0.105904092604038,ZMU60508:0.01701208383807174)Node3:0.05972259836120912); 231s Tree actinTree2=(ZMU60513:0.01013433247873647,ZMU60514:0.02362266936808758,((((((ZMU60511:0.03959926850963617,ZMU60510:0.02870478512134468)Node8:0.04599109182442013,OSRAC2:0.1281540501826964)Node7:0.02274865176629471,(OSRAC1:0.04039890987490254,SVSOAC1:0.0553286130063774)Node12:0.0905395571679606)Node6:0.02100488746729546,((OSRAC3:0.1082126627070749,ZMU60507:0.07345368472804116)Node16:0.05601401247636992,ZMU60509:0.1117304891545221)Node15:0.02915321876146179)Node5:0.04980904638864664,(MZEACT1G:0.1070193486175715,OSRAC7:0.09559226343698206)Node20:0.02269013920069791)Node4:0.04831903334853681,ZMU60508:0.02346472825105576)Node3:0.05650090551461232); 231s + for i in *.bf 231s + '[' -f HKY852blocks2models.bf ']' 231s + hyphy HKY852blocks2models.bf 231s 231s ----- RESULTS ----- 231s Log Likelihood = -6049.33430509219; 231s Tree actinTree1=(ZMU60513:0.01368065835946704,ZMU60514:0.06662560144432099,((((((ZMU60511:0.1014698393343548,ZMU60510:0.08941869435591956)Node8:0.2110383153534773,OSRAC2:0.3684369266868493)Node7:0.06393319699898629,(OSRAC1:0.04344267527694522,SVSOAC1:0.2445300038759274)Node12:0.4077968913614998)Node6:0.1004066359203368,((OSRAC3:0.1861632105151208,ZMU60507:0.3287949285775706)Node16:0.1592030395019906,ZMU60509:0.4442382581177137)Node15:0.04671926403427797)Node5:0.1895203615491486,(MZEACT1G:0.3244981794276043,OSRAC7:0.2477753232924249)Node20:0.009414964421613197)Node4:0.2663190361503114,ZMU60508:0.01033901940751635)Node3:0.2230500126676203); 231s Tree actinTree2=(ZMU60513:0.004498640605527752,ZMU60514:0.004482898757018348,((((((ZMU60511:0.004483072442852635,ZMU60510:0.005993388586689664)Node8:0.004874092480403656,OSRAC2:0.04744636325973004)Node7:0.003178294515027827,(OSRAC1:0.01209268208445469,SVSOAC1:0.007445167231502748)Node12:0.02729855311737739)Node6:0,((OSRAC3:0.04642967638294117,ZMU60507:0.009175845755993344)Node16:0.01045215429481289,ZMU60509:0.0244781963857302)Node15:0)Node5:0.01926914288035394,(MZEACT1G:0.03379329078628768,OSRAC7:0.03062841308654933)Node20:0.006213356233780941)Node4:0.007801168753207949,ZMU60508:0.004487784516264148)Node3:0.015116075995397); 231s + for i in *.bf 231s + '[' -f HKY85relrate.bf ']' 231s + hyphy HKY85relrate.bf 231s 231s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371751632041; 231s Tree threeTaxaTree=(a:0.08473003191111293,b:0.07473137624491773,c:0.1740645452720764); 231s 231s 231s 1). Outgroup at taxon #1 231s a). Transition rate test. P-Value = 0.02098226517412549 231s + for i in *.bf 231s + '[' -f HKY85relratio.bf ']' 231s + hyphy HKY85relratio.bf 231s Log Likelihood = -924.03588402071; 231s Tree threeTaxaTree=(a:0.08099122821686185,b:0.1064970285402011,c:0.1431287318444799); 231s 231s b). Transversion rate test. P-Value = 0.03655174810897788 231s Log Likelihood = -923.557339860284; 231s Tree threeTaxaTree=(a:0.08438586068793587,b:0.09108496737387296,c:0.157793239649387); 231s 231s c). Both rates test. P-Value = 0.006323998283663035 231s Log Likelihood = -926.435155263128; 231s Tree threeTaxaTree=(a:0.08054168133397031,b:0.1248197487342514,c:0.1248197487342514); 231s 231s 231s 2). Outgroup at taxon #2 231s a). Transition rate test. P-Value = 0.02758028957244585 231s Log Likelihood = -923.798808189913; 231s Tree threeTaxaTree=(a:0.1157945381968907,b:0.07102316558833002,c:0.1442792954664215); 231s 231s b). Transversion rate test. P-Value = 0.1106456954879589 231s Log Likelihood = -922.644238895678; 231s Tree threeTaxaTree=(a:0.09762132950835234,b:0.07463526436014642,c:0.160897156664404); 231s 231s c). Both rates test. P-Value = 0.0219950008118095 231s Log Likelihood = -925.188691719365; 231s Tree threeTaxaTree=(a:0.1299135243067527,b:0.07078650482744393,c:0.1299135243067527); 231s 231s 231s 3). Outgroup at taxon #3 231s a). Transition rate test. P-Value = 0.9291732747688928 231s Log Likelihood = -921.375701906994; 231s Tree threeTaxaTree=(a:0.08354359190419325,b:0.07588179938172648,c:0.1740455814250527); 231s 231s b). Transversion rate test. P-Value = 0.5919879226055667 231s Log Likelihood = -921.515376853629; 231s Tree threeTaxaTree=(a:0.08115158798052034,b:0.07834975239261983,c:0.1740032070467013); 231s 231s c). Both rates test. P-Value = 0.8615417053068671 231s Log Likelihood = -921.520783446112; 231s Tree threeTaxaTree=(a:0.07974274672476114,b:0.07974274672476114,c:0.174097726933251); 231s 231s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78444360881; 231s Tree fourTaxaTree1=((1:0.1138486705938774,2:0.1110122462972651)Node1:0.104102842106571,3:0.3524784878138216,4:0.3311404413991695); 231s Tree fourTaxaTree2=((1:0.0860597386392196,2:0.09356343941933419)Node1:0.08032201490231416,3:0.3858914607428712,4:0.3896179276135943); 231s 231s 231s 1). Relative ratio constraint on transitions; the P-value is:0.5738662884098752 231s Log Likelihood = -2541.23688749921; 231s Global Parameters: 231s R=0.8575284325133654; 231s 231s Tree fourTaxaTree1=((1:0.1086649864354847,2:0.09424031379397739)Node1:0.111620122827603,3:0.3553976425639594,4:0.3553083906830451); 231s Tree fourTaxaTree2=((1:0.09036354678634317,2:0.1091988683375492)Node1:0.07301594252847129,3:0.3837981988164835,4:0.3656297801660289); 231s 231s 231s 2). Relative ratio constraint on transversions; the P-value is:0.5738627516274089 231s Log Likelihood = -2541.23689790555; 231s Global Parameters: 231s R=0.85825951450135; 231s 231s Tree fourTaxaTree1=((1:0.1086625191715241,2:0.09426238845211039)Node1:0.1116480307060316,3:0.3552777897755875,4:0.3552083160672975); 231s Tree fourTaxaTree2=((1:0.09039762776903866,2:0.1092537393704408)Node1:0.07309817242646641,3:0.3840137782019722,4:0.3657793455039087); 231s 231s 231s 3). Relative ratio constraint on both rates; the P-value is:0.6565969025918279 231s Log Likelihood = -2543.19086999415; 231s Global Parameters: 231s R=0.9964954639800966; 231s 231s Tree fourTaxaTree1=((1:0.1004904775311104,2:0.1007304508148404)Node1:0.09257492961864017,3:0.3715249546720786,4:0.3582649192759509); 231s Tree fourTaxaTree2=((1:0.1003215762759256,2:0.1007202855739472)Node1:0.09286598060944462,3:0.3699568886876284,4:0.357722170418195); 231s + for i in *.bf 231s + '[' -f HKY85shared.bf ']' 231s + hyphy HKY85shared.bf 231s Log Likelihood = -1165.70301127147; 231s Global Parameters: 231s R=2.970524885533917; 231s 231s Tree givenTree=(256:0.01208775338325542,(822:0.02960968859585506,159:0.004651897379088246)Node2:0.003524577290327657,((113:0.0218031141251108,9939:0.0794195761547906)Node6:0.004908086009945949,(6760:0.07148879456878611,((317:0.03799252030357465,6767:0.07150930824234027)Node12:0.01178345206858378,((135:0.02022927720301946,(529:0.03405040173466748,105r:0.01304699573961813)Node18:0.02630176613069551)Node16:0.005817017418013274,(719:0.02973913964285991,136:0.008132530317728802)Node21:0.04877233392933042)Node15:0.01555697405185011)Node11:0.01396228297512418)Node9:0.02325904761636235)Node5:0.02146761028962216); 231s + for i in *.bf 231s + '[' -f JC69.bf ']' 231s + hyphy JC69.bf 231s Log Likelihood = -1227.45123451939; 231s Tree givenTree=(256:0.01208132378741086,(822:0.02897031120684837,159:0.004654690199997344)Node2:0.003646466641669312,((113:0.02417961708467097,9939:0.07265778198907162)Node6:0.005829014238445143,(6760:0.06388799683505494,((317:0.04027387637637774,6767:0.06819735681028999)Node12:0.01441604714363964,((135:0.0242734433643081,(529:0.03328072256381603,105r:0.01296055910155082)Node18:0.01988332856887562)Node16:0.003612544702306865,(719:0.02786537888441625,136:0.009982165852536065)Node21:0.05116795319458452)Node15:0.01668528231338159)Node11:0.008473522540836919)Node9:0.02634101151157303)Node5:0.02075182753820698); 231s + for i in *.bf 231s + '[' -f K2P.bf ']' 231s + hyphy K2P.bf 231s Log Likelihood = -1198.26189231186; 231s Tree givenTree=(256:0.01176910305654432,(822:0.02927352642982053,159:0.004287897193840723)Node2:0.003666638179085252,((113:0.02368483463279736,9939:0.07265294425600895)Node6:0.003381518624634053,(6760:0.06223538160532885,((317:0.0407374314051176,6767:0.06835321688034353)Node12:0.01245065810213201,((135:0.02259928814936616,(529:0.03395729246298833,105r:0.01240107392534691)Node18:0.02141967588130321)Node16:0.00449235792631839,(719:0.02880184618664692,136:0.008841875309372457)Node21:0.05084948701327376)Node15:0.01732969308569131)Node11:0.01112009431307714)Node9:0.02820939857869801)Node5:0.02370247369599254); 231s + for i in *.bf 231s + '[' -f K2Pshared.bf ']' 231s + hyphy K2Pshared.bf 232s Log Likelihood = -1210.49426595799; 232s Global Parameters: 232s R=2.615269647870584; 232s 232s Tree givenTree=(256:0.01222199849007476,(822:0.02897035218554136,159:0.00477714541146832)Node2:0.003545897261880193,((113:0.02375458958827501,9939:0.0749091377084513)Node6:0.005890435198643676,(6760:0.0649295420105835,((317:0.0397090245869384,6767:0.06948376439991623)Node12:0.01423214146310314,((135:0.02390228433170875,(529:0.03396509897647851,105r:0.01262329197452233)Node18:0.02071313860718839)Node16:0.003967941189956443,(719:0.02813193832889056,136:0.009506313249870686)Node21:0.05080798320925575)Node15:0.01659426317214061)Node11:0.008794881328943547)Node9:0.0262605646979837)Node5:0.02011433136081846); 232s + for i in *.bf 232s + '[' -f MatrixIndexing.bf ']' 232s + hyphy MatrixIndexing.bf 232s 232s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 232s { 232s {0.2368444619320436, 0.04061059398590833, 0.666988711260955, 0.8374601839663135, 0.9539458555993497, 0.7244865060142442} 232s {0.4943931180737897, 0.1304117765115601, 0.4871892050111641, 0.9874883391865269, 0.8220359889841722, 0.2285692126556694} 232s {0.4300463801319819, 0.4704307013820928, 0.6582157916059289, 0.9443289991338571, 0.6833268009785858, 0.3765939263106775} 232s {0.5688868517914989, 0.03677048674709408, 0.5196713112573306, 0.541605647546613, 0.5224114238569539, 0.7647312147926379} 232s {0.7027866853640384, 0.5839060993362, 0.8579163611535719, 0.9300499358051573, 0.3902173848799936, 0.8671559814520078} 232s } 232s 232s 2). Accessing a second-row third-column element and a random element. 232s 232s matrix[1][2]=0.4871892050111641 232s matrix[0][2]=0.666988711260955 232s 232s 3). Accessing the fourth row. 232s 232s matrix[3][-1]= 232s { 232s {0.5688868517914989, 0.03677048674709408, 0.5196713112573306, 0.541605647546613, 0.5224114238569539, 0.7647312147926379} 232s } 232s 232s 4). Accessing the first column. 232s 232s matrix[-1][0]= 232s { 232s {0.2368444619320436} 232s {0.4943931180737897} 232s {0.4300463801319819} 232s {0.5688868517914989} 232s {0.7027866853640384} 232s } 232s 232s 5). Populating a matrix template (below the diagonal). 232s 232s { 232s {0, 0, 0, 0, 0, 0} 232s {1, 0, 0, 0, 0, 0} 232s {1, 1, 0, 0, 0, 0} 232s {1, 1, 1, 0, 0, 0} 232s {1, 1, 1, 1, 0, 0} 232s } 232s 232s 6). Extracting (by row) matrix elements using the template. 232s 232s { 232s {0.4943931180737897, 0.4300463801319819, 0.4704307013820928, 0.5688868517914989, 0.03677048674709408, 0.5196713112573306, 0.7027866853640384, 0.5839060993362, 0.8579163611535719, 0.9300499358051573} 232s } 232s 232s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 232s 232s matrix[{{1,1}}][{{3,2}}]= 232s { 232s {0.1304117765115601, 0.4871892050111641} 232s {0.4704307013820928, 0.6582157916059289} 232s {0.03677048674709408, 0.5196713112573306} 232s } 232s 232s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 232s 232s 232s { 232s {0.05609529914787927, 1.001649220343888, 1.44487394094955, 1.701339559728892, 1.910012695415175, 1.524880697396727} 232s {0.2444245551987241, 0.01700723145290111, 1.23735332147941, 1.975133220029365, 1.675743167185186, 1.052243884974033} 232s {0.1849398890646211, 0.2213050448028478, 0.4332480283194197, 1.891757258605153, 1.466935516935628, 1.141822985334092} 232s {0.3236322501412428, 0.001352068695618221, 0.2700582717439133, 0.293336677454386, 1.27291369577625, 1.584813830878224} 232s {0.4939091251249719, 0.3409463328420162, 0.7360204827349861, 0.8649928830911772, 0.152269607462581, 1.751959496167995} 232s } 232s + for i in *.bf 232s + '[' -f MolecularClockF81.bf ']' 232s + hyphy MolecularClockF81.bf 232s 232s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124455898; 232s Tree theTree=(HVRNASS:0.02574343818698083,(RICRSS3:0.05627616267647488,((ZMSUCS1:0.07160732998770968,(OSRSS1A:0.0605882871342691,(TASUCSYN1:0.02788189879694929,HVSSYNMR:0.02037311730942106)Internal1:0.05182863735260022)Node9:0.02015511134557432)Node7:0.1581453919621747,(MZESUS1:0.0766455265177465,ORRSS2:0.05437554665156652)Internal2:0.02506690253273259)Node6:0.03254407420921539)Node4:0.05900645921387682,TAAJ153:0.0137240823557105); 232s 232s 232s 1). Global Molecular Clock; the P-value is:0 232s Log Likelihood = -11927.6152937369; 232s Tree theTree=(HVRNASS:0.02157256105224451,(RICRSS3:0.1233391624335933,((ZMSUCS1:0.05658068351739532,(OSRSS1A:0.04751103199830189,(TASUCSYN1:0.01824592668340718,HVSSYNMR:0.01824592668340718)Internal1:0.02926510531489471)Node9:0.009069651519093433)Node7:0.05762932995774125,(MZESUS1:0.07014505382594971,ORRSS2:0.07014505382594971)Internal2:0.04406495964918684)Node6:0.009129148958456767)Node4:0.0271554279855623,TAAJ153:0.1504945904191556); 232s 232s 232s 2). Molecular Clock starting at Internal1; the P-value is:0.1603800996417838 232s Log Likelihood = -11476.6977648658; 232s Tree theTree=(HVRNASS:0.02574463877872497,(RICRSS3:0.05630537922293165,((ZMSUCS1:0.07170663228293392,(OSRSS1A:0.06051692341998914,(TASUCSYN1:0.0241183626915089,HVSSYNMR:0.0241183626915089)Internal1:0.05180646849531016)Node9:0.02017647183178858)Node7:0.1580963980052938,(MZESUS1:0.07663695353693974,ORRSS2:0.05441168358245108)Internal2:0.02507735229076212)Node6:0.03252990279147008)Node4:0.05896342842216468,TAAJ153:0.01372807420946328); 232s 232s 232s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.0161019722752217 232s Log Likelihood = -11479.8412591028; 232s Tree theTree=(HVRNASS:0.02577199027361876,(RICRSS3:0.0565088634272685,((ZMSUCS1:0.07148106086700545,(OSRSS1A:0.06062414834514016,(TASUCSYN1:0.02412281644248133,HVSSYNMR:0.02412281644248133)Internal1:0.0516691688196029)Node9:0.02036313732843775)Node7:0.1580479219859107,(MZESUS1:0.06553054265699038,ORRSS2:0.06553054265699038)Internal2:0.0250209971949034)Node6:0.0323579537198934)Node4:0.05873963393381004,TAAJ153:0.01369897052902781); 232s + for i in *.bf 232s + '[' -f MolecularClockHKY85.bf ']' 232s + hyphy MolecularClockHKY85.bf 232s 232s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013196361; 232s Tree theTree=(HVRNASS:0.02587907737396311,(RICRSS3:0.0572894124085676,((ZMSUCS1:0.07272709601044716,(OSRSS1A:0.06095570992118214,(TASUCSYN1:0.02742497968105604,HVSSYNMR:0.02082031616288811)Node11:0.05283536750873715)Node9:0.02050572458204564)Node7:0.1590163318162333,(MZESUS1:0.0776144692251914,ORRSS2:0.05414212880562341)Node14:0.02601315280911412)Node6:0.03166660548063902)Node4:0.06041546479717889,TAAJ153:0.01384412085712321); 232s 232s 232s 1). Global Molecular Clock on transition rates; the P-value is:0 232s Log Likelihood = -11434.7016033383; 232s Tree theTree=(HVRNASS:0.02319733761553288,(RICRSS3:0.08334085055188765,((ZMSUCS1:0.06367266227632011,(OSRSS1A:0.05485169643806629,(TASUCSYN1:0.0232551460867506,HVSSYNMR:0.01890604954545845)Node11:0.04016831567262675)Node9:0.01328538420556341)Node7:0.1273995940933478,(MZESUS1:0.07240244266209002,ORRSS2:0.06226503778212443)Node14:0.03460943298177104)Node6:0.02068820627130245)Node4:0.03899425489109949,TAAJ153:0.08890804672536808); 233s 233s 233s 2). Global Molecular Clock on transversion rates; the P-value is:0 233s Log Likelihood = -11497.3782386367; 233s Tree theTree=(HVRNASS:0.02484528756261216,(RICRSS3:0.09397660711566694,((ZMSUCS1:0.06900744557579687,(OSRSS1A:0.05468497070692049,(TASUCSYN1:0.0227716508779853,HVSSYNMR:0.02034233073929944)Node11:0.04373646643512617)Node9:0.01673694266275387)Node7:0.09971901063820572,(MZESUS1:0.07447177543760836,ORRSS2:0.06134376047192384)Node14:0.03386900175600831)Node6:0.02079418106193919)Node4:0.05008072898660467,TAAJ153:0.07306008055237165); 233s 233s 233s 3). Global Molecular Clock on both rates; the P-value is:0 233s Log Likelihood = -11703.6261452004; 233s Tree theTree=(HVRNASS:0.02209626591814473,(RICRSS3:0.1239907399586609,((ZMSUCS1:0.05799737347185272,(OSRSS1A:0.04854802437863659,(TASUCSYN1:0.01832984801726247,HVSSYNMR:0.01832984801726247)Node11:0.03021817636137412)Node9:0.009449349093216129)Node7:0.05733994328761582,(MZESUS1:0.07024387052667865,ORRSS2:0.07024387052667865)Node14:0.04509344623278988)Node6:0.008653423199192328)Node4:0.02801466046190713,TAAJ153:0.152005400420568); 233s + for i in *.bf 233s + '[' -f Non-Rev.bf ']' 233s + hyphy Non-Rev.bf 233s Log Likelihood = -1152.7868429868; 233s Global Parameters: 233s GC=0.2667937090867484; 233s CG=0.1887231922033225; 233s GA=1.908118102904802; 233s CT=1.256649571389755; 233s GT=0.08643485457487809; 233s CA=0.9159944421582883; 233s AT=0.4295957929127387; 233s AG=1.579700626736878; 233s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2554491561489715; 233s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.033634750032359; 233s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7964622428218343; 233s 233s Tree givenTree=(256:0.01345535227860117,(822:0.02845066843173148,159:0.006118674072625591)Node2:0.003450784603022853,((113:0.02186926391938918,9939:0.07932206531419443)Node6:0.004993984679151328,(6760:0.07323441798101694,((317:0.04007662861081602,6767:0.06980780579195063)Node12:0.01161543649697462,((135:0.02155486255895556,(529:0.03497766937138842,105r:0.01423697410192226)Node18:0.02377184479755287)Node16:0.005235161748841306,(719:0.02862577134253361,136:0.009576312326589276)Node21:0.04929836933270873)Node15:0.01635720663752303)Node11:0.01272076015602887)Node9:0.02192877750939732)Node5:0.02026047422639026); 233s + for i in *.bf 233s + '[' -f PBootstrapHetRates.bf ']' 233s + hyphy PBootstrapHetRates.bf 233s 233s ----ORIGINAL DATA---- 233s Log Likelihood = -1127.31560726467; 233s Global Parameters: 233s alpha=0.3189019521637245; 233s kappa=0.323634843422934; 233s 233s Tree givenTree=(256:0.01258500542706293,(822:0.03175318657470722,159:0.004691996269708359)Node2:0.003777657874653248,((113:0.02291425151829138,9939:0.09712404277422883)Node6:0.001963873996793157,(6760:0.08715253670421785,((317:0.04570163939234655,6767:0.08106912982648756)Node12:0.007409764477276542,((135:0.01863677865921079,(529:0.03693823573662843,105r:0.01499278826225312)Node18:0.03033449865114696)Node16:0.007147086743127492,(719:0.03339487747583827,136:0.007167238341417949)Node21:0.05751756487654235)Node15:0.01788782180184505)Node11:0.0188402524940454)Node9:0.02369234296522092)Node5:0.02500545734330536); 233s 233s Using the seed: 234s 1710603434 234s Category variable name: TRUE 234s Site Rate 234s 0 0.00000 234s 1 0.00000 234s 2 0.00001 234s 3 0.00003 234s 4 0.00004 234s 5 0.00005 234s 6 0.00006 234s 7 0.00006 234s 8 0.00009 234s 9 0.00010 234s 10 0.00011 234s 11 0.00012 234s 12 0.00016 234s 13 0.00016 234s 14 0.00020 234s 15 0.00022 234s 16 0.00023 234s 17 0.00027 234s 18 0.00037 234s 19 0.00044 234s 20 0.00049 234s 21 0.00052 234s 22 0.00058 234s 23 0.00066 234s 24 0.00080 234s 25 0.00140 234s 26 0.00217 234s 27 0.00220 234s 28 0.00222 234s 29 0.00242 234s 30 0.00247 234s 31 0.00258 234s 32 0.00275 234s 33 0.00281 234s 34 0.00282 234s 35 0.00304 234s 36 0.00373 234s 37 0.00425 234s 38 0.00496 234s 39 0.00562 234s 40 0.00565 234s 41 0.00569 234s 42 0.00696 234s 43 0.00707 234s 44 0.00746 234s 45 0.00754 234s 46 0.00767 234s 47 0.00804 234s 48 0.00808 234s 49 0.01083 234s 50 0.01093 234s 51 0.01248 234s 52 0.01250 234s 53 0.01411 234s 54 0.01740 234s 55 0.01798 234s 56 0.01867 234s 57 0.01962 234s 58 0.02102 234s 59 0.02391 234s 60 0.02408 234s 61 0.02617 234s 62 0.03018 234s 63 0.03228 234s 64 0.03246 234s 65 0.03372 234s 66 0.03654 234s 67 0.03704 234s 68 0.03836 234s 69 0.03848 234s 70 0.04137 234s 71 0.04159 234s 72 0.04190 234s 73 0.04825 234s 74 0.05952 234s 75 0.06064 234s 76 0.06161 234s 77 0.06326 234s 78 0.06526 234s 79 0.06722 234s 80 0.07073 234s 81 0.07252 234s 82 0.07597 234s 83 0.07827 234s 84 0.07895 234s 85 0.08119 234s 86 0.08206 234s 87 0.08511 234s 88 0.08639 234s 89 0.09200 234s 90 0.09253 234s 91 0.09260 234s 92 0.09379 234s 93 0.09718 234s 94 0.09759 234s 95 0.10069 234s 96 0.10267 234s 97 0.10369 234s 98 0.10637 234s 99 0.10812 234s 100 0.11584 234s 101 0.11592 234s 102 0.12615 234s 103 0.13340 234s 104 0.13516 234s 105 0.14248 234s 106 0.14494 234s 107 0.15570 234s 108 0.15787 234s 109 0.15792 234s 110 0.16146 234s 111 0.16318 234s 112 0.16677 234s 113 0.16821 234s 114 0.16871 234s 115 0.16984 234s 116 0.16986 234s 117 0.17337 234s 118 0.17405 234s 119 0.18979 234s 120 0.19911 234s 121 0.20044 234s 122 0.20580 234s 123 0.21369 234s 124 0.22253 234s 125 0.22593 234s 126 0.22759 234s 127 0.23971 234s 128 0.24682 234s 129 0.24996 234s 130 0.25081 234s 131 0.26422 234s 132 0.26684 234s 133 0.30531 234s 134 0.33161 234s 135 0.34358 234s 136+ for i in *.bf 234s + '[' -f REV.bf ']' 234s + hyphy REV.bf 234s 0.35707 234s 137 0.36401 234s 138 0.36869 234s 139 0.37786 234s 140 0.38406 234s 141 0.38455 234s 142 0.40213 234s 143 0.40221 234s 144 0.41873 234s 145 0.42309 234s 146 0.44187 234s 147 0.44626 234s 148 0.45742 234s 149 0.46540 234s 150 0.46934 234s 151 0.47543 234s 152 0.48980 234s 153 0.49050 234s 154 0.49355 234s 155 0.49387 234s 156 0.49437 234s 157 0.51325 234s 158 0.52779 234s 159 0.52990 234s 160 0.54153 234s 161 0.54693 234s 162 0.55994 234s 163 0.57051 234s 164 0.59507 234s 165 0.59944 234s 166 0.60250 234s 167 0.61002 234s 168 0.61975 234s 169 0.64132 234s 170 0.64904 234s 171 0.67836 234s 172 0.67955 234s 173 0.67997 234s 174 0.68137 234s 175 0.68255 234s 176 0.69233 234s 177 0.69629 234s 178 0.69955 234s 179 0.71042 234s 180 0.71857 234s 181 0.72588 234s 182 0.75581 234s 183 0.76730 234s 184 0.78404 234s 185 0.80935 234s 186 0.81033 234s 187 0.82305 234s 188 0.82750 234s 189 0.82814 234s 190 0.86226 234s 191 0.94022 234s 192 0.94282 234s 193 0.98364 234s 194 1.03374 234s 195 1.06944 234s 196 1.07518 234s 197 1.08130 234s 198 1.08505 234s 199 1.09417 234s 200 1.11832 234s 201 1.11838 234s 202 1.12100 234s 203 1.12553 234s 204 1.14080 234s 205 1.15248 234s 206 1.15728 234s 207 1.15930 234s 208 1.21213 234s 209 1.23810 234s 210 1.24099 234s 211 1.26329 234s 212 1.34288 234s 213 1.39225 234s 214 1.40733 234s 215 1.45721 234s 216 1.52821 234s 217 1.56304 234s 218 1.56732 234s 219 1.58113 234s 220 1.58917 234s 221 1.62925 234s 222 1.63564 234s 223 1.64652 234s 224 1.69293 234s 225 1.72024 234s 226 1.75252 234s 227 1.76135 234s 228 1.78028 234s 229 1.89572 234s 230 1.94091 234s 231 1.96619 234s 232 1.96708 234s 233 1.97301 234s 234 2.01164 234s 235 2.02563 234s 236 2.22722 234s 237 2.23594 234s 238 2.30386 234s 239 2.31548 234s 240 2.35750 234s 241 2.39559 234s 242 2.42100 234s 243 2.48788 234s 244 2.53034 234s 245 2.59092 234s 246 2.75817 234s 247 2.84160 234s 248 2.95757 234s 249 3.20111 234s 250 3.26702 234s 251 3.37779 234s 252 3.43552 234s 253 3.71226 234s 254 3.80712 234s 255 3.94186 234s 256 3.96277 234s 257 3.98485 234s 258 4.32463 234s 259 4.88504 234s 260 4.97102 234s 261 5.03900 234s 262 5.52099 234s 263 6.42840 234s 264 6.46565 234s 265 6.80207 234s 266 6.81017 234s 267 6.88301 234s 268 7.70257 234s 269 8.49202 234s 270 9.35220 234s 271 11.13399 234s 272 11.19335 234s 234s Mean = 1.01639416089865 234s Var = 3.13125029024409 (1/alpha) = 3.135760045415461 234s Log Likelihood = -1100.00325192825; 234s Tree givenTree=(256:0.02246875114337755,(822:0.01867823122043897,159:0.01469059913175439)Node2:0.003780035603908842,((113:0.01829385606031696,9939:0.07804100019464809)Node6:0.007456159322626059,(6760:0.07113582386827495,((317:0.03719085130056347,6767:0.07206936945595187)Node12:0.01019125089869471,((135:0.02036489400110258,(529:0.03424008585662204,105r:0.01130059017016288)Node18:0.0285116839730642)Node16:0.006571188750754679,(719:0.02830813536460677,136:0.009595572687636146)Node21:0.04404096153060984)Node15:0.01655093511589027)Node11:0.01315864559716088)Node9:0.02915629967554301)Node5:0.009980424315425578); 234s + for i in *.bf 234s + '[' -f REVshared.bf ']' 234s + hyphy REVshared.bf 234s Log Likelihood = -1156.62548891656; 234s Global Parameters: 234s AT=0.3618422195106666; 234s GT=0.4591848014349445; 234s CG=0.2458226660545487; 234s AG=1.842836886938053; 234s CT=1.196790957516014; 234s 234s Tree givenTree=(256:0.0120849443891866,(822:0.02974480620049809,159:0.004669448660303607)Node2:0.003489904910174796,((113:0.02207977238258231,9939:0.07977360902457309)Node6:0.004706047666819394,(6760:0.07205077737979429,((317:0.0390946747526612,6767:0.07105937428611539)Node12:0.01083776419000808,((135:0.02050612528374597,(529:0.03436945795905898,105r:0.01468004972546612)Node18:0.02466827485670234)Node16:0.00555941424528441,(719:0.02873374717341659,136:0.009464694805887797)Node21:0.04909369045408175)Node15:0.01584715826584453)Node11:0.01425933999551002)Node9:0.02296161961066105)Node5:0.02145184527825768); 234s + for i in *.bf 234s + '[' -f ReplicateConstraint1.bf ']' 234s + hyphy ReplicateConstraint1.bf 234s 1).Unconstrained HKY85 234s 234s Log Likelihood = -1152.88; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.317.trvs 234s Parameter 2 : hivTree.317.trst 234s Parameter 3 : hivTree.6767.trvs 234s Parameter 4 : hivTree.6767.trst 234s Parameter 5 : hivTree.Node2.trvs 234s Parameter 6 : hivTree.Node2.trst 234s Parameter 7 : hivTree.135.trvs 234s Parameter 8 : hivTree.135.trst 234s Parameter 9 : hivTree.529.trvs 234s Parameter 10 : hivTree.529.trst 234s Parameter 11 : hivTree.105r.trvs 234s Parameter 12 : hivTree.105r.trst 234s Parameter 13 : hivTree.Node8.trvs 234s Parameter 14 : hivTree.Node8.trst 234s Parameter 15 : hivTree.iNode1.trvs 234s Parameter 16 : hivTree.iNode1.trst 234s Parameter 17 : hivTree.719.trvs 234s Parameter 18 : hivTree.719.trst 234s Parameter 19 : hivTree.136.trvs 234s Parameter 20 : hivTree.136.trst 234s Parameter 21 : hivTree.Node11.trvs 234s Parameter 22 : hivTree.Node11.trst 234s Parameter 23 : hivTree.Node5.trvs 234s Parameter 24 : hivTree.Node5.trst 234s Parameter 25 : hivTree.Node1.trvs 234s Parameter 26 : hivTree.Node1.trst 234s Parameter 27 : hivTree.6760.trvs 234s Parameter 28 : hivTree.6760.trst 234s Parameter 29 : hivTree.113.trvs 234s Parameter 30 : hivTree.113.trst 234s Parameter 31 : hivTree.9939.trvs 234s Parameter 32 : hivTree.9939.trst 234s Parameter 33 : hivTree.Node16.trvs 234s Parameter 34 : hivTree.Node16.trst 234s Parameter 35 : hivTree.256.trvs 234s Parameter 36 : hivTree.256.trst 234s Parameter 37 : hivTree.822.trvs 234s Parameter 38 : hivTree.822.trst 234s Parameter 39 : hivTree.159.trvs 234s Parameter 40 : hivTree.159.trst 234s Parameter 41 : hivTree.Node21.trvs 234s Parameter 42 : hivTree.Node21.trst 234s Parameter 43 : hivTree.iNode2.trvs 234s Parameter 44 : hivTree.iNode2.trst 234s Parameter 45 : hivTree.Node15.trvs 234s Parameter 46 : hivTree.Node15.trst 234s 234s 2).HKY85 constrained to F81 234s 234s Log Likelihood = -1187.55; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.317.trvs 234s Parameter 2 : hivTree.6767.trvs 234s Parameter 3 : hivTree.Node2.trvs 234s Parameter 4 : hivTree.135.trvs 234s Parameter 5 : hivTree.529.trvs 234s Parameter 6 : hivTree.105r.trvs 234s Parameter 7 : hivTree.Node8.trvs 234s Parameter 8 : hivTree.iNode1.trvs 234s Parameter 9 : hivTree.719.trvs 234s Parameter 10 : hivTree.136.trvs 234s Parameter 11 : hivTree.Node11.trvs 234s Parameter 12 : hivTree.Node5.trvs 234s Parameter 13 : hivTree.Node1.trvs 234s Parameter 14 : hivTree.6760.trvs 234s Parameter 15 : hivTree.113.trvs 234s Parameter 16 : hivTree.9939.trvs 234s Parameter 17 : hivTree.Node16.trvs 234s Parameter 18 : hivTree.256.trvs 234s Parameter 19 : hivTree.822.trvs 234s Parameter 20 : hivTree.159.trvs 234s Parameter 21 : hivTree.Node21.trvs 234s Parameter 22 : hivTree.iNode2.trvs 234s Parameter 23 : hivTree.Node15.trvs 234s 234s Constrained Parameters List 234s 234s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 234s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 234s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 234s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 234s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 234s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 234s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 234s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 234s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 234s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 234s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 234s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 234s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 234s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 234s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 234s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 234s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 234s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 234s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 234s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 234s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 234s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 234s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 234s 234s 3).HKY85 constrained to F81 on internal branches 234s 234s Log Likelihood = -1167.99; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.Node2.trvs 234s Parameter 2 : hivTree.Node8.trvs 234s Parameter 3 : hivTree.iNode1.trvs 234s Parameter 4 : hivTree.Node11.trvs 234s Parameter 5 : hivTree.Node5.trvs 234s Parameter 6 : hivTree.Node1.trvs 234s Parameter 7 : hivTree.Node16.trvs 234s Parameter 8 : hivTree.Node21.trvs 234s Parameter 9 : hivTree.iNode2.trvs 234s Parameter 10 : hivTree.Node15.trvs 234s Parameter 11 : hivTree.317.trst 234s Parameter 12 : hivTree.317.trvs 234s Parameter 13 : hivTree.6767.trvs 234s Parameter 14 : hivTree.6767.trst 234s Parameter 15 : hivTree.135.trst 234s Parameter 16 : hivTree.135.trvs 234s Parameter 17 : hivTree.529.trvs 234s Parameter 18 : hivTree.529.trst 234s Parameter 19 : hivTree.105r.trst 234s Parameter 20 : hivTree.105r.trvs 234s Parameter 21 : hivTree.719.trvs 234s Parameter 22 : hivTree.719.trst 234s Parameter 23 : hivTree.136.trvs 234s Parameter 24 : hivTree.136.trst 234s Parameter 25 : hivTree.6760.trvs 234s Parameter 26 : hivTree.6760.trst 234s Parameter 27 : hivTree.113.trvs 234s Parameter 28 : hivTree.113.trst 234s Parameter 29 : hivTree.9939.trst 234s Parameter 30 : hivTree.9939.trvs 234s Parameter 31 : hivTree.256.trvs 234s Parameter 32 : hivTree.256.trst 234s Parameter 33 : hivTree.822.trvs 234s Parameter 34 : hivTree.822.trst 234s Parameter 35 : hivTree.159.trst 234s Parameter 36 : hivTree.159.trvs 234s 234s Constrained Parameters List 234s 234s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 234s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 234s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 234s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 234s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 234s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 234s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 234s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 234s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 234s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 234s 234s 4).HKY85 with shared ratio. 234s 234s Log Likelihood = -1165.7; 234s 234s Independent Parameters List 234s 234s Parameter 1 : R 234s Parameter 2 : hivTree.317.trst 234s Parameter 3 : hivTree.6767.trst 234s Parameter 4 : hivTree.Node2.trst 234s Parameter 5 : hivTree.135.trst 234s Parameter 6 : hivTree.529.trst 234s Parameter 7 : hivTree.105r.trst 234s Parameter 8 : hivTree.Node8.trst 234s Parameter 9 : hivTree.iNode1.trst 234s Parameter 10 : hivTree.719.trst 234s Parameter 11 : hivTree.136.trst 234s Parameter 12 : hivTree.Node11.trst 234s Parameter 13 : hivTree.Node5.trst 234s Parameter 14 : hivTree.Node1.trst 234s Parameter 15 : hivTree.6760.trst 234s Parameter 16 : hivTree.113.trst 234s Parameter 17 : hivTree.9939.trst 234s Parameter 18 : hivTree.Node16.trst 234s Parameter 19 : hivTree.256.trst 234s Parameter 20 : hivTree.822.trst 234s Parameter 21 : hivTree.159.trst 234s Parameter 22 : hivTree.Node21.trst 234s Parameter 23 : hivTree.iNode2.trst 234s Parameter 24 : hivTree.Node15.trst 234s 234s Constrained Parameters List 234s 234s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 234s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 234s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 234s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 234s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 234s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 234s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 234s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 234s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 234s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 234s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 234s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 234s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 234s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 234s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 234s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 234s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 234s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 234s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 234s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 234s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 234s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 234s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 234s + '[' -f ReplicateConstraint2.bf ']' 234s + hyphy ReplicateConstraint2.bf 234s 1).Unconstrained HKY85 234s 234s Log Likelihood = -1152.88; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.317.trvs 234s Parameter 2 : hivTree.317.trst 234s Parameter 3 : hivTree.6767.trvs 234s Parameter 4 : hivTree.6767.trst 234s Parameter 5 : hivTree.Node2.trvs 234s Parameter 6 : hivTree.Node2.trst 234s Parameter 7 : hivTree.135.trvs 234s Parameter 8 : hivTree.135.trst 234s Parameter 9 : hivTree.529.trvs 234s Parameter 10 : hivTree.529.trst 234s Parameter 11 : hivTree.105r.trvs 234s Parameter 12 : hivTree.105r.trst 234s Parameter 13 : hivTree.Node8.trvs 234s Parameter 14 : hivTree.Node8.trst 234s Parameter 15 : hivTree.iNode1.trvs 234s Parameter 16 : hivTree.iNode1.trst 234s Parameter 17 : hivTree.719.trvs 234s Parameter 18 : hivTree.719.trst 234s Parameter 19 : hivTree.136.trvs 234s Parameter 20 : hivTree.136.trst 234s Parameter 21 : hivTree.Node11.trvs 234s Parameter 22 : hivTree.Node11.trst 234s Parameter 23 : hivTree.Node5.trvs 234s Parameter 24 : hivTree.Node5.trst 234s Parameter 25 : hivTree.Node1.trvs 234s Parameter 26 : hivTree.Node1.trst 234s Parameter 27 : hivTree.6760.trvs 234s Parameter 28 : hivTree.6760.trst 234s Parameter 29 : hivTree.113.trvs 234s Parameter 30 : hivTree.113.trst 234s Parameter 31 : hivTree.9939.trvs 234s Parameter 32 : hivTree.9939.trst 234s Parameter 33 : hivTree.Node16.trvs 234s Parameter 34 : hivTree.Node16.trst 234s Parameter 35 : hivTree.256.trvs 234s Parameter 36 : hivTree.256.trst 234s Parameter 37 : hivTree.822.trvs 234s Parameter 38 : hivTree.822.trst 234s Parameter 39 : hivTree.159.trvs 234s Parameter 40 : hivTree.159.trst 234s Parameter 41 : hivTree.Node21.trvs 234s Parameter 42 : hivTree.Node21.trst 234s Parameter 43 : hivTree.iNode2.trvs 234s Parameter 44 : hivTree.iNode2.trst 234s Parameter 45 : hivTree.Node15.trvs 234s Parameter 46 : hivTree.Node15.trst 234s 234s 2).HKY85 constrained to F81 on the "iNode1" subtree 234s 234s Log Likelihood = -1157.82; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.135.trvs 234s Parameter 2 : hivTree.529.trvs 234s Parameter 3 : hivTree.105r.trvs 234s Parameter 4 : hivTree.Node8.trvs 234s Parameter 5 : hivTree.317.trvs 234s Parameter 6 : hivTree.317.trst 234s Parameter 7 : hivTree.6767.trst 234s Parameter 8 : hivTree.6767.trvs 234s Parameter 9 : hivTree.Node2.trst 234s Parameter 10 : hivTree.Node2.trvs 234s Parameter 11 : hivTree.iNode1.trvs 234s Parameter 12 : hivTree.iNode1.trst 234s Parameter 13 : hivTree.719.trvs 234s Parameter 14 : hivTree.719.trst 234s Parameter 15 : hivTree.136.trvs 234s Parameter 16 : hivTree.136.trst 234s Parameter 17 : hivTree.Node11.trvs 234s Parameter 18 : hivTree.Node11.trst 234s Parameter 19 : hivTree.Node5.trvs 234s Parameter 20 : hivTree.Node5.trst 234s Parameter 21 : hivTree.Node1.trvs 234s Parameter 22 : hivTree.Node1.trst 234s Parameter 23 : hivTree.6760.trvs 234s Parameter 24 : hivTree.6760.trst 234s Parameter 25 : hivTree.113.trvs 234s Parameter 26 : hivTree.113.trst 234s Parameter 27 : hivTree.9939.trvs 234s Parameter 28 : hivTree.9939.trst 234s Parameter 29 : hivTree.Node16.trvs 234s Parameter 30 : hivTree.Node16.trst 234s Parameter 31 : hivTree.256.trvs 234s Parameter 32 : hivTree.256.trst 234s Parameter 33 : hivTree.822.trvs 234s Parameter 34 : hivTree.822.trst 234s Parameter 35 : hivTree.159.trvs 234s Parameter 36 : hivTree.159.trst 234s Parameter 37 : hivTree.Node21.trvs 234s Parameter 38 : hivTree.Node21.trst 234s Parameter 39 : hivTree.iNode2.trvs 234s Parameter 40 : hivTree.iNode2.trst 234s Parameter 41 : hivTree.Node15.trvs 234s Parameter 42 : hivTree.Node15.trst 234s 234s Constrained Parameters List 234s 234s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 234s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 234s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 234s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 234s 234s 3).HKY85 constrained to F81 on the "iNode1" branch 234s 234s Log Likelihood = -1152.88; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.317.trvs 234s Parameter 2 : hivTree.317.trst 234s Parameter 3 : hivTree.6767.trvs 234s Parameter 4 : hivTree.6767.trst 234s Parameter 5 : hivTree.Node2.trvs 234s Parameter 6 : hivTree.Node2.trst 234s Parameter 7 : hivTree.135.trvs 234s Parameter 8 : hivTree.135.trst 234s Parameter 9 : hivTree.529.trvs 234s Parameter 10 : hivTree.529.trst 234s Parameter 11 : hivTree.105r.trvs 234s Parameter 12 : hivTree.105r.trst 234s Parameter 13 : hivTree.Node8.trvs 234s Parameter 14 : hivTree.Node8.trst 234s Parameter 15 : hivTree.iNode1.trvs 234s Parameter 16 : hivTree.iNode1.trst 234s Parameter 17 : hivTree.719.trvs 234s Parameter 18 : hivTree.719.trst 234s Parameter 19 : hivTree.136.trvs 234s Parameter 20 : hivTree.136.trst 234s Parameter 21 : hivTree.Node11.trvs 234s Parameter 22 : hivTree.Node11.trst 234s Parameter 23 : hivTree.Node5.trvs 234s Parameter 24 : hivTree.Node5.trst 234s Parameter 25 : hivTree.Node1.trvs 234s Parameter 26 : hivTree.Node1.trst 234s Parameter 27 : hivTree.6760.trvs 234s Parameter 28 : hivTree.6760.trst 234s Parameter 29 : hivTree.113.trvs 234s Parameter 30 : hivTree.113.trst 234s Parameter 31 : hivTree.9939.trvs 234s Parameter 32 : hivTree.9939.trst 234s Parameter 33 : hivTree.Node16.trvs 234s Parameter 34 : hivTree.Node16.trst 234s Parameter 35 : hivTree.256.trvs 234s Parameter 36 : hivTree.256.trst 234s Parameter 37 : hivTree.822.trvs 234s Parameter 38 : hivTree.822.trst 234s Parameter 39 : hivTree.159.trvs 234s Parameter 40 : hivTree.159.trst 234s Parameter 41 : hivTree.Node21.trvs 234s Parameter 42 : hivTree.Node21.trst 234s Parameter 43 : hivTree.iNode2.trvs 234s Parameter 44 : hivTree.iNode2.trst 234s Parameter 45 : hivTree.Node15.trvs 234s Parameter 46 : hivTree.Node15.trst 234s 234s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 234s 234s Log Likelihood = -1152.88; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.317.trvs 234s Parameter 2 : hivTree.317.trst 234s Parameter 3 : hivTree.6767.trvs 234s Parameter 4 : hivTree.6767.trst 234s Parameter 5 : hivTree.Node2.trvs 234s Parameter 6 : hivTree.Node2.trst 234s Parameter 7 : hivTree.135.trvs 234s Parameter 8 : hivTree.135.trst 234s Parameter 9 : hivTree.529.trvs 234s Parameter 10 : hivTree.529.trst 234s Parameter 11 : hivTree.105r.trvs 234s Parameter 12 : hivTree.105r.trst 234s Parameter 13 : hivTree.Node8.trvs 234s Parameter 14 : hivTree.Node8.trst 234s Parameter 15 : hivTree.iNode1.trvs 234s Parameter 16 : hivTree.iNode1.trst 234s Parameter 17 : hivTree.719.trvs 234s Parameter 18 : hivTree.719.trst 234s Parameter 19 : hivTree.136.trvs 234s Parameter 20 : hivTree.136.trst 234s Parameter 21 : hivTree.Node11.trvs 234s Parameter 22 : hivTree.Node11.trst 234s Parameter 23 : hivTree.Node5.trvs 234s Parameter 24 : hivTree.Node5.trst 234s Parameter 25 : hivTree.Node1.trvs 234s Parameter 26 : hivTree.Node1.trst 234s Parameter 27 : hivTree.6760.trvs 234s Parameter 28 : hivTree.6760.trst 234s Parameter 29 : hivTree.113.trvs 234s Parameter 30 : hivTree.113.trst 234s Parameter 31 : hivTree.9939.trvs 234s Parameter 32 : hivTree.9939.trst 234s Parameter 33 : hivTree.Node16.trvs 234s Parameter 34 : hivTree.Node16.trst 234s Parameter 35 : hivTree.256.trvs 234s Parameter 36 : hivTree.256.trst 234s Parameter 37 : hivTree.822.trvs 234s Parameter 38 : hivTree.822.trst 234s Parameter 39 : hivTree.159.trvs 234s Parameter 40 : hivTree.159.trst 234s Parameter 41 : hivTree.Node21.trvs 234s Parameter 42 : hivTree.Node21.trst 234s Parameter 43 : hivTree.iNode2.trvs 234s Parameter 44 : hivTree.iNode2.trst 234s Parameter 45 : hivTree.Node15.trvs 234s Parameter 46 : hivTree.Node15.trst 234s 234s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 234s 234s Log Likelihood = -1152.88; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.317.trvs 234s Parameter 2 : hivTree.317.trst 234s Parameter 3 : hivTree.6767.trvs 234s Parameter 4 : hivTree.6767.trst 234s Parameter 5 : hivTree.Node2.trvs 234s Parameter 6 : hivTree.Node2.trst 234s Parameter 7 : hivTree.135.trvs 234s Parameter 8 : hivTree.135.trst 234s Parameter 9 : hivTree.529.trvs 234s Parameter 10 : hivTree.529.trst 234s Parameter 11 : hivTree.105r.trvs 234s Parameter 12 : hivTree.105r.trst 234s Parameter 13 : hivTree.Node8.trvs 234s Parameter 14 : hivTree.Node8.trst 234s Parameter 15 : hivTree.iNode1.trvs 234s Parameter 16 : hivTree.iNode1.trst 234s Parameter 17 : hivTree.719.trvs 234s Parameter 18 : hivTree.719.trst 234s Parameter 19 : hivTree.136.trvs 234s Parameter 20 : hivTree.136.trst 234s Parameter 21 : hivTree.Node11.trvs 234s Parameter 22 : hivTree.Node11.trst 234s Parameter 23 : hivTree.Node5.trvs 234s Parameter 24 : hivTree.Node5.trst 234s Parameter 25 : hivTree.Node1.trvs 234s Parameter 26 : hivTree.Node1.trst 234s Parameter 27 : hivTree.6760.trvs 234s Parameter 28 : hivTree.6760.trst 234s Parameter 29 : hivTree.113.trvs 234s Parameter 30 : hivTree.113.trst 234s Parameter 31 : hivTree.9939.trvs 234s Parameter 32 : hivTree.9939.trst 234s Parameter 33 : hivTree.Node16.trvs 234s Parameter 34 : hivTree.Node16.trst 234s Parameter 35 : hivTree.256.trvs 234s Parameter 36 : hivTree.256.trst 234s Parameter 37 : hivTree.822.trvs 234s Parameter 38 : hivTree.822.trst 234s Parameter 39 : hivTree.159.trvs 234s Parameter 40 : hivTree.159.trst 234s Parameter 41 : hivTree.Node21.trvs 234s Parameter 42 : hivTree.Node21.trst 234s Parameter 43 : hivTree.iNode2.trvs 234s Parameter 44 : hivTree.iNode2.trst 234s Parameter 45 : hivTree.Node15.trvs 234s Parameter 46 : hivTree.Node15.trst 234s 234s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 234s 234s Log Likelihood = -1157.82; 234s 234s Independent Parameters List 234s 234s Parameter 1 : hivTree.135.trst 234s Parameter 2 : hivTree.529.trst 234s Parameter 3 : hivTree.105r.trst 234s Parameter 4 : hivTree.Node8.trst 234s Parameter 5 : hivTree.317.trvs 234s Parameter 6 : hivTree.317.trst 234s Parameter 7 : hivTree.6767.trst 234s Parameter 8 : hivTree.6767.trvs 234s Parameter 9 : hivTree.Node2.trst 234s Parameter 10 : hivTree.Node2.trvs 234s Parameter 11 : hivTree.iNode1.trvs 234s Parameter 12 : hivTree.iNode1.trst 234s Parameter 13 : hivTree.719.trvs 234s Parameter 14 : hivTree.719.trst 234s Parameter 15 : hivTree.136.trvs 234s Parameter 16 : hivTree.136.trst 234s Parameter 17 : hivTree.Node11.trvs 234s Parameter 18 : hivTree.Node11.trst 234s Parameter 19 : hivTree.Node5.trvs 234s Parameter 20 : hivTree.Node5.trst 234s Parameter 21 : hivTree.Node1.trvs 234s Parameter 22 : hivTree.Node1.trst 234s Parameter 23 : hivTree.6760.trvs 234s Parameter 24 : hivTree.6760.trst 234s Parameter 25 : hivTree.113.trvs 234s Parameter 26 : hivTree.113.trst 234s Parameter 27 : hivTree.9939.trvs 234s Parameter 28 : hivTree.9939.trst 234s Parameter 29 : hivTree.Node16.trvs 234s Parameter 30 : hivTree.Node16.trst 234s Parameter 31 : hivTree.256.trvs 234s Parameter 32 : hivTree.256.trst 234s Parameter 33 : hivTree.822.trvs 234s Parameter 34 : hivTree.822.trst 234s Parameter 35 : hivTree.159.trvs 234s Parameter 36 : hivTree.159.trst 234s Parameter 37 : hivTree.Node21.trvs 234s Parameter 38 : hivTree.Node21.trst 234s Parameter 39 : hivTree.iNode2.trvs 234s Parameter 40 : hivTree.iNode2.trst 234s Parameter 41 : hivTree.Node15.trvs 234s Parameter 42 : hivTree.Node15.trst 234s 234s Constrained Parameters List 234s 234s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 234s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 234s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 234s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 234s + '[' -f aa.bf ']' 234s + hyphy aa.bf 235s Log Likelihood = -1134.73158903913; 235s Tree theTree=(((Langur:0.07430927355753303,Baboon:0.03832845958677486)Node2:0.02339192532927102,Human:0.05949975683358704)Node1:0.02006656431022491,Rat:0.2458809238984347,(Cow:0.2552868260837879,Horse:0.5627637212219557)Node7:0.07060308849528245); 235s + for i in *.bf 235s + '[' -f definitions2.bf ']' 235s + hyphy definitions2.bf 235s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 235s 235s Sample by MEAN: 235s 235s Sample mean = 0.5 (sample variance = 0.2450374540764348) 235s 235s Rate[0]= 0.06847689 (weight=0.2500000) 235s Rate[1]= 0.23837593 (weight=0.2500000) 235s Rate[2]= 0.50000000 (weight=0.2500000) 235s Rate[3]= 1.19314718 (weight=0.2500000) 235s ------------------------------------------------ 235s 235s Sample by MEDIAN: 235s 235s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 235s 235s Rate[0]= 0.06676570 (weight=0.2500000) 235s Rate[1]= 0.23500181 (weight=0.2500000) 235s Rate[2]= 0.49041463 (weight=0.2500000) 235s Rate[3]= 1.03972077 (weight=0.2500000) 235s ------------------------------------------------ 235s 235s Sample by SCALED_MEDIAN: 235s 235s Sample mean = 0.5 (sample variance = 0.2154404122636025) 235s 235s Rate[0]= 0.07289218 (weight=0.2500000) 235s Rate[1]= 0.25656580 (weight=0.2500000) 235s Rate[2]= 0.53541552 (weight=0.2500000) 235s Rate[3]= 1.13512650 (weight=0.2500000) 235s ------------------------------------------------ 235s 235s Sample by MEAN (numerical averaging): 235s 235s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 235s 235s Rate[0]= 0.06846096 (weight=0.2500000) 235s Rate[1]= 0.23834015 (weight=0.2500000) 235s Rate[2]= 0.49996411 (weight=0.2500000) 235s Rate[3]= 1.19314889 (weight=0.2500000) 235s ------------------------------------------------ 235s 235s Sample by MEAN (numerical CDF and averaging): 235s 235s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 235s 235s Rate[0]= 0.06849282 (weight=0.2500000) 235s Rate[1]= 0.23835613 (weight=0.2500000) 235s Rate[2]= 0.49994751 (weight=0.2500000) 235s Rate[3]= 1.19311765 (weight=0.2500000) 235s ------------------------------------------------ 235s 2). Equiprobable rates sampled from Exponential with lambda = 2 235s 235s Sample by MEDIAN (3 rate classes): 235s 235s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 235s 235s Rate[0]= 0.09116078 (weight=0.3333333) 235s Rate[1]= 0.34657359 (weight=0.3333333) 235s Rate[2]= 0.89587973 (weight=0.3333333) 235s ------------------------------------------------ 235s 235s Sample by MEDIAN (9 rate classes): 235s 235s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 235s 235s Rate[0]= 0.02857921 (weight=0.1111111) 235s Rate[1]= 0.09116078 (weight=0.1111111) 235s Rate[2]= 0.16271120 (weight=0.1111111) 235s Rate[3]= 0.24623824 (weight=0.1111111) 235s Rate[4]= 0.34657359 (weight=0.1111111) 235s Rate[5]= 0.47223080 (weight=0.1111111) 235s Rate[6]= 0.64046692 (weight=0.1111111) 235s Rate[7]= 0.89587973 (weight=0.1111111) 235s Rate[8]= 1.44518588 (weight=0.1111111) 235s ------------------------------------------------ 235s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 235s 235s Sample by MEAN (10 rate classes): 235s 235s Sample mean = 1 (sample variance = 0.1057310289486733) 235s 235s Rate[0]= 0.52447499 (weight=0.1000000) 235s Rate[1]= 0.67866972 (weight=0.1000000) 235s Rate[2]= 0.77209919 (weight=0.1000000) 235s Rate[3]= 0.85214884 (weight=0.1000000) 235s Rate[4]= 0.92850815 (weight=0.1000000) 235s Rate[5]= 1.00664500 (weight=0.1000000) 235s Rate[6]= 1.09192933 (weight=0.1000000) 235s Rate[7]= 1.19267960 (weight=0.1000000) 235s Rate[8]= 1.32858029 (weight=0.1000000) 235s Rate[9]= 1.62426489 (weight=0.1000000) 235s ------------------------------------------------ 235s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 235s 235s Sample by MEAN (10 rate classes): 235s 235s Sample mean = 2 (sample variance = 0.04259071282256012) 235s 235s Rate[0]= 1.66431246 (weight=0.1000000) 235s Rate[1]= 1.79212822 (weight=0.1000000) 235s Rate[2]= 1.86123411 (weight=0.1000000) 235s Rate[3]= 1.91722052 (weight=0.1000000) 235s Rate[4]= 1.96832799 (weight=0.1000000) 235s Rate[5]= 2.01862937 (weight=0.1000000) 235s Rate[6]= 2.07152664 (weight=0.1000000) 235s Rate[7]= 2.13166629 (weight=0.1000000) 235s Rate[8]= 2.20930216 (weight=0.1000000) 235s Rate[9]= 2.36565224 (weight=0.1000000) 235s ------------------------------------------------ 235s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 235s 235s Sample by MEAN (8 rate classes): 235s 235s Sample mean = 0.5 (sample variance = 0.09375000225643569) 235s 235s Rate[0]= 0.06250000 (weight=0.1250000) 235s Rate[1]= 0.18750000 (weight=0.1250000) 235s Rate[2]= 0.31250001 (weight=0.1250000) 235s Rate[3]= 0.43750001 (weight=0.1250000) 235s Rate[4]= 0.56249993 (weight=0.1250000) 235s Rate[5]= 0.68750001 (weight=0.1250000) 235s Rate[6]= 0.81250002 (weight=0.1250000) 235s Rate[7]= 0.93750002 (weight=0.1250000) 235s ------------------------------------------------ 235s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 235s 235s Sample by MEAN (8 rate classes): 235s 235s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 235s 235s Rate[0]= 2.17658588 (weight=0.1250000) 235s Rate[1]= 2.55230783 (weight=0.1250000) 235s Rate[2]= 2.75432532 (weight=0.1250000) 235s Rate[3]= 2.92101185 (weight=0.1250000) 235s Rate[4]= 3.07898815 (weight=0.1250000) 235s Rate[5]= 3.24567468 (weight=0.1250000) 235s Rate[6]= 3.44769217 (weight=0.1250000) 235s Rate[7]= 3.82341415 (weight=0.1250000) 235s ------------------------------------------------ 235s + for i in *.bf 235s + '[' -f definitions3.bf ']' 235s + hyphy definitions3.bf 235s 235s 235s Sample mean = 1 (sample variance = 0.9920002887656187) 235s 235s Rate[0]= 0.05175536 (weight=0.1000000) 235s Rate[1]= 0.16309623 (weight=0.1000000) 235s Rate[2]= 0.28842380 (weight=0.1000000) 235s Rate[3]= 0.43177086 (weight=0.1000000) 235s Rate[4]= 0.59921784 (weight=0.1000000) 235s Rate[5]= 0.80057298 (weight=0.1000000) 235s Rate[6]= 1.05324451 (weight=0.1000000) 235s Rate[7]= 1.39304259 (weight=0.1000000) 235s Rate[8]= 1.91629073 (weight=0.1000000) 235s Rate[9]= 3.30258509 (weight=0.1000000) 235s ------------------------------------------------ 235s + for i in *.bf 235s + '[' -f displayFunction.bf ']' 235s + hyphy displayFunction.bf 235s + for i in *.bf 235s + '[' -f profile_test.bf ']' 235s + hyphy profile_test.bf 235s 235s Total run time (seconds) : 0.000000 235s Total number of steps : 1500005 235s 235s 1 : s=0; 235s Call count: 1 235s Time (seconds): 5.3e-11 235s 2 : m={5,1}; 235s Call count: 1 235s Time (seconds): 6.5e-11 235s 3 : k=0; 235s Call count: 1 235s Time (seconds): 7e-12 235s 4 : Branch under condition 'k<250000' 235s to 235s s=s+k; 235s else 235s #profilePAUSE, ; 235s Call count: 250001 235s Time (seconds): 5.823900000003703e-08 235s 5 : s=s+k; 235s Call count: 250000 235s Time (seconds): 6.059800000003875e-08 235s 6 : t=Random(0,5); 235s Call count: 250000 235s Time (seconds): 5.88790000000363e-08 235s 7 : m[t]=m[t]+1; 235s Call count: 250000 235s Time (seconds): 1.643110000001407e-07 235s 8 : k=k+1; 235s Call count: 250000 235s Time (seconds): 6.268600000003954e-08 235s 9 : Go to step 4 235s Call count: 250000 235s Time (seconds): 1.576699999999511e-08 235s 10 : #profilePAUSE, ; 235s Call count: 1 235s Time (seconds): 3e-12 235s + for i in *.bf 235s + '[' -f shared.bf ']' 235s + hyphy shared.bf 235s + rm -f '*messages.log*' '*errors.log*' 236s autopkgtest [14:55:28]: test run-unit-tests: -----------------------] 236s autopkgtest [14:55:28]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 236s run-unit-tests PASS 237s autopkgtest [14:55:29]: @@@@@@@@@@@@@@@@@@@@ summary 237s run-unit-tests PASS 249s Creating nova instance adt-noble-arm64-hyphy-20240316-145132-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...