0s autopkgtest [16:49:36]: starting date and time: 2024-03-17 16:49:36+0000 0s autopkgtest [16:49:36]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [16:49:36]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6nao053u/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-ppc64el-2.secgroup --name adt-noble-ppc64el-hyphy-20240317-164936-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/ 87s autopkgtest [16:51:03]: testbed dpkg architecture: ppc64el 87s autopkgtest [16:51:03]: testbed apt version: 2.7.12 87s autopkgtest [16:51:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 88s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 88s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 88s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 88s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3671 kB] 90s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [482 kB] 90s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [641 kB] 90s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 90s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 90s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 90s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3965 kB] 91s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 91s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [48.2 kB] 91s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 93s Fetched 8996 kB in 3s (2689 kB/s) 94s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Calculating upgrade... 96s The following packages have been kept back: 96s curl 96s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 96s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 97s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 97s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 97s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 97s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 98s Reading package lists... 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 99s The following packages have been kept back: 99s curl 99s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 102s autopkgtest [16:51:18]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 102s autopkgtest [16:51:18]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (dsc) [2417 B] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (tar) [2613 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (diff) [17.2 kB] 105s gpgv: Signature made Sat Mar 16 06:59:46 2024 UTC 105s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 105s gpgv: issuer "steve.langasek@ubuntu.com" 105s gpgv: Can't check signature: No public key 105s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.59+dfsg-1build2.dsc: no acceptable signature found 105s autopkgtest [16:51:21]: testing package hyphy version 2.5.59+dfsg-1build2 106s autopkgtest [16:51:22]: build not needed 107s autopkgtest [16:51:23]: test run-unit-tests: preparing testbed 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 109s The following additional packages will be installed: 109s curl hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 109s libcurl3t64-gnutls libcurl4t64 libdrm-amdgpu1 libevent-pthreads-2.1-7 109s libfabric1 libgnutls30t64 libgomp1 libhogweed6t64 libhsa-runtime64-1 109s libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 libmunge2 libnettle8t64 109s libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 librdmacm1t64 libssl3t64 109s libucx0 libxnvctrl0 ocl-icd-libopencl1 109s Suggested packages: 109s gnutls-bin opencl-icd 109s The following packages will be REMOVED: 109s libcurl3-gnutls libcurl4 libgnutls30 libhogweed6 libnettle8 libpsl5 libssl3 109s The following NEW packages will be installed: 109s autopkgtest-satdep hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 109s libamdhip64-5 libcurl3t64-gnutls libcurl4t64 libdrm-amdgpu1 109s libevent-pthreads-2.1-7 libfabric1 libgnutls30t64 libgomp1 libhogweed6t64 109s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 109s libmunge2 libnettle8t64 libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 109s librdmacm1t64 libssl3t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 109s The following packages will be upgraded: 109s curl 109s 1 upgraded, 30 newly installed, 7 to remove and 0 not upgraded. 109s Need to get 62.1 MB/62.1 MB of archives. 109s After this operation, 266 MB of additional disk space will be used. 109s Get:1 /tmp/autopkgtest.06szZY/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 109s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2 [226 kB] 109s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2 [208 kB] 109s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu2 [1154 kB] 109s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu1 [2168 kB] 109s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl4t64 ppc64el 8.5.0-2ubuntu7 [428 kB] 109s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el curl ppc64el 8.5.0-2ubuntu7 [234 kB] 109s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpsl5t64 ppc64el 0.21.2-1.1 [59.0 kB] 109s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl3t64-gnutls ppc64el 8.5.0-2ubuntu7 [419 kB] 109s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el hyphy-common all 2.5.59+dfsg-1build2 [624 kB] 109s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 109s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-9 [7844 B] 109s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el librdmacm1t64 ppc64el 50.0-2 [80.9 kB] 109s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfabric1 ppc64el 1.17.0-3 [677 kB] 110s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] 110s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmunge2 ppc64el 0.5.15-3ubuntu1 [17.6 kB] 110s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] 110s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] 110s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] 110s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] 110s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix2t64 ppc64el 5.0.1-4.1 [765 kB] 110s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libllvm17 ppc64el 1:17.0.6-5build1 [27.3 MB] 110s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3 [15.3 MB] 111s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] 111s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsakmt1 ppc64el 5.7.0-1 [76.5 kB] 111s Get:26 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-1 [330 kB] 111s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamdhip64-5 ppc64el 5.2.3-12 [5004 kB] 111s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el libucx0 ppc64el 1.16.0+ds-4 [1203 kB] 111s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-6ubuntu1 [2721 kB] 111s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el hyphy-mpi ppc64el 2.5.59+dfsg-1build2 [1364 kB] 111s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el hyphy-pt ppc64el 2.5.59+dfsg-1build2 [1323 kB] 111s Fetched 62.1 MB in 2s (28.9 MB/s) 111s dpkg: libhogweed6:ppc64el: dependency problems, but removing anyway as you requested: 111s librtmp1:ppc64el depends on libhogweed6. 111s libjcat1:ppc64el depends on libhogweed6. 111s libgnutls30:ppc64el depends on libhogweed6 (>= 3.6). 111s 111s (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 ... 70095 files and directories currently installed.) 111s Removing libhogweed6:ppc64el (3.9.1-2) ... 111s dpkg: libnettle8:ppc64el: dependency problems, but removing anyway as you requested: 111s librtmp1:ppc64el depends on libnettle8. 111s libgnutls30:ppc64el depends on libnettle8 (>= 3.9~). 111s libcurl3-gnutls:ppc64el depends on libnettle8. 111s libarchive13:ppc64el depends on libnettle8. 111s 111s Removing libnettle8:ppc64el (3.9.1-2) ... 111s Selecting previously unselected package libnettle8t64:ppc64el. 111s (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 ... 70083 files and directories currently installed.) 111s Preparing to unpack .../libnettle8t64_3.9.1-2.2_ppc64el.deb ... 111s Unpacking libnettle8t64:ppc64el (3.9.1-2.2) ... 111s Selecting previously unselected package libhogweed6t64:ppc64el. 111s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_ppc64el.deb ... 111s Unpacking libhogweed6t64:ppc64el (3.9.1-2.2) ... 111s dpkg: libgnutls30:ppc64el: dependency problems, but removing anyway as you requested: 111s librtmp1:ppc64el depends on libgnutls30 (>= 3.7.2). 111s libldap2:ppc64el depends on libgnutls30 (>= 3.8.2). 111s libjcat1:ppc64el depends on libgnutls30 (>= 3.7.3). 111s libcurl3-gnutls:ppc64el depends on libgnutls30 (>= 3.8.2). 111s fwupd depends on libgnutls30 (>= 3.7.3). 111s dirmngr depends on libgnutls30 (>= 3.8.1). 111s apt depends on libgnutls30 (>= 3.8.1). 111s 111s (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 ... 70097 files and directories currently installed.) 111s Removing libgnutls30:ppc64el (3.8.3-1ubuntu1) ... 111s Selecting previously unselected package libgnutls30t64:ppc64el. 111s (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 ... 70088 files and directories currently installed.) 111s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_ppc64el.deb ... 111s Unpacking libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ... 112s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 112s wget depends on libssl3 (>= 3.0.0). 112s tnftp depends on libssl3 (>= 3.0.0). 112s tcpdump depends on libssl3 (>= 3.0.0). 112s systemd-resolved depends on libssl3 (>= 3.0.0). 112s systemd depends on libssl3 (>= 3.0.0). 112s sudo depends on libssl3 (>= 3.0.0). 112s rsync depends on libssl3 (>= 3.0.0). 112s python3-cryptography depends on libssl3 (>= 3.0.0). 112s openssl depends on libssl3 (>= 3.0.9). 112s openssh-server depends on libssl3 (>= 3.0.10). 112s openssh-client depends on libssl3 (>= 3.0.10). 112s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 112s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 112s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 112s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 112s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 112s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 112s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 112s libnvme1 depends on libssl3 (>= 3.0.0). 112s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 112s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 112s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 112s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 112s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 112s kmod depends on libssl3 (>= 3.0.0). 112s dhcpcd-base depends on libssl3 (>= 3.0.0). 112s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 112s 112s (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 ... 70116 files and directories currently installed.) 112s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 112s Selecting previously unselected package libssl3t64:ppc64el. 112s (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 ... 70105 files and directories currently installed.) 112s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_ppc64el.deb ... 112s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 112s dpkg: libcurl4:ppc64el: dependency problems, but removing anyway as you requested: 112s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 112s 112s (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 ... 70118 files and directories currently installed.) 112s Removing libcurl4:ppc64el (8.5.0-2ubuntu2) ... 112s Selecting previously unselected package libcurl4t64:ppc64el. 112s (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 ... 70113 files and directories currently installed.) 112s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_ppc64el.deb ... 112s Unpacking libcurl4t64:ppc64el (8.5.0-2ubuntu7) ... 112s Preparing to unpack .../curl_8.5.0-2ubuntu7_ppc64el.deb ... 112s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 112s dpkg: libpsl5:ppc64el: dependency problems, but removing anyway as you requested: 112s wget depends on libpsl5 (>= 0.16.0). 112s libcurl3-gnutls:ppc64el depends on libpsl5 (>= 0.16.0). 112s 112s (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 ... 70119 files and directories currently installed.) 112s Removing libpsl5:ppc64el (0.21.2-1build1) ... 112s Selecting previously unselected package libpsl5t64:ppc64el. 112s (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 ... 70114 files and directories currently installed.) 112s Preparing to unpack .../libpsl5t64_0.21.2-1.1_ppc64el.deb ... 112s Unpacking libpsl5t64:ppc64el (0.21.2-1.1) ... 112s dpkg: libcurl3-gnutls:ppc64el: dependency problems, but removing anyway as you requested: 112s libfwupd2:ppc64el depends on libcurl3-gnutls (>= 7.63.0). 112s fwupd depends on libcurl3-gnutls (>= 7.63.0). 112s 112s (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 ... 70120 files and directories currently installed.) 112s Removing libcurl3-gnutls:ppc64el (8.5.0-2ubuntu2) ... 112s Selecting previously unselected package libcurl3t64-gnutls:ppc64el. 112s (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 ... 70113 files and directories currently installed.) 112s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu7_ppc64el.deb ... 112s Unpacking libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu7) ... 112s Selecting previously unselected package hyphy-common. 112s Preparing to unpack .../01-hyphy-common_2.5.59+dfsg-1build2_all.deb ... 112s Unpacking hyphy-common (2.5.59+dfsg-1build2) ... 112s Selecting previously unselected package libgomp1:ppc64el. 112s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 112s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 112s Selecting previously unselected package libevent-pthreads-2.1-7:ppc64el. 112s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9_ppc64el.deb ... 112s Unpacking libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 112s Selecting previously unselected package librdmacm1t64:ppc64el. 112s Preparing to unpack .../04-librdmacm1t64_50.0-2_ppc64el.deb ... 112s Unpacking librdmacm1t64:ppc64el (50.0-2) ... 112s Selecting previously unselected package libfabric1:ppc64el. 112s Preparing to unpack .../05-libfabric1_1.17.0-3_ppc64el.deb ... 112s Unpacking libfabric1:ppc64el (1.17.0-3) ... 112s Selecting previously unselected package libhwloc15:ppc64el. 112s Preparing to unpack .../06-libhwloc15_2.10.0-1_ppc64el.deb ... 112s Unpacking libhwloc15:ppc64el (2.10.0-1) ... 112s Selecting previously unselected package libmunge2:ppc64el. 112s Preparing to unpack .../07-libmunge2_0.5.15-3ubuntu1_ppc64el.deb ... 112s Unpacking libmunge2:ppc64el (0.5.15-3ubuntu1) ... 112s Selecting previously unselected package libpciaccess0:ppc64el. 112s Preparing to unpack .../08-libpciaccess0_0.17-3_ppc64el.deb ... 112s Unpacking libpciaccess0:ppc64el (0.17-3) ... 112s Selecting previously unselected package libxnvctrl0:ppc64el. 112s Preparing to unpack .../09-libxnvctrl0_510.47.03-0ubuntu1_ppc64el.deb ... 112s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 112s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 112s Preparing to unpack .../10-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... 112s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 112s Selecting previously unselected package libhwloc-plugins:ppc64el. 112s Preparing to unpack .../11-libhwloc-plugins_2.10.0-1_ppc64el.deb ... 112s Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... 112s Selecting previously unselected package libpmix2t64:ppc64el. 112s Preparing to unpack .../12-libpmix2t64_5.0.1-4.1_ppc64el.deb ... 112s Unpacking libpmix2t64:ppc64el (5.0.1-4.1) ... 112s Selecting previously unselected package libllvm17:ppc64el. 112s Preparing to unpack .../13-libllvm17_1%3a17.0.6-5build1_ppc64el.deb ... 112s Unpacking libllvm17:ppc64el (1:17.0.6-5build1) ... 113s Selecting previously unselected package libamd-comgr2:ppc64el. 113s Preparing to unpack .../14-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_ppc64el.deb ... 113s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 114s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 114s Preparing to unpack .../15-libdrm-amdgpu1_2.4.120-2_ppc64el.deb ... 114s Unpacking libdrm-amdgpu1:ppc64el (2.4.120-2) ... 114s Selecting previously unselected package libhsakmt1:ppc64el. 114s Preparing to unpack .../16-libhsakmt1_5.7.0-1_ppc64el.deb ... 114s Unpacking libhsakmt1:ppc64el (5.7.0-1) ... 114s Selecting previously unselected package libhsa-runtime64-1. 114s Preparing to unpack .../17-libhsa-runtime64-1_5.7.1-1_ppc64el.deb ... 114s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 114s Selecting previously unselected package libamdhip64-5. 114s Preparing to unpack .../18-libamdhip64-5_5.2.3-12_ppc64el.deb ... 114s Unpacking libamdhip64-5 (5.2.3-12) ... 114s Selecting previously unselected package libucx0:ppc64el. 114s Preparing to unpack .../19-libucx0_1.16.0+ds-4_ppc64el.deb ... 114s Unpacking libucx0:ppc64el (1.16.0+ds-4) ... 114s Selecting previously unselected package libopenmpi3t64:ppc64el. 114s Preparing to unpack .../20-libopenmpi3t64_4.1.6-6ubuntu1_ppc64el.deb ... 114s Unpacking libopenmpi3t64:ppc64el (4.1.6-6ubuntu1) ... 114s Selecting previously unselected package hyphy-mpi. 114s Preparing to unpack .../21-hyphy-mpi_2.5.59+dfsg-1build2_ppc64el.deb ... 114s Unpacking hyphy-mpi (2.5.59+dfsg-1build2) ... 114s Selecting previously unselected package hyphy-pt. 114s Preparing to unpack .../22-hyphy-pt_2.5.59+dfsg-1build2_ppc64el.deb ... 114s Unpacking hyphy-pt (2.5.59+dfsg-1build2) ... 114s Selecting previously unselected package autopkgtest-satdep. 114s Preparing to unpack .../23-1-autopkgtest-satdep.deb ... 114s Unpacking autopkgtest-satdep (0) ... 114s Setting up libpciaccess0:ppc64el (0.17-3) ... 114s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 114s Setting up libpsl5t64:ppc64el (0.21.2-1.1) ... 114s Setting up hyphy-common (2.5.59+dfsg-1build2) ... 114s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 114s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 114s Setting up libnettle8t64:ppc64el (3.9.1-2.2) ... 114s Setting up libmunge2:ppc64el (0.5.15-3ubuntu1) ... 114s Setting up libhwloc15:ppc64el (2.10.0-1) ... 114s Setting up libhogweed6t64:ppc64el (3.9.1-2.2) ... 114s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 114s Setting up librdmacm1t64:ppc64el (50.0-2) ... 114s Setting up libllvm17:ppc64el (1:17.0.6-5build1) ... 114s Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 114s Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... 114s Setting up libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ... 114s Setting up libfabric1:ppc64el (1.17.0-3) ... 114s Setting up libcurl4t64:ppc64el (8.5.0-2ubuntu7) ... 114s Setting up libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu7) ... 114s Setting up hyphy-pt (2.5.59+dfsg-1build2) ... 114s Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... 114s Setting up libpmix2t64:ppc64el (5.0.1-4.1) ... 114s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 114s Setting up curl (8.5.0-2ubuntu7) ... 114s Setting up libhsakmt1:ppc64el (5.7.0-1) ... 114s Setting up libhsa-runtime64-1 (5.7.1-1) ... 114s Setting up libamdhip64-5 (5.2.3-12) ... 114s Setting up libucx0:ppc64el (1.16.0+ds-4) ... 114s Setting up libopenmpi3t64:ppc64el (4.1.6-6ubuntu1) ... 114s Setting up hyphy-mpi (2.5.59+dfsg-1build2) ... 114s Setting up autopkgtest-satdep (0) ... 114s Processing triggers for man-db (2.12.0-3) ... 115s Processing triggers for libc-bin (2.39-0ubuntu2) ... 117s (Reading database ... 71024 files and directories currently installed.) 117s Removing autopkgtest-satdep (0) ... 118s autopkgtest [16:51:34]: test run-unit-tests: [----------------------- 118s + for i in *.bf 118s + '[' -f ExonIntron.bf ']' 118s + hyphy ExonIntron.bf 119s Log Likelihood = -1113.3452348024; 119s 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); 119s 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); 119s 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); 119s + for i in *.bf 119s + '[' -f F81.bf ']' 119s + hyphy F81.bf 119s Log Likelihood = -1187.54702793712; 119s 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); 119s + for i in *.bf 119s + '[' -f F81relrate.bf ']' 119s + hyphy F81relrate.bf 119s 119s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001001418486; 119s Tree threeTaxaTree=(a:0.08501458081697648,b:0.0733761297957005,c:0.1653894109016959); 119s 119s 119s 1). With the outgroup at taxon #1, the P-value is:0.002155106158058917 119s Log Likelihood = -948.707253867892; 119s Tree threeTaxaTree=(a:0.08228741153904655,b:0.119450759858316,c:0.119450759858316); 119s 119s 119s 2). With the outgroup at taxon #2, the P-value is:0.008353404399322084 119s Log Likelihood = -947.479050125766; 119s Tree threeTaxaTree=(a:0.1250762630043411,b:0.07125949122322148,c:0.1250762630043411); 119s 119s 119s 3). With the outgroup at taxon #3, the P-value is:0.6669137053248184 119s Log Likelihood = -944.093618166699; 119s Tree threeTaxaTree=(a:0.07922729811878117,b:0.07922729811878117,c:0.165333983818582); 119s + for i in *.bf 119s + '[' -f F81relratio.bf ']' 119s + hyphy F81relratio.bf 119s + for i in *.bf 119s + '[' -f HKY85.bf ']' 119s + hyphy HKY85.bf 119s 119s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059583111; 119s Tree fourTaxaTree1=((1:0.1129103974967786,2:0.1073438667590712)Node1:0.09978716101100081,3:0.3469444073497459,4:0.321901988109122); 119s Tree fourTaxaTree2=((1:0.08585822407067131,2:0.09338071137963387)Node1:0.07364164481371639,3:0.3933120496818053,4:0.3801922686510784); 119s 119s 119s 1). Relative ratio constraint; the P-value is:0.6933531589969584 119s Log Likelihood = -2575.74610909071; 119s Global Parameters: 119s R=1.007290914989641; 119s 119s Tree fourTaxaTree1=((1:0.09948363759362119,2:0.09943036934765574)Node1:0.0869682813941792,3:0.3687236032519883,4:0.3489177318846092); 119s Tree fourTaxaTree2=((1:0.1000737336848971,2:0.100020149473568)Node1:0.08748414153115294,3:0.3709107202724674,4:0.3509873686082183); 119s Log Likelihood = -1152.88077773909; 119s 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); 119s + for i in *.bf 119s + '[' -f HKY852blocks.bf ']' 119s + hyphy HKY852blocks.bf 119s 119s ----- RESULTS ----- 119s Log Likelihood = -6801.91478425276; 119s 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); 119s 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); 119s + for i in *.bf 119s + '[' -f HKY852blocks2models.bf ']' 119s + hyphy HKY852blocks2models.bf 119s 119s ----- RESULTS ----- 119s Log Likelihood = -6049.33413410755; 119s 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); 119s 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); 119s + for i in *.bf 119s + '[' -f HKY85relrate.bf ']' 119s + hyphy HKY85relrate.bf 119s 119s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371751632424; 119s Tree threeTaxaTree=(a:0.08473003175317764,b:0.07473137597643539,c:0.174064542689109); 119s 119s 119s 1). Outgroup at taxon #1 119s a). Transition rate test. P-Value = 0.02098226516725465 119s Log Likelihood = -924.035884021378; 119s Tree threeTaxaTree=(a:0.08099123330674669,b:0.1064970277501439,c:0.1431287422547734); 119s 119s b). Transversion rate test. P-Value = 0.03655174813200768 119s Log Likelihood = -923.55733986013; 119s Tree threeTaxaTree=(a:0.084385863180111,b:0.09108496720824998,c:0.1577932370277693); 119s 119s c). Both rates test. P-Value = 0.00632399828374719 119s Log Likelihood = -926.435155263498; 119s Tree threeTaxaTree=(a:0.08054167256686441,b:0.1248197388549912,c:0.1248197388549912); 119s 119s 119s 2). Outgroup at taxon #2 119s a). Transition rate test. P-Value = 0.02758028958440228 119s Log Likelihood = -923.798808189923; 119s Tree threeTaxaTree=(a:0.1157945362947561,b:0.0710231672763683,c:0.1442792954111021); 119s 119s b). Transversion rate test. P-Value = 0.1106456954857765 119s Log Likelihood = -922.644238896077; 119s Tree threeTaxaTree=(a:0.09762132520456517,b:0.07463527366174004,c:0.1608971533992973); 119s 119s c). Both rates test. P-Value = 0.02199500082285188 119s Log Likelihood = -925.188691719246; 119s Tree threeTaxaTree=(a:0.1299135255623827,b:0.07078650465677661,c:0.1299135255623827); 119s 119s 119s 3). Outgroup at taxon #3 119s a). Transition rate test. P-Value = 0.9291732773304646 119s Log Likelihood = -921.37570190709; 119s Tree threeTaxaTree=(a:0.08354358737958395,b:0.07588180027038632,c:0.1740455829900139); 119s 119s b). Transversion rate test. P-Value = 0.5919879178907992 119s Log Likelihood = -921.515376857668; 119s Tree threeTaxaTree=(a:0.08115157531975309,b:0.07834973653854679,c:0.1740031943295483); 119s 119s c). Both rates test. P-Value = 0.8615417030144421 119s + for i in *.bf 119s Log Likelihood = -921.520783449156; 119s Tree threeTaxaTree=(a:0.07974273880137919,b:0.07974273880137919,c:0.1740977261800018); 119s + '[' -f HKY85relratio.bf ']' 119s + hyphy HKY85relratio.bf 119s 119s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78442604578; 119s Tree fourTaxaTree1=((1:0.113791381333629,2:0.1109812084398387)Node1:0.1041142737713125,3:0.3523124007351069,4:0.3312024761326549); 119s Tree fourTaxaTree2=((1:0.08607518432405536,2:0.09347854528016543)Node1:0.08034238812430958,3:0.3860171002678663,4:0.3896629274258822); 119s 119s 119s 1). Relative ratio constraint on transitions; the P-value is:0.5738619496010586 119s Log Likelihood = -2541.23688270234; 119s Global Parameters: 119s R=0.857859886787587; 119s 119s Tree fourTaxaTree1=((1:0.1086802469370478,2:0.09422126334199116)Node1:0.1116166730257614,3:0.3552433767353616,4:0.3552103925067623); 119s Tree fourTaxaTree2=((1:0.09038010622587356,2:0.1091768128240128)Node1:0.07302607950862043,3:0.3839597771249044,4:0.3656457444895455); 119s 119s 119s 2). Relative ratio constraint on transversions; the P-value is:0.5738586713323656 119s Log Likelihood = -2541.23689234809; 119s Global Parameters: 119s R=0.8583181346135639; 119s 119s Tree fourTaxaTree1=((1:0.108676326355565,2:0.09420490762588636)Node1:0.1115472480453758,3:0.3552507058813295,4:0.3551641378526289); 119s Tree fourTaxaTree2=((1:0.0903829267380851,2:0.1092126253201284)Node1:0.07300223899624374,3:0.383998103571856,4:0.3657564835059527); 119s 119s 119s 3). Relative ratio constraint on both rates; the P-value is:0.656593458642062 119s Log Likelihood = -2543.19086899059; 119s Global Parameters: 119s R=0.99658305319929; 119s 119s Tree fourTaxaTree1=((1:0.1004912977418655,2:0.1007192360110612)Node1:0.09258175841483439,3:0.3715174282866335,4:0.3582233653223759); 119s Tree fourTaxaTree2=((1:0.1003311983863386,2:0.1007179506033033)Node1:0.09288090482056402,3:0.369982009902517,4:0.357712490363656); 119s + for i in *.bf 119s + '[' -f HKY85shared.bf ']' 119s + hyphy HKY85shared.bf 120s Log Likelihood = -1165.7030112399; 120s Global Parameters: 120s R=2.970525480369322; 120s 120s 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); 120s + for i in *.bf 120s + '[' -f JC69.bf ']' 120s + hyphy JC69.bf 120s Log Likelihood = -1230.82014326801; 120s 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); 120s + for i in *.bf 120s + '[' -f K2P.bf ']' 120s + hyphy K2P.bf 120s Log Likelihood = -1198.26189040159; 120s 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); 120s + for i in *.bf 120s + '[' -f K2Pshared.bf ']' 120s + hyphy K2Pshared.bf 120s Log Likelihood = -1210.49419565614; 120s Global Parameters: 120s R=2.61677690422922; 120s 120s 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); 120s + for i in *.bf 120s + '[' -f MatrixIndexing.bf ']' 120s + hyphy MatrixIndexing.bf 120s 120s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 120s { 120s {0.431645126415334, 0.83327813093394, 0.4397485517989259, 0.7614810533731899, 0.7129074231984344, 0.3337489334712151} 120s {0.6414772350437653, 0.3583661032278012, 0.81824477012694, 0.1650213157211014, 0.161452558860521, 0.3888730535723439} 120s {0.5458675267980125, 0.4336546865370252, 0.2231853534987162, 0.7848680898977602, 0.5948883354651947, 0.8844013469955887} 120s {0.6161882666908642, 0.9562113385079921, 0.3203041563556306, 0.298652764479316, 0.4844835180520274, 0.308877068876493} 120s {0.8332488347853647, 0.6544911034066442, 0.7909521760397945, 0.4291895736076845, 0.1539410560284604, 0.1228612750123398} 120s } 120s 120s 2). Accessing a second-row third-column element and a random element. 120s 120s matrix[1][2]=0.81824477012694 120s matrix[2][5]=0.8844013469955887 120s 120s 3). Accessing the fourth row. 120s 120s matrix[3][-1]= 120s { 120s {0.6161882666908642, 0.9562113385079921, 0.3203041563556306, 0.298652764479316, 0.4844835180520274, 0.308877068876493} 120s } 120s 120s 4). Accessing the first column. 120s 120s matrix[-1][0]= 120s { 120s {0.431645126415334} 120s {0.6414772350437653} 120s {0.5458675267980125} 120s {0.6161882666908642} 120s {0.8332488347853647} 120s } 120s 120s 5). Populating a matrix template (below the diagonal). 120s 120s { 120s {0, 0, 0, 0, 0, 0} 120s {1, 0, 0, 0, 0, 0} 120s {1, 1, 0, 0, 0, 0} 120s {1, 1, 1, 0, 0, 0} 120s {1, 1, 1, 1, 0, 0} 120s } 120s 120s 6). Extracting (by row) matrix elements using the template. 120s 120s { 120s {0.6414772350437653, 0.5458675267980125, 0.4336546865370252, 0.6161882666908642, 0.9562113385079921, 0.3203041563556306, 0.8332488347853647, 0.6544911034066442, 0.7909521760397945, 0.4291895736076845} 120s } 120s 120s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 120s 120s matrix[{{1,1}}][{{3,2}}]= 120s { 120s {0.3583661032278012, 0.81824477012694} 120s {0.4336546865370252, 0.2231853534987162} 120s {0.9562113385079921, 0.3203041563556306} 120s } 120s 120s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 120s 120s 120s { 120s {0.1863175151581097, 1.694352443492761, 1.193378788809253, 1.579853394646343, 1.508236994051432, 1.111388350593174} 120s {0.4114930430793941, 0.128426263942679, 1.669524503840089, 1.027232034642323, 1.02606692876261, 1.151222251794679} 120s {0.2979713568125789, 0.1880563871555256, 0.04981170201634692, 1.616017918539759, 1.35389213167255, 1.782165742567612} 120s {0.3796879800074917, 0.9143401238912459, 0.1025947525786923, 0.08919347373113778, 1.234724279264069, 1.095405043677734} 120s {0.694303620671168, 0.4283586044384466, 0.6256053447820861, 0.184203690093546, 0.02369784873115758, 1.015094892897658} 120s }+ for i in *.bf 120s + '[' -f MolecularClockF81.bf ']' 120s + hyphy MolecularClockF81.bf 120s 120s 120s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124421372; 120s 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); 120s 120s 120s 1). Global Molecular Clock; the P-value is:0 120s Log Likelihood = -11927.6152937466; 120s 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); 120s 120s 120s 2). Molecular Clock starting at Internal1; the P-value is:0.160379891009284 120s Log Likelihood = -11476.6977623965; 120s 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); 120s 120s 120s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:+ for i in *.bf 120s 0.01610191699969754 120s Log Likelihood = -11479.841259083; 120s 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); 120s + '[' -f MolecularClockHKY85.bf ']' 120s + hyphy MolecularClockHKY85.bf 120s 120s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013283038; 120s 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); 120s 120s 120s 1). Global Molecular Clock on transition rates; the P-value is:0 120s Log Likelihood = -11434.7016033505; 120s 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); 120s 120s 120s 2). Global Molecular Clock on transversion rates; the P-value is:0 120s Log Likelihood = -11497.3782660734; 120s 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); 120s 120s 120s 3). Global Molecular Clock on both rates; the P-value is:0 120s Log Likelihood = -11703.6261633936; 120s 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); 120s + for i in *.bf 120s + '[' -f Non-Rev.bf ']' 120s + hyphy Non-Rev.bf 121s Log Likelihood = -1152.78520340395; 121s Global Parameters: 121s GC=0.2678176856372157; 121s CG=0.1884973640941212; 121s GA=1.912366120233473; 121s CT=1.257799996215937; 121s GT=0.08662166487777689; 121s CA=0.9177395876329193; 121s AT=0.4308014505060968; 121s AG=1.583788301379299; 121s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2554263860968757; 121s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.037425186642276; 121s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7977713671122841; 121s 121s Tree givenTree=(256:0.01346212869771218,(822:0.02845742754211651,159:0.006126935908451817)Node2:0.003448052196685787,((113:0.02186772779547555,9939:0.07933718188906294)Node6:0.004992805885283978,(6760:0.07325913150885933,((317:0.0400929491970593,6767:0.06984473760899462)Node12:0.01159515839219042,((135:0.02157162556005525,(529:0.0349722790555065,105r:0.01422325021017295)Node18:0.02378716753369394)Node16:0.005237148438691484,(719:0.02864169200271327,136:0.009563392914063508)Node21:0.04929092279141361)Node15:0.01636543479511182)Node11:0.01273278646018296)Node9:0.02193514648855319)Node5:0.02026421359766841); 121s + for i in *.bf 121s + '[' -f PBootstrapHetRates.bf ']' 121s + hyphy PBootstrapHetRates.bf 121s 121s ----ORIGINAL DATA---- 121s Log Likelihood = -1127.31557906324; 121s Global Parameters: 121s alpha=0.3190248733457374; 121s kappa=0.3235517732929273; 121s 121s 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); 121s 121s Using the seed: 121s 1710696948 121s Category variable name: TRUE 121s Site Rate 121s 0 0.00000 121s 1 0.00000 121s 2 0.00004 121s 3 0.00005 121s 4 0.00009 121s 5 0.00011 121s 6 0.00031 121s 7 0.00034 121s 8 0.00052 121s 9 0.00061 121s 10 0.00062 121s 11 0.00065 121s 12 0.00130 121s 13 0.00133 121s 14 0.00147 121s 15 0.00189 121s 16 0.00206 121s 17 0.00224 121s 18 0.00229 121s 19 0.00244 121s 20 0.00282 121s 21 0.00295 121s 22 0.00323 121s 23 0.00372 121s 24 0.00373 121s 25 0.00378 121s 26 0.00553 121s 27 0.00574 121s 28 0.00621 121s 29 0.00638 121s 30 0.00659 121s 31 0.00730 121s 32 0.00755 121s 33 0.00880 121s 34 0.00933 121s 35 0.00951 121s 36 0.01012 121s 37 0.01209 121s 38 0.01241 121s 39 0.01351 121s 40 0.01447 121s 41 0.01638 121s 42 0.01717 121s 43 0.01741 121s 44 0.01986 121s 45 0.02069 121s 46 0.02077 121s 47 0.02106 121s 48 0.02208 121s 49 0.02290 121s 50 0.02319 121s 51 0.02485 121s 52 0.02586 121s 53 0.02639 121s 54 0.02655 121s 55 0.02658 121s 56 0.02711 121s 57 0.02728 121s 58 0.02773 121s 59 0.02876 121s 60 0.02916 121s 61 0.02964 121s 62 0.03008 121s 63 0.03080 121s 64 0.03241 121s 65 0.03445 121s 66 0.03747 121s 67 0.04185 121s 68 0.04357 121s 69 0.04384 121s 70 0.04547 121s 71 0.04827 121s 72 0.04902 121s 73 0.04938 121s 74 0.05000 121s 75 0.05035 121s 76 0.05088 121s 77 0.05097 121s 78 0.05251 121s 79 0.05352 121s 80 0.05636 121s 81 0.06704 121s 82 0.06914 121s 83 0.07249 121s 84 0.07628 121s 85 0.07908 121s 86 0.07950 121s 87 0.08516 121s 88 0.08774 121s 89 0.08933 121s 90 0.09098 121s 91 0.09697 121s 92 0.09998 121s 93 0.10160 121s 94 0.10212 121s 95 0.10247 121s 96 0.10287 121s 97 0.10567 121s 98 0.10731 121s 99 0.11188 121s 100 0.11628 121s 101 0.11706 121s 102 0.12231 121s 103 0.12307 121s 104 0.13315 121s 105 0.13340 121s 106 0.13691 121s 107 0.13828 121s 108 0.14695 121s 109 0.14702 121s 110 0.14948 121s 111 0.15325 121s 112 0.15554 121s 113 0.15873 121s 114 0.16161 121s 115 0.16548 121s 116 0.16585 121s 117 0.17411 121s 118 0.17527 121s 119 0.17704 121s 120 0.18325 121s 121 0.18445 121s 122 0.18613 121s 123 0.19067 121s 124 0.19260 121s 125 0.19324 121s 126 0.19793 121s 127 0.20056 121s 128 0.20520 121s 129 0.20568 121s 130 0.20798 121s 131 0.21076 121s 132 0.21540 121s 133 0.21820 121s 134 0.22208 121s 135 0.22426 121s 136 0.22575 121s 137 0.23183 121s 138 0.23651 121s 139 0.23763 121s 140 0.24131 121s 141 0.24934 121s 142 0.25469 121s 143 0.25881 121s 144 0.26928 121s 145 0.28524 121s 146 0.29446 121s 147 0.30991 121s 148 0.31417 121s 149 0.32941 121s 150 0.33010 121s 151 0.33135 121s 152 0.33162 121s 153 0.34122 121s 154 0.34386 121s 155 0.35474 121s 156 0.36052 121s 157 0.36232 121s 158 0.36571 121s 159 0.37770 121s 160 0.38066 121s 161 0.39461 121s 162 0.40538 121s 163 0.41075 121s 164 0.41346 121s 165 0.42851 121s 166 0.43696 121s 167 0.47668 121s 168 0.47684 121s 169 0.51507 121s 170 0.51698 121s 171 0.53319 121s 172 0.53383 121s 173 0.55172 121s 174 0.58841 121s 175 0.61297 121s 176 0.62360 121s 177 0.62672 121s 178 0.65193 121s 179 0.66595 121s 180 0.66851 121s 181 0.67651 121s 182 0.70260 121s 183 0.74260 121s 184 0.75367 121s 185 0.75824 121s 186 0.76656 121s 187 0.77097 121s 188 0.77709 121s 189 0.78433 121s 190 0.79221 121s 191 0.81271 121s 192 0.82296 121s 193 0.82903 121s 194 0.86426 121s 195 0.88744 121s 196 0.92034 121s 197 0.92713 121s 198 0.93034 121s 199 1.02051 121s 200 1.03157 121s 201 1.05334 121s 202 1.06816 121s 203 1.06878 121s 204 1.08101 121s 205 1.09129+ for i in *.bf 121s + '[' -f REV.bf ']' 121s + hyphy REV.bf 121s 121s 206 1.25344 121s 207 1.26404 121s 208 1.29189 121s 209 1.29565 121s 210 1.34371 121s 211 1.35582 121s 212 1.46832 121s 213 1.47396 121s 214 1.49947 121s 215 1.56144 121s 216 1.57281 121s 217 1.57745 121s 218 1.60348 121s 219 1.63370 121s 220 1.74920 121s 221 1.80025 121s 222 1.84070 121s 223 1.84833 121s 224 1.84912 121s 225 1.86197 121s 226 1.86446 121s 227 1.97483 121s 228 2.03410 121s 229 2.04537 121s 230 2.06133 121s 231 2.15123 121s 232 2.20957 121s 233 2.30301 121s 234 2.40703 121s 235 2.47627 121s 236 2.53434 121s 237 2.62139 121s 238 2.77458 121s 239 2.84178 121s 240 2.84316 121s 241 2.85008 121s 242 3.07376 121s 243 3.08949 121s 244 3.16568 121s 245 3.26732 121s 246 3.57441 121s 247 3.60130 121s 248 3.71527 121s 249 3.73835 121s 250 3.80440 121s 251 3.80495 121s 252 3.85100 121s 253 3.92368 121s 254 3.92838 121s 255 4.04667 121s 256 4.25520 121s 257 4.35084 121s 258 4.42295 121s 259 4.45285 121s 260 4.53822 121s 261 4.77496 121s 262 5.16480 121s 263 5.29014 121s 264 5.32174 121s 265 5.32779 121s 266 5.77825 121s 267 5.98434 121s 268 6.38247 121s 269 6.54081 121s 270 7.09878 121s 271 8.84733 121s 272 11.32130 121s 121s Mean = 0.9857220487181991 121s Var = 2.684168472215171 (1/alpha) = 3.134551828240264 121s Log Likelihood = -1100.00325191866; 121s 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); 121s + for i in *.bf 121s + '[' -f REVshared.bf ']' 121s + hyphy REVshared.bf 121s Log Likelihood = -1156.6254044555; 121s Global Parameters: 121s AT=0.3620866660397165; 121s GT=0.4597052642244015; 121s CG=0.2460538300724483; 121s AG=1.843832202866545; 121s CT=1.197638573724416; 121s 121s 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); 121s + for i in *.bf 121s + '[' -f ReplicateConstraint1.bf ']' 121s + hyphy ReplicateConstraint1.bf 121s 1).Unconstrained HKY85 121s 121s Log Likelihood = -1152.88; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.317.trvs 121s Parameter 2 : hivTree.317.trst 121s Parameter 3 : hivTree.6767.trvs 121s Parameter 4 : hivTree.6767.trst 121s Parameter 5 : hivTree.Node2.trvs 121s Parameter 6 : hivTree.Node2.trst 121s Parameter 7 : hivTree.135.trvs 121s Parameter 8 : hivTree.135.trst 121s Parameter 9 : hivTree.529.trvs 121s Parameter 10 : hivTree.529.trst 121s Parameter 11 : hivTree.105r.trvs 121s Parameter 12 : hivTree.105r.trst 121s Parameter 13 : hivTree.Node8.trvs 121s Parameter 14 : hivTree.Node8.trst 121s Parameter 15 : hivTree.iNode1.trvs 121s Parameter 16 : hivTree.iNode1.trst 121s Parameter 17 : hivTree.719.trvs 121s Parameter 18 : hivTree.719.trst 121s Parameter 19 : hivTree.136.trvs 121s Parameter 20 : hivTree.136.trst 121s Parameter 21 : hivTree.Node11.trvs 121s Parameter 22 : hivTree.Node11.trst 121s Parameter 23 : hivTree.Node5.trvs 121s Parameter 24 : hivTree.Node5.trst 121s Parameter 25 : hivTree.Node1.trvs 121s Parameter 26 : hivTree.Node1.trst 121s Parameter 27 : hivTree.6760.trvs 121s Parameter 28 : hivTree.6760.trst 121s Parameter 29 : hivTree.113.trvs 121s Parameter 30 : hivTree.113.trst 121s Parameter 31 : hivTree.9939.trvs 121s Parameter 32 : hivTree.9939.trst 121s Parameter 33 : hivTree.Node16.trvs 121s Parameter 34 : hivTree.Node16.trst 121s Parameter 35 : hivTree.256.trvs 121s Parameter 36 : hivTree.256.trst 121s Parameter 37 : hivTree.822.trvs 121s Parameter 38 : hivTree.822.trst 121s Parameter 39 : hivTree.159.trvs 121s Parameter 40 : hivTree.159.trst 121s Parameter 41 : hivTree.Node21.trvs 121s Parameter 42 : hivTree.Node21.trst 121s Parameter 43 : hivTree.iNode2.trvs 121s Parameter 44 : hivTree.iNode2.trst 121s Parameter 45 : hivTree.Node15.trvs 121s Parameter 46 : hivTree.Node15.trst 121s 121s 2).HKY85 constrained to F81 121s 121s Log Likelihood = -1187.55; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.317.trvs 121s Parameter 2 : hivTree.6767.trvs 121s Parameter 3 : hivTree.Node2.trvs 121s Parameter 4 : hivTree.135.trvs 121s Parameter 5 : hivTree.529.trvs 121s Parameter 6 : hivTree.105r.trvs 121s Parameter 7 : hivTree.Node8.trvs 121s Parameter 8 : hivTree.iNode1.trvs 121s Parameter 9 : hivTree.719.trvs 121s Parameter 10 : hivTree.136.trvs 121s Parameter 11 : hivTree.Node11.trvs 121s Parameter 12 : hivTree.Node5.trvs 121s Parameter 13 : hivTree.Node1.trvs 121s Parameter 14 : hivTree.6760.trvs 121s Parameter 15 : hivTree.113.trvs 121s Parameter 16 : hivTree.9939.trvs 121s Parameter 17 : hivTree.Node16.trvs 121s Parameter 18 : hivTree.256.trvs 121s Parameter 19 : hivTree.822.trvs 121s Parameter 20 : hivTree.159.trvs 121s Parameter 21 : hivTree.Node21.trvs 121s Parameter 22 : hivTree.iNode2.trvs 121s Parameter 23 : hivTree.Node15.trvs 121s 121s Constrained Parameters List 121s 121s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 121s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 121s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 121s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 121s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 121s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 121s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 121s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 121s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 121s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 121s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 121s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 121s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 121s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 121s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 121s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 121s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 121s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 121s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 121s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 121s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 121s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 121s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 121s 121s 3).HKY85 constrained to F81 on internal branches 121s 121s Log Likelihood = -1167.99; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.Node2.trvs 121s Parameter 2 : hivTree.Node8.trvs 121s Parameter 3 : hivTree.iNode1.trvs 121s Parameter 4 : hivTree.Node11.trvs 121s Parameter 5 : hivTree.Node5.trvs 121s Parameter 6 : hivTree.Node1.trvs 121s Parameter 7 : hivTree.Node16.trvs 121s Parameter 8 : hivTree.Node21.trvs 121s Parameter 9 : hivTree.iNode2.trvs 121s Parameter 10 : hivTree.Node15.trvs 121s Parameter 11 : hivTree.317.trst 121s Parameter 12 : hivTree.317.trvs 121s Parameter 13 : hivTree.6767.trvs 121s Parameter 14 : hivTree.6767.trst 121s Parameter 15 : hivTree.135.trst 121s Parameter 16 : hivTree.135.trvs 121s Parameter 17 : hivTree.529.trvs 121s Parameter 18 : hivTree.529.trst 121s Parameter 19 : hivTree.105r.trst 121s Parameter 20 : hivTree.105r.trvs 121s Parameter 21 : hivTree.719.trvs 121s Parameter 22 : hivTree.719.trst 121s Parameter 23 : hivTree.136.trvs 121s Parameter 24 : hivTree.136.trst 121s Parameter 25 : hivTree.6760.trvs 121s Parameter 26 : hivTree.6760.trst 121s Parameter 27 : hivTree.113.trvs 121s Parameter 28 : hivTree.113.trst 121s Parameter 29 : hivTree.9939.trst 121s Parameter 30 : hivTree.9939.trvs 121s Parameter 31 : hivTree.256.trvs 121s Parameter 32 : hivTree.256.trst 121s Parameter 33 : hivTree.822.trvs 121s Parameter 34 : hivTree.822.trst 121s Parameter 35 : hivTree.159.trst 121s Parameter 36 : hivTree.159.trvs 121s 121s Constrained Parameters List 121s 121s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 121s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 121s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 121s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 121s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 121s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 121s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 121s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 121s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 121s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 121s 121s 4).HKY85 with shared ratio. 121s 121s Log Likelihood = -1165.7; 121s 121s Independent Parameters List 121s 121s Parameter 1 : R 121s Parameter 2 : hivTree.317.trst 121s Parameter 3 : hivTree.6767.trst 121s Parameter 4 : hivTree.Node2.trst 121s Parameter 5 : hivTree.135.trst 121s Parameter 6 : hivTree.529.trst 121s Parameter 7 : hivTree.105r.trst 121s Parameter 8 : hivTree.Node8.trst 121s Parameter 9 : hivTree.iNode1.trst 121s Parameter 10 : hivTree.719.trst 121s Parameter 11 : hivTree.136.trst 121s Parameter 12 : hivTree.Node11.trst 121s Parameter 13 : hivTree.Node5.trst 121s Parameter 14 : hivTree.Node1.trst 121s Parameter 15 : hivTree.6760.trst 121s Parameter 16 : hivTree.113.trst 121s Parameter 17 : hivTree.9939.trst 121s Parameter 18 : hivTree.Node16.trst 121s Parameter 19 : hivTree.256.trst 121s Parameter 20 : hivTree.822.trst 121s Parameter 21 : hivTree.159.trst 121s Parameter 22 : hivTree.Node21.trst 121s Parameter 23 : hivTree.iNode2.trst 121s Parameter 24 : hivTree.Node15.trst 121s 121s Constrained Parameters List 121s 121s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 121s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 121s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 121s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 121s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 121s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 121s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 121s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 121s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 121s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 121s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 121s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 121s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 121s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 121s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 121s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 121s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 121s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 121s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 121s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 121s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 121s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 121s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 121s + '[' -f ReplicateConstraint2.bf ']' 121s + hyphy ReplicateConstraint2.bf 121s 1).Unconstrained HKY85 121s 121s Log Likelihood = -1152.88; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.317.trvs 121s Parameter 2 : hivTree.317.trst 121s Parameter 3 : hivTree.6767.trvs 121s Parameter 4 : hivTree.6767.trst 121s Parameter 5 : hivTree.Node2.trvs 121s Parameter 6 : hivTree.Node2.trst 121s Parameter 7 : hivTree.135.trvs 121s Parameter 8 : hivTree.135.trst 121s Parameter 9 : hivTree.529.trvs 121s Parameter 10 : hivTree.529.trst 121s Parameter 11 : hivTree.105r.trvs 121s Parameter 12 : hivTree.105r.trst 121s Parameter 13 : hivTree.Node8.trvs 121s Parameter 14 : hivTree.Node8.trst 121s Parameter 15 : hivTree.iNode1.trvs 121s Parameter 16 : hivTree.iNode1.trst 121s Parameter 17 : hivTree.719.trvs 121s Parameter 18 : hivTree.719.trst 121s Parameter 19 : hivTree.136.trvs 121s Parameter 20 : hivTree.136.trst 121s Parameter 21 : hivTree.Node11.trvs 121s Parameter 22 : hivTree.Node11.trst 121s Parameter 23 : hivTree.Node5.trvs 121s Parameter 24 : hivTree.Node5.trst 121s Parameter 25 : hivTree.Node1.trvs 121s Parameter 26 : hivTree.Node1.trst 121s Parameter 27 : hivTree.6760.trvs 121s Parameter 28 : hivTree.6760.trst 121s Parameter 29 : hivTree.113.trvs 121s Parameter 30 : hivTree.113.trst 121s Parameter 31 : hivTree.9939.trvs 121s Parameter 32 : hivTree.9939.trst 121s Parameter 33 : hivTree.Node16.trvs 121s Parameter 34 : hivTree.Node16.trst 121s Parameter 35 : hivTree.256.trvs 121s Parameter 36 : hivTree.256.trst 121s Parameter 37 : hivTree.822.trvs 121s Parameter 38 : hivTree.822.trst 121s Parameter 39 : hivTree.159.trvs 121s Parameter 40 : hivTree.159.trst 121s Parameter 41 : hivTree.Node21.trvs 121s Parameter 42 : hivTree.Node21.trst 121s Parameter 43 : hivTree.iNode2.trvs 121s Parameter 44 : hivTree.iNode2.trst 121s Parameter 45 : hivTree.Node15.trvs 121s Parameter 46 : hivTree.Node15.trst 121s 121s 2).HKY85 constrained to F81 on the "iNode1" subtree 121s 121s Log Likelihood = -1157.82; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.135.trvs 121s Parameter 2 : hivTree.529.trvs 121s Parameter 3 : hivTree.105r.trvs 121s Parameter 4 : hivTree.Node8.trvs 121s Parameter 5 : hivTree.317.trvs 121s Parameter 6 : hivTree.317.trst 121s Parameter 7 : hivTree.6767.trst 121s Parameter 8 : hivTree.6767.trvs 121s Parameter 9 : hivTree.Node2.trst 121s Parameter 10 : hivTree.Node2.trvs 121s Parameter 11 : hivTree.iNode1.trvs 121s Parameter 12 : hivTree.iNode1.trst 121s Parameter 13 : hivTree.719.trvs 121s Parameter 14 : hivTree.719.trst 121s Parameter 15 : hivTree.136.trvs 121s Parameter 16 : hivTree.136.trst 121s Parameter 17 : hivTree.Node11.trvs 121s Parameter 18 : hivTree.Node11.trst 121s Parameter 19 : hivTree.Node5.trvs 121s Parameter 20 : hivTree.Node5.trst 121s Parameter 21 : hivTree.Node1.trvs 121s Parameter 22 : hivTree.Node1.trst 121s Parameter 23 : hivTree.6760.trvs 121s Parameter 24 : hivTree.6760.trst 121s Parameter 25 : hivTree.113.trvs 121s Parameter 26 : hivTree.113.trst 121s Parameter 27 : hivTree.9939.trvs 121s Parameter 28 : hivTree.9939.trst 121s Parameter 29 : hivTree.Node16.trvs 121s Parameter 30 : hivTree.Node16.trst 121s Parameter 31 : hivTree.256.trvs 121s Parameter 32 : hivTree.256.trst 121s Parameter 33 : hivTree.822.trvs 121s Parameter 34 : hivTree.822.trst 121s Parameter 35 : hivTree.159.trvs 121s Parameter 36 : hivTree.159.trst 121s Parameter 37 : hivTree.Node21.trvs 121s Parameter 38 : hivTree.Node21.trst 121s Parameter 39 : hivTree.iNode2.trvs 121s Parameter 40 : hivTree.iNode2.trst 121s Parameter 41 : hivTree.Node15.trvs 121s Parameter 42 : hivTree.Node15.trst 121s 121s Constrained Parameters List 121s 121s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 121s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 121s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 121s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 121s 121s 3).HKY85 constrained to F81 on the "iNode1" branch 121s 121s Log Likelihood = -1152.88; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.317.trvs 121s Parameter 2 : hivTree.317.trst 121s Parameter 3 : hivTree.6767.trvs 121s Parameter 4 : hivTree.6767.trst 121s Parameter 5 : hivTree.Node2.trvs 121s Parameter 6 : hivTree.Node2.trst 121s Parameter 7 : hivTree.135.trvs 121s Parameter 8 : hivTree.135.trst 121s Parameter 9 : hivTree.529.trvs 121s Parameter 10 : hivTree.529.trst 121s Parameter 11 : hivTree.105r.trvs 121s Parameter 12 : hivTree.105r.trst 121s Parameter 13 : hivTree.Node8.trvs 121s Parameter 14 : hivTree.Node8.trst 121s Parameter 15 : hivTree.iNode1.trvs 121s Parameter 16 : hivTree.iNode1.trst 121s Parameter 17 : hivTree.719.trvs 121s Parameter 18 : hivTree.719.trst 121s Parameter 19 : hivTree.136.trvs 121s Parameter 20 : hivTree.136.trst 121s Parameter 21 : hivTree.Node11.trvs 121s Parameter 22 : hivTree.Node11.trst 121s Parameter 23 : hivTree.Node5.trvs 121s Parameter 24 : hivTree.Node5.trst 121s Parameter 25 : hivTree.Node1.trvs 121s Parameter 26 : hivTree.Node1.trst 121s Parameter 27 : hivTree.6760.trvs 121s Parameter 28 : hivTree.6760.trst 121s Parameter 29 : hivTree.113.trvs 121s Parameter 30 : hivTree.113.trst 121s Parameter 31 : hivTree.9939.trvs 121s Parameter 32 : hivTree.9939.trst 121s Parameter 33 : hivTree.Node16.trvs 121s Parameter 34 : hivTree.Node16.trst 121s Parameter 35 : hivTree.256.trvs 121s Parameter 36 : hivTree.256.trst 121s Parameter 37 : hivTree.822.trvs 121s Parameter 38 : hivTree.822.trst 121s Parameter 39 : hivTree.159.trvs 121s Parameter 40 : hivTree.159.trst 121s Parameter 41 : hivTree.Node21.trvs 121s Parameter 42 : hivTree.Node21.trst 121s Parameter 43 : hivTree.iNode2.trvs 121s Parameter 44 : hivTree.iNode2.trst 121s Parameter 45 : hivTree.Node15.trvs 121s Parameter 46 : hivTree.Node15.trst 121s 121s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 121s 121s Log Likelihood = -1152.88; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.317.trvs 121s Parameter 2 : hivTree.317.trst 121s Parameter 3 : hivTree.6767.trvs 121s Parameter 4 : hivTree.6767.trst 121s Parameter 5 : hivTree.Node2.trvs 121s Parameter 6 : hivTree.Node2.trst 121s Parameter 7 : hivTree.135.trvs 121s Parameter 8 : hivTree.135.trst 121s Parameter 9 : hivTree.529.trvs 121s Parameter 10 : hivTree.529.trst 121s Parameter 11 : hivTree.105r.trvs 121s Parameter 12 : hivTree.105r.trst 121s Parameter 13 : hivTree.Node8.trvs 121s Parameter 14 : hivTree.Node8.trst 121s Parameter 15 : hivTree.iNode1.trvs 121s Parameter 16 : hivTree.iNode1.trst 121s Parameter 17 : hivTree.719.trvs 121s Parameter 18 : hivTree.719.trst 121s Parameter 19 : hivTree.136.trvs 121s Parameter 20 : hivTree.136.trst 121s Parameter 21 : hivTree.Node11.trvs 121s Parameter 22 : hivTree.Node11.trst 121s Parameter 23 : hivTree.Node5.trvs 121s Parameter 24 : hivTree.Node5.trst 121s Parameter 25 : hivTree.Node1.trvs 121s Parameter 26 : hivTree.Node1.trst 121s Parameter 27 : hivTree.6760.trvs 121s Parameter 28 : hivTree.6760.trst 121s Parameter 29 : hivTree.113.trvs 121s Parameter 30 : hivTree.113.trst 121s Parameter 31 : hivTree.9939.trvs 121s Parameter 32 : hivTree.9939.trst 121s Parameter 33 : hivTree.Node16.trvs 121s Parameter 34 : hivTree.Node16.trst 121s Parameter 35 : hivTree.256.trvs 121s Parameter 36 : hivTree.256.trst 121s Parameter 37 : hivTree.822.trvs 121s Parameter 38 : hivTree.822.trst 121s Parameter 39 : hivTree.159.trvs 121s Parameter 40 : hivTree.159.trst 121s Parameter 41 : hivTree.Node21.trvs 121s Parameter 42 : hivTree.Node21.trst 121s Parameter 43 : hivTree.iNode2.trvs 121s Parameter 44 : hivTree.iNode2.trst 121s Parameter 45 : hivTree.Node15.trvs 121s Parameter 46 : hivTree.Node15.trst 121s 121s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 121s 121s Log Likelihood = -1152.88; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.317.trvs 121s Parameter 2 : hivTree.317.trst 121s Parameter 3 : hivTree.6767.trvs 121s Parameter 4 : hivTree.6767.trst 121s Parameter 5 : hivTree.Node2.trvs 121s Parameter 6 : hivTree.Node2.trst 121s Parameter 7 : hivTree.135.trvs 121s Parameter 8 : hivTree.135.trst 121s Parameter 9 : hivTree.529.trvs 121s Parameter 10 : hivTree.529.trst 121s Parameter 11 : hivTree.105r.trvs 121s Parameter 12 : hivTree.105r.trst 121s Parameter 13 : hivTree.Node8.trvs 121s Parameter 14 : hivTree.Node8.trst 121s Parameter 15 : hivTree.iNode1.trvs 121s Parameter 16 : hivTree.iNode1.trst 121s Parameter 17 : hivTree.719.trvs 121s Parameter 18 : hivTree.719.trst 121s Parameter 19 : hivTree.136.trvs 121s Parameter 20 : hivTree.136.trst 121s Parameter 21 : hivTree.Node11.trvs 121s Parameter 22 : hivTree.Node11.trst 121s Parameter 23 : hivTree.Node5.trvs 121s Parameter 24 : hivTree.Node5.trst 121s Parameter 25 : hivTree.Node1.trvs 121s Parameter 26 : hivTree.Node1.trst 121s Parameter 27 : hivTree.6760.trvs 121s Parameter 28 : hivTree.6760.trst 121s Parameter 29 : hivTree.113.trvs 121s Parameter 30 : hivTree.113.trst 121s Parameter 31 : hivTree.9939.trvs 121s Parameter 32 : hivTree.9939.trst 121s Parameter 33 : hivTree.Node16.trvs 121s Parameter 34 : hivTree.Node16.trst 121s Parameter 35 : hivTree.256.trvs 121s Parameter 36 : hivTree.256.trst 121s Parameter 37 : hivTree.822.trvs 121s Parameter 38 : hivTree.822.trst 121s Parameter 39 : hivTree.159.trvs 121s Parameter 40 : hivTree.159.trst 121s Parameter 41 : hivTree.Node21.trvs 121s Parameter 42 : hivTree.Node21.trst 121s Parameter 43 : hivTree.iNode2.trvs 121s Parameter 44 : hivTree.iNode2.trst 121s Parameter 45 : hivTree.Node15.trvs 121s Parameter 46 : hivTree.Node15.trst 121s 121s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 121s 121s Log Likelihood = -1157.82; 121s 121s Independent Parameters List 121s 121s Parameter 1 : hivTree.135.trst 121s Parameter 2 : hivTree.529.trst 121s Parameter 3 : hivTree.105r.trst 121s Parameter 4 : hivTree.Node8.trst 121s Parameter 5 : hivTree.317.trvs 121s Parameter 6 : hivTree.317.trst 121s Parameter 7 : hivTree.6767.trst 121s Parameter 8 : hivTree.6767.trvs 121s Parameter 9 : hivTree.Node2.trst 121s Parameter 10 : hivTree.Node2.trvs 121s Parameter 11 : hivTree.iNode1.trvs 121s Parameter 12 : hivTree.iNode1.trst 121s Parameter 13 : hivTree.719.trvs 121s Parameter 14 : hivTree.719.trst 121s Parameter 15 : hivTree.136.trvs 121s Parameter 16 : hivTree.136.trst 121s Parameter 17 : hivTree.Node11.trvs 121s Parameter 18 : hivTree.Node11.trst 121s Parameter 19 : hivTree.Node5.trvs 121s Parameter 20 : hivTree.Node5.trst 121s Parameter 21 : hivTree.Node1.trvs 121s Parameter 22 : hivTree.Node1.trst 121s Parameter 23 : hivTree.6760.trvs 121s Parameter 24 : hivTree.6760.trst 121s Parameter 25 : hivTree.113.trvs 121s Parameter 26 : hivTree.113.trst 121s Parameter 27 : hivTree.9939.trvs 121s Parameter 28 : hivTree.9939.trst 121s Parameter 29 : hivTree.Node16.trvs 121s Parameter 30 : hivTree.Node16.trst 121s Parameter 31 : hivTree.256.trvs 121s Parameter 32 : hivTree.256.trst 121s Parameter 33 : hivTree.822.trvs 121s Parameter 34 : hivTree.822.trst 121s Parameter 35 : hivTree.159.trvs 121s Parameter 36 : hivTree.159.trst 121s Parameter 37 : hivTree.Node21.trvs 121s Parameter 38 : hivTree.Node21.trst 121s Parameter 39 : hivTree.iNode2.trvs 121s Parameter 40 : hivTree.iNode2.trst 121s Parameter 41 : hivTree.Node15.trvs 121s Parameter 42 : hivTree.Node15.trst 121s 121s Constrained Parameters List 121s 121s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 121s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 121s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 121s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 121s + '[' -f aa.bf ']' 121s + hyphy aa.bf 121s Log Likelihood = -1134.73158903811; 121s 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); 121s + for i in *.bf 121s + '[' -f definitions2.bf ']' 121s + hyphy definitions2.bf 121s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 121s 121s Sample by MEAN: 121s 121s Sample mean = 0.5 (sample variance = 0.2450374540764348) 121s 121s Rate[0]= 0.06847689 (weight=0.2500000) 121s Rate[1]= 0.23837593 (weight=0.2500000) 121s Rate[2]= 0.50000000 (weight=0.2500000) 121s Rate[3]= 1.19314718 (weight=0.2500000) 121s ------------------------------------------------ 121s 121s Sample by MEDIAN: 121s 121s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 121s 121s Rate[0]= 0.06676570 (weight=0.2500000) 121s Rate[1]= 0.23500181 (weight=0.2500000) 121s Rate[2]= 0.49041463 (weight=0.2500000) 121s Rate[3]= 1.03972077 (weight=0.2500000) 121s ------------------------------------------------ 121s 121s Sample by SCALED_MEDIAN: 121s 121s Sample mean = 0.5 (sample variance = 0.2154404122636025) 121s 121s Rate[0]= 0.07289218 (weight=0.2500000) 121s Rate[1]= 0.25656580 (weight=0.2500000) 121s Rate[2]= 0.53541552 (weight=0.2500000) 121s Rate[3]= 1.13512650 (weight=0.2500000) 121s ------------------------------------------------ 121s 121s Sample by MEAN (numerical averaging): 121s 121s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 121s 121s Rate[0]= 0.06846096 (weight=0.2500000) 121s Rate[1]= 0.23834015 (weight=0.2500000) 121s Rate[2]= 0.49996411 (weight=0.2500000) 121s Rate[3]= 1.19314889 (weight=0.2500000) 121s ------------------------------------------------ 121s 121s Sample by MEAN (numerical CDF and averaging): 121s 121s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 121s 121s Rate[0]= 0.06849282 (weight=0.2500000) 121s Rate[1]= 0.23835613 (weight=0.2500000) 121s Rate[2]= 0.49994751 (weight=0.2500000) 121s Rate[3]= 1.19311765 (weight=0.2500000) 121s ------------------------------------------------ 121s 2). Equiprobable rates sampled from Exponential with lambda = 2 121s 121s Sample by MEDIAN (3 rate classes): 121s 121s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 121s 121s Rate[0]= 0.09116078 (weight=0.3333333) 121s Rate[1]= 0.34657359 (weight=0.3333333) 121s Rate[2]= 0.89587973 (weight=0.3333333) 121s ------------------------------------------------ 121s 121s Sample by MEDIAN (9 rate classes): 121s 121s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 121s 121s Rate[0]= 0.02857921 (weight=0.1111111) 121s Rate[1]= 0.09116078 (weight=0.1111111) 121s Rate[2]= 0.16271120 (weight=0.1111111) 121s Rate[3]= 0.24623824 (weight=0.1111111) 121s Rate[4]= 0.34657359 (weight=0.1111111) 121s Rate[5]= 0.47223080 (weight=0.1111111) 121s Rate[6]= 0.64046692 (weight=0.1111111) 121s Rate[7]= 0.89587973 (weight=0.1111111) 121s Rate[8]= 1.44518588 (weight=0.1111111) 121s ------------------------------------------------ 121s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 121s 121s Sample by MEAN (10 rate classes): 121s 121s Sample mean = 1 (sample variance = 0.1057310289486733) 121s 121s Rate[0]= 0.52447499 (weight=0.1000000) 121s Rate[1]= 0.67866972 (weight=0.1000000) 121s Rate[2]= 0.77209919 (weight=0.1000000) 121s Rate[3]= 0.85214884 (weight=0.1000000) 121s Rate[4]= 0.92850815 (weight=0.1000000) 121s Rate[5]= 1.00664500 (weight=0.1000000) 121s Rate[6]= 1.09192933 (weight=0.1000000) 121s Rate[7]= 1.19267960 (weight=0.1000000) 121s Rate[8]= 1.32858029 (weight=0.1000000) 121s Rate[9]= 1.62426489 (weight=0.1000000) 121s ------------------------------------------------ 121s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 121s 121s Sample by MEAN (10 rate classes): 121s 121s Sample mean = 2 (sample variance = 0.04259071282256012) 121s 121s Rate[0]= 1.66431246 (weight=0.1000000) 121s Rate[1]= 1.79212822 (weight=0.1000000) 121s Rate[2]= 1.86123411 (weight=0.1000000) 121s Rate[3]= 1.91722052 (weight=0.1000000) 121s Rate[4]= 1.96832799 (weight=0.1000000) 121s Rate[5]= 2.01862937 (weight=0.1000000) 121s Rate[6]= 2.07152664 (weight=0.1000000) 121s Rate[7]= 2.13166629 (weight=0.1000000) 121s Rate[8]= 2.20930216 (weight=0.1000000) 121s Rate[9]= 2.36565224 (weight=0.1000000) 121s ------------------------------------------------ 121s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 121s 121s Sample by MEAN (8 rate classes): 121s 121s Sample mean = 0.5 (sample variance = 0.09375000225643569) 121s 121s Rate[0]= 0.06250000 (weight=0.1250000) 121s Rate[1]= 0.18750000 (weight=0.1250000) 121s Rate[2]= 0.31250001 (weight=0.1250000) 121s Rate[3]= 0.43750001 (weight=0.1250000) 121s Rate[4]= 0.56249993 (weight=0.1250000) 121s Rate[5]= 0.68750001 (weight=0.1250000) 121s Rate[6]= 0.81250002 (weight=0.1250000) 121s Rate[7]= 0.93750002 (weight=0.1250000) 121s ------------------------------------------------ 121s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 121s 121s Sample by MEAN (8 rate classes): 121s 121s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 121s 121s Rate[0]= 2.17658588 (weight=0.1250000) 121s Rate[1]= 2.55230783 (weight=0.1250000) 121s Rate[2]= 2.75432532 (weight=0.1250000) 121s Rate[3]= 2.92101185 (weight=0.1250000) 121s Rate[4]= 3.07898815 (weight=0.1250000) 121s Rate[5]= 3.24567468 (weight=0.1250000) 121s Rate[6]= 3.44769217 (weight=0.1250000) 121s Rate[7]= 3.82341415 (weight=0.1250000) 121s ------------------------------------------------ 121s + for i in *.bf 121s + '[' -f definitions3.bf ']' 121s + hyphy definitions3.bf 121s 121s 121s Sample mean = 1 (sample variance = + for i in *.bf 121s + '[' -f displayFunction.bf ']' 121s 0.9920002887656187) 121s 121s Rate[0]= 0.05175536 (weight=0.1000000) 121s Rate[1]= 0.16309623 (weight=0.1000000) 121s Rate[2]= 0.28842380 (weight=0.1000000) 121s Rate[3]= 0.43177086 (weight=0.1000000) 121s Rate[4]= 0.59921784 (weight=0.1000000) 121s Rate[5]= 0.80057298 (weight=0.1000000) 121s Rate[6]= 1.05324451 (weight=0.1000000) 121s Rate[7]= 1.39304259 (weight=0.1000000) 121s Rate[8]= 1.91629073 (weight=0.1000000) 121s Rate[9]= 3.30258509 (weight=0.1000000) 121s ------------------------------------------------ 121s + hyphy displayFunction.bf 121s + for i in *.bf 121s + '[' -f profile_test.bf ']' 121s + hyphy profile_test.bf 122s 122s Total run time (seconds) : 0.000000 122s Total number of steps : + for i in *.bf 122s 1500005 122s 122s 1 : s=0; 122s Call count: 1 122s Time (seconds): 1.3e-11 122s 2 : m={5,1}; 122s Call count: 1 122s Time (seconds): 1.5e-11 122s 3 : k=0; 122s Call count: 1 122s Time (seconds): 3e-12 122s 4 : Branch under condition 'k<250000' 122s to 122s s=s+k; 122s else 122s #profilePAUSE, ; 122s Call count: 250001 122s Time (seconds): 3.534500000001454e-08 122s 5 : s=s+k; 122s Call count: 250000 122s Time (seconds): 4.132800000002059e-08 122s 6 : t=Random(0,5); 122s Call count: 250000 122s Time (seconds): 4.059700000001978e-08 122s 7 : m[t]=m[t]+1; 122s Call count: 250000 122s Time (seconds): 1.343430000001133e-07 122s 8 : k=k+1; 122s Call count: 250000 122s Time (seconds): 5.438000000003369e-08 122s 9 : Go to step 4 122s Call count: 250000 122s Time (seconds): 1.212499999999755e-08 122s 10 : #profilePAUSE, ; 122s Call count: 1 122s Time (seconds): 0 122s + '[' -f shared.bf ']' 122s + hyphy shared.bf 122s + rm -f '*messages.log*' '*errors.log*' 122s autopkgtest [16:51:38]: test run-unit-tests: -----------------------] 122s run-unit-tests PASS 122s autopkgtest [16:51:38]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 123s autopkgtest [16:51:39]: @@@@@@@@@@@@@@@@@@@@ summary 123s run-unit-tests PASS 136s Creating nova instance adt-noble-ppc64el-hyphy-20240317-164936-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240316.img (UUID 5f323cde-6357-475d-9beb-0cc93b49185c)...