0s autopkgtest [17:00:26]: starting date and time: 2024-03-16 17:00:26+0000 0s autopkgtest [17:00:26]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:00:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1aih06gp/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-s390x-4.secgroup --name adt-noble-s390x-hyphy-20240316-170026-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-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/ 201s autopkgtest [17:03:47]: testbed dpkg architecture: s390x 201s autopkgtest [17:03:47]: testbed apt version: 2.7.12 201s autopkgtest [17:03:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 202s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 202s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 203s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 203s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 203s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 203s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [632 kB] 203s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 203s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 203s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 203s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3736 kB] 203s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 203s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [33.5 kB] 203s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 206s Fetched 8735 kB in 3s (3362 kB/s) 206s Reading package lists... 209s Reading package lists... 209s Building dependency tree... 209s Reading state information... 210s Calculating upgrade... 210s The following packages have been kept back: 210s curl 210s The following packages will be upgraded: 210s ubuntu-minimal ubuntu-standard 210s 2 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 210s Need to get 21.3 kB of archives. 210s After this operation, 0 B of additional disk space will be used. 210s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-minimal s390x 1.536 [10.7 kB] 210s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-standard s390x 1.536 [10.7 kB] 211s Fetched 21.3 kB in 0s (99.2 kB/s) 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 ... 52171 files and directories currently installed.) 211s Preparing to unpack .../ubuntu-minimal_1.536_s390x.deb ... 211s Unpacking ubuntu-minimal (1.536) over (1.535) ... 211s Preparing to unpack .../ubuntu-standard_1.536_s390x.deb ... 211s Unpacking ubuntu-standard (1.536) over (1.535) ... 211s Setting up ubuntu-minimal (1.536) ... 211s Setting up ubuntu-standard (1.536) ... 211s Reading package lists... 211s Building dependency tree... 211s Reading state information... 212s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 212s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 212s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 212s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 212s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 214s Reading package lists... 214s Reading package lists... 214s Building dependency tree... 214s Reading state information... 215s Calculating upgrade... 215s The following packages have been kept back: 215s curl 215s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 216s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 219s autopkgtest [17:04:05]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 219s autopkgtest [17:04:05]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 222s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (dsc) [2417 B] 222s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (tar) [2613 kB] 222s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe hyphy 2.5.59+dfsg-1build2 (diff) [17.2 kB] 222s gpgv: Signature made Sat Mar 16 06:59:46 2024 UTC 222s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 222s gpgv: issuer "steve.langasek@ubuntu.com" 222s gpgv: Can't check signature: No public key 222s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.59+dfsg-1build2.dsc: no acceptable signature found 222s autopkgtest [17:04:08]: testing package hyphy version 2.5.59+dfsg-1build2 223s autopkgtest [17:04:09]: build not needed 226s autopkgtest [17:04:12]: test run-unit-tests: preparing testbed 230s Reading package lists... 230s Building dependency tree... 230s Reading state information... 231s Starting pkgProblemResolver with broken count: 0 231s Starting 2 pkgProblemResolver with broken count: 0 231s Done 231s The following additional packages will be installed: 231s curl hyphy-common hyphy-mpi hyphy-pt libatomic1 libcurl3t64-gnutls 231s libcurl4t64 libevent-pthreads-2.1-7 libfabric1 libgnutls30t64 libgomp1 231s libhogweed6t64 libhwloc-plugins libhwloc15 libmunge2 libnettle8t64 231s libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 librdmacm1 libssl3t64 231s libxnvctrl0 ocl-icd-libopencl1 231s Suggested packages: 231s gnutls-bin opencl-icd 231s The following packages will be REMOVED: 231s libcurl3-gnutls libcurl4 libgnutls30 libhogweed6 libnettle8 libpsl5 libssl3 231s The following NEW packages will be installed: 231s autopkgtest-satdep hyphy-common hyphy-mpi hyphy-pt libatomic1 231s libcurl3t64-gnutls libcurl4t64 libevent-pthreads-2.1-7 libfabric1 231s libgnutls30t64 libgomp1 libhogweed6t64 libhwloc-plugins libhwloc15 libmunge2 231s libnettle8t64 libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 librdmacm1 231s libssl3t64 libxnvctrl0 ocl-icd-libopencl1 231s The following packages will be upgraded: 231s curl 231s 1 upgraded, 24 newly installed, 7 to remove and 0 not upgraded. 231s Need to get 11.8 MB/11.8 MB of archives. 231s After this operation, 26.6 MB of additional disk space will be used. 231s Get:1 /tmp/autopkgtest.AgnAOI/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [724 B] 231s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnettle8t64 s390x 3.9.1-2.2 [210 kB] 232s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libhogweed6t64 s390x 3.9.1-2.2 [204 kB] 232s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu2 [1044 kB] 232s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu1 [1652 kB] 232s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x curl s390x 8.5.0-2ubuntu7 [227 kB] 232s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl4t64 s390x 8.5.0-2ubuntu7 [364 kB] 232s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpsl5t64 s390x 0.21.2-1.1 [57.6 kB] 232s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl3t64-gnutls s390x 8.5.0-2ubuntu7 [356 kB] 232s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x hyphy-common all 2.5.59+dfsg-1build2 [624 kB] 232s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 232s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libevent-pthreads-2.1-7 s390x 2.1.12-stable-9 [7692 B] 232s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] 232s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x librdmacm1 s390x 50.0-1 [73.9 kB] 232s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x libfabric1 s390x 1.17.0-3 [513 kB] 232s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc15 s390x 2.10.0-1 [174 kB] 232s Get:17 http://ftpmaster.internal/ubuntu noble/universe s390x libmunge2 s390x 0.5.15-3ubuntu1 [17.3 kB] 232s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libpciaccess0 s390x 0.17-3 [18.5 kB] 232s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu1 [11.7 kB] 232s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1 [39.1 kB] 232s Get:21 http://ftpmaster.internal/ubuntu noble/universe s390x libhwloc-plugins s390x 2.10.0-1 [16.1 kB] 232s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libpmix2t64 s390x 5.0.1-4.1 [727 kB] 232s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libopenmpi3t64 s390x 4.1.6-6ubuntu1 [2437 kB] 232s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x hyphy-mpi s390x 2.5.59+dfsg-1build2 [1468 kB] 232s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x hyphy-pt s390x 2.5.59+dfsg-1build2 [1424 kB] 233s Fetched 11.8 MB in 1s (10.6 MB/s) 233s dpkg: libhogweed6:s390x: dependency problems, but removing anyway as you requested: 233s librtmp1:s390x depends on libhogweed6. 233s libjcat1:s390x depends on libhogweed6. 233s libgnutls30:s390x depends on libhogweed6 (>= 3.6). 233s 233s (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 ... 52171 files and directories currently installed.) 233s Removing libhogweed6:s390x (3.9.1-2) ... 233s dpkg: libnettle8:s390x: dependency problems, but removing anyway as you requested: 233s librtmp1:s390x depends on libnettle8. 233s libgnutls30:s390x depends on libnettle8 (>= 3.9~). 233s libcurl3-gnutls:s390x depends on libnettle8. 233s libarchive13:s390x depends on libnettle8. 233s 233s Removing libnettle8:s390x (3.9.1-2) ... 233s Selecting previously unselected package libnettle8t64:s390x. 233s (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 ... 52159 files and directories currently installed.) 233s Preparing to unpack .../libnettle8t64_3.9.1-2.2_s390x.deb ... 233s Unpacking libnettle8t64:s390x (3.9.1-2.2) ... 233s Selecting previously unselected package libhogweed6t64:s390x. 233s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_s390x.deb ... 233s Unpacking libhogweed6t64:s390x (3.9.1-2.2) ... 233s dpkg: libgnutls30:s390x: dependency problems, but removing anyway as you requested: 233s librtmp1:s390x depends on libgnutls30 (>= 3.7.2). 233s libldap2:s390x depends on libgnutls30 (>= 3.8.2). 233s libjcat1:s390x depends on libgnutls30 (>= 3.7.3). 233s libcurl3-gnutls:s390x depends on libgnutls30 (>= 3.8.2). 233s fwupd depends on libgnutls30 (>= 3.7.3). 233s dirmngr depends on libgnutls30 (>= 3.8.1). 233s apt depends on libgnutls30 (>= 3.8.1). 233s 233s (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 ... 52173 files and directories currently installed.) 233s Removing libgnutls30:s390x (3.8.3-1ubuntu1) ... 233s Selecting previously unselected package libgnutls30t64:s390x. 233s (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 ... 52164 files and directories currently installed.) 233s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_s390x.deb ... 233s Unpacking libgnutls30t64:s390x (3.8.3-1.1ubuntu2) ... 233s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 233s wget depends on libssl3 (>= 3.0.0). 233s tnftp depends on libssl3 (>= 3.0.0). 233s tcpdump depends on libssl3 (>= 3.0.0). 233s systemd-resolved depends on libssl3 (>= 3.0.0). 233s systemd depends on libssl3 (>= 3.0.0). 233s sudo depends on libssl3 (>= 3.0.0). 233s s390-tools depends on libssl3 (>= 3.0.0). 233s rsync depends on libssl3 (>= 3.0.0). 233s python3-cryptography depends on libssl3 (>= 3.0.0). 233s openssl depends on libssl3 (>= 3.0.9). 233s openssh-server depends on libssl3 (>= 3.0.10). 233s openssh-client depends on libssl3 (>= 3.0.10). 233s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 233s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 233s libssh-4:s390x depends on libssl3 (>= 3.0.0). 233s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 233s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 233s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 233s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 233s libnvme1 depends on libssl3 (>= 3.0.0). 233s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 233s libkmod2:s390x depends on libssl3 (>= 3.0.0). 233s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 233s libcurl4:s390x depends on libssl3 (>= 3.0.0). 233s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 233s kmod depends on libssl3 (>= 3.0.0). 233s dhcpcd-base depends on libssl3 (>= 3.0.0). 233s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 233s 233s (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 ... 52192 files and directories currently installed.) 233s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 233s Selecting previously unselected package libssl3t64:s390x. 233s (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 ... 52181 files and directories currently installed.) 233s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_s390x.deb ... 233s Unpacking libssl3t64:s390x (3.0.13-0ubuntu1) ... 233s Preparing to unpack .../curl_8.5.0-2ubuntu7_s390x.deb ... 233s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 233s dpkg: libcurl4:s390x: dependency problems, but removing anyway as you requested: 233s s390-tools depends on libcurl4 (>= 7.16.2). 233s 233s (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 ... 52194 files and directories currently installed.) 233s Removing libcurl4:s390x (8.5.0-2ubuntu2) ... 233s Selecting previously unselected package libcurl4t64:s390x. 233s (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 ... 52189 files and directories currently installed.) 233s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_s390x.deb ... 233s Unpacking libcurl4t64:s390x (8.5.0-2ubuntu7) ... 233s dpkg: libpsl5:s390x: dependency problems, but removing anyway as you requested: 233s wget depends on libpsl5 (>= 0.16.0). 233s libcurl3-gnutls:s390x depends on libpsl5 (>= 0.16.0). 233s 233s (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 ... 52195 files and directories currently installed.) 233s Removing libpsl5:s390x (0.21.2-1build1) ... 233s Selecting previously unselected package libpsl5t64:s390x. 233s (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 ... 52190 files and directories currently installed.) 233s Preparing to unpack .../libpsl5t64_0.21.2-1.1_s390x.deb ... 233s Unpacking libpsl5t64:s390x (0.21.2-1.1) ... 234s dpkg: libcurl3-gnutls:s390x: dependency problems, but removing anyway as you requested: 234s libfwupd2:s390x depends on libcurl3-gnutls (>= 7.63.0). 234s fwupd depends on libcurl3-gnutls (>= 7.63.0). 234s 234s (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 ... 52196 files and directories currently installed.) 234s Removing libcurl3-gnutls:s390x (8.5.0-2ubuntu2) ... 234s Selecting previously unselected package libcurl3t64-gnutls:s390x. 234s (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 ... 52189 files and directories currently installed.) 234s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu7_s390x.deb ... 234s Unpacking libcurl3t64-gnutls:s390x (8.5.0-2ubuntu7) ... 234s Selecting previously unselected package hyphy-common. 234s Preparing to unpack .../01-hyphy-common_2.5.59+dfsg-1build2_all.deb ... 234s Unpacking hyphy-common (2.5.59+dfsg-1build2) ... 234s Selecting previously unselected package libgomp1:s390x. 234s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 234s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 234s Selecting previously unselected package libevent-pthreads-2.1-7:s390x. 234s Preparing to unpack .../03-libevent-pthreads-2.1-7_2.1.12-stable-9_s390x.deb ... 234s Unpacking libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 234s Selecting previously unselected package libatomic1:s390x. 234s Preparing to unpack .../04-libatomic1_14-20240303-1ubuntu1_s390x.deb ... 234s Unpacking libatomic1:s390x (14-20240303-1ubuntu1) ... 234s Selecting previously unselected package librdmacm1:s390x. 234s Preparing to unpack .../05-librdmacm1_50.0-1_s390x.deb ... 234s Unpacking librdmacm1:s390x (50.0-1) ... 234s Selecting previously unselected package libfabric1:s390x. 234s Preparing to unpack .../06-libfabric1_1.17.0-3_s390x.deb ... 234s Unpacking libfabric1:s390x (1.17.0-3) ... 234s Selecting previously unselected package libhwloc15:s390x. 234s Preparing to unpack .../07-libhwloc15_2.10.0-1_s390x.deb ... 234s Unpacking libhwloc15:s390x (2.10.0-1) ... 234s Selecting previously unselected package libmunge2:s390x. 234s Preparing to unpack .../08-libmunge2_0.5.15-3ubuntu1_s390x.deb ... 234s Unpacking libmunge2:s390x (0.5.15-3ubuntu1) ... 234s Selecting previously unselected package libpciaccess0:s390x. 234s Preparing to unpack .../09-libpciaccess0_0.17-3_s390x.deb ... 234s Unpacking libpciaccess0:s390x (0.17-3) ... 234s Selecting previously unselected package libxnvctrl0:s390x. 234s Preparing to unpack .../10-libxnvctrl0_510.47.03-0ubuntu1_s390x.deb ... 234s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 234s Selecting previously unselected package ocl-icd-libopencl1:s390x. 234s Preparing to unpack .../11-ocl-icd-libopencl1_2.3.2-1_s390x.deb ... 234s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1) ... 234s Selecting previously unselected package libhwloc-plugins:s390x. 234s Preparing to unpack .../12-libhwloc-plugins_2.10.0-1_s390x.deb ... 234s Unpacking libhwloc-plugins:s390x (2.10.0-1) ... 234s Selecting previously unselected package libpmix2t64:s390x. 234s Preparing to unpack .../13-libpmix2t64_5.0.1-4.1_s390x.deb ... 234s Unpacking libpmix2t64:s390x (5.0.1-4.1) ... 234s Selecting previously unselected package libopenmpi3t64:s390x. 234s Preparing to unpack .../14-libopenmpi3t64_4.1.6-6ubuntu1_s390x.deb ... 234s Unpacking libopenmpi3t64:s390x (4.1.6-6ubuntu1) ... 234s Selecting previously unselected package hyphy-mpi. 234s Preparing to unpack .../15-hyphy-mpi_2.5.59+dfsg-1build2_s390x.deb ... 234s Unpacking hyphy-mpi (2.5.59+dfsg-1build2) ... 234s Selecting previously unselected package hyphy-pt. 234s Preparing to unpack .../16-hyphy-pt_2.5.59+dfsg-1build2_s390x.deb ... 234s Unpacking hyphy-pt (2.5.59+dfsg-1build2) ... 234s Selecting previously unselected package autopkgtest-satdep. 234s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 234s Unpacking autopkgtest-satdep (0) ... 234s Setting up librdmacm1:s390x (50.0-1) ... 234s Setting up libpciaccess0:s390x (0.17-3) ... 234s Setting up libssl3t64:s390x (3.0.13-0ubuntu1) ... 234s Setting up libpsl5t64:s390x (0.21.2-1.1) ... 234s Setting up hyphy-common (2.5.59+dfsg-1build2) ... 234s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 234s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu1) ... 234s Setting up libnettle8t64:s390x (3.9.1-2.2) ... 234s Setting up libmunge2:s390x (0.5.15-3ubuntu1) ... 234s Setting up libhwloc15:s390x (2.10.0-1) ... 234s Setting up libatomic1:s390x (14-20240303-1ubuntu1) ... 234s Setting up libhogweed6t64:s390x (3.9.1-2.2) ... 234s Setting up ocl-icd-libopencl1:s390x (2.3.2-1) ... 234s Setting up libevent-pthreads-2.1-7:s390x (2.1.12-stable-9) ... 234s Setting up libgnutls30t64:s390x (3.8.3-1.1ubuntu2) ... 234s Setting up libfabric1:s390x (1.17.0-3) ... 234s Setting up libcurl4t64:s390x (8.5.0-2ubuntu7) ... 234s Setting up libcurl3t64-gnutls:s390x (8.5.0-2ubuntu7) ... 234s Setting up hyphy-pt (2.5.59+dfsg-1build2) ... 234s Setting up libhwloc-plugins:s390x (2.10.0-1) ... 234s Setting up libpmix2t64:s390x (5.0.1-4.1) ... 234s Setting up libopenmpi3t64:s390x (4.1.6-6ubuntu1) ... 234s Setting up curl (8.5.0-2ubuntu7) ... 234s Setting up hyphy-mpi (2.5.59+dfsg-1build2) ... 234s Setting up autopkgtest-satdep (0) ... 234s Processing triggers for man-db (2.12.0-3) ... 235s Processing triggers for libc-bin (2.39-0ubuntu2) ... 238s (Reading database ... 53028 files and directories currently installed.) 238s Removing autopkgtest-satdep (0) ... 239s autopkgtest [17:04:25]: test run-unit-tests: [----------------------- 239s + for i in *.bf 239s + '[' -f ExonIntron.bf ']' 239s + hyphy ExonIntron.bf 240s Log Likelihood = -1113.34523097096; 240s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134922360054386,(ZMUBIS27F:0,(ZMU29160:0.05439434932282533,ZMU29161:0.03970999166190733)Node8:0.01201941509476627)Node6:0)Node4:0.02459325579552285,BLYMUB1:0.01185776317071451); 240s Tree exon2Tree=(BLYMUB2:0.03542712686531091,(RICRMA630:0.02935212677492443,(ZMUBIS27F:0.07545618687547105,(ZMU29160:0.09103008402713363,ZMU29161:0.02595058167991688)Node8:0.01157418952698801)Node6:0.04928334034159242)Node4:0.02930702521183928,BLYMUB1:0.02204339627174455); 240s Tree intronTree=(BLYMUB2:0.03120148612094109,(RICRMA630:0.04155588332931375,(ZMUBIS27F:0.0204450048634299,(ZMU29160:0.02069042064766667,ZMU29161:0.01019777223217759)Node8:0.02068977427005251)Node6:0)Node4:0,BLYMUB1:0.01036597601511323); 240s + for i in *.bf 240s + '[' -f F81.bf ']' 240s + hyphy F81.bf 240s Log Likelihood = -1187.54702793555; 240s Tree givenTree=(256:0.01194349931817215,(822:0.02944831511822758,159:0.004470548006066492)Node2:0.003652057115312472,((113:0.02244745718091993,9939:0.07632906548672694)Node6:0.00507764978158866,(6760:0.06903114752200892,((317:0.03751818519773164,6767:0.07086144671073689)Node12:0.01229344742288747,((135:0.02045618794857804,(529:0.03338016174521963,105r:0.01322043982245651)Node18:0.02586876645680794)Node16:0.005414265333512922,(719:0.02965903204975293,136:0.008234207161007853)Node21:0.04882998782707906)Node15:0.01525962110033743)Node11:0.01379934486338241)Node9:0.02422267836472632)Node5:0.02148378205726027); 240s + for i in *.bf 240s + '[' -f F81relrate.bf ']' 240s + hyphy F81relrate.bf 240s 240s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.001001418486; 240s Tree threeTaxaTree=(a:0.08501458081831741,b:0.07337612979570049,c:0.1653894109016897); 240s 240s 240s 1). With the outgroup at taxon #1, the P-value is:0.002155106158058695 240s Log Likelihood = -948.707253867892; 240s Tree threeTaxaTree=(a:0.08228741153904655,b:0.119450759858316,c:0.119450759858316); 240s 240s 240s 2). With the outgroup at taxon #2, the P-value is:0.008353404399320974 240s Log Likelihood = -947.479050125766; 240s Tree threeTaxaTree=(a:0.1250762630043411,b:0.07125949122322148,c:0.1250762630043411); 240s 240s 240s 3). With the outgroup at taxon #3, the P-value is:0.6669137053246262 240s Log Likelihood = -944.093618166699; 240s Tree threeTaxaTree=(a:0.07922729811878117,b:0.07922729811878117,c:0.165333983818582); 240s 240s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.63059583061; 240s Tree fourTaxaTree1=((1:0.1129103837257227,2:0.107343860013683)Node1:0.09978718076111803,3:0.3469443804232114,4:0.3219019795642176); 240s Tree fourTaxaTree2=((1:0.08585822862919713,2:0.09338072181116867)Node1:0.07364163086656983,3:0.3933120522865876,4:0.3801922663729329); 240s + for i in *.bf 240s + '[' -f F81relratio.bf ']' 240s + hyphy F81relratio.bf 240s 240s 240s 1). Relative ratio constraint; the P-value is:0.6933531570010261 240s Log Likelihood = -2575.74610909567; 240s Global Parameters: 240s R=1.00729085341613; 240s 240s Tree fourTaxaTree1=((1:0.09948365505806882,2:0.09943037138794089)Node1:0.08696829308802421,3:0.3687235960126604,4:0.3489177338272059); 240s Tree fourTaxaTree2=((1:0.100073745135645,2:0.1000201454119401)Node1:0.08748414794664425,3:0.3709106903172302,4:0.3509873491072399); 240s + for i in *.bf 240s + '[' -f HKY85.bf ']' 240s + hyphy HKY85.bf 240s Log Likelihood = -1152.88077773909; 240s 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); 240s + for i in *.bf 240s + '[' -f HKY852blocks.bf ']' 240s + hyphy HKY852blocks.bf 240s 240s ----- RESULTS ----- 240s Log Likelihood = -6801.91478425276; 240s 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); 240s 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); 240s + for i in *.bf 240s + '[' -f HKY852blocks2models.bf ']' 240s + hyphy HKY852blocks2models.bf 240s 240s ----- RESULTS ----- 240s Log Likelihood = -6049.33413410755; 240s 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); 240s 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); 240s + for i in *.bf 240s + '[' -f HKY85relrate.bf ']' 240s + hyphy HKY85relrate.bf 240s 240s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371751632424; 240s Tree threeTaxaTree=(a:0.08473003175317764,b:0.07473137597643539,c:0.174064542689109); 240s 240s 240s 1). Outgroup at taxon #1 240s a). Transition rate test. P-Value = 0.02098226516725465 240s Log Likelihood = -924.035884021378; 240s Tree threeTaxaTree=(a:0.08099123330674669,b:0.1064970277501439,c:0.1431287422547734); 240s 240s b). Transversion rate test. P-Value = 0.03655174813200768 240s Log Likelihood = -923.55733986013; 240s Tree threeTaxaTree=(a:0.084385863180111,b:0.09108496720824998,c:0.1577932370277693); 240s 240s c). Both rates test. P-Value = 0.00632399828374719 240s Log Likelihood = -926.435155263498; 240s Tree threeTaxaTree=(a:0.08054167256686441,b:0.1248197388549912,c:0.1248197388549912); 240s 240s 240s 2). Outgroup at taxon #2 240s a). Transition rate test. P-Value = 0.02758028958440228 240s Log Likelihood = -923.798808189923; 240s Tree threeTaxaTree=(a:0.1157945362947561,b:0.0710231672763683,c:0.1442792954111021); 240s 240s b). Transversion rate test. P-Value = 0.1106456954857765 240s Log Likelihood = -922.644238896077; 240s Tree threeTaxaTree=(a:0.09762132520456517,b:0.07463527366174004,c:0.1608971533992973); 240s 240s c). Both rates test. P-Value = 0.02199500082285188 240s Log Likelihood = -925.188691719246; 240s Tree threeTaxaTree=(a:0.1299135255623827,b:0.07078650465677661,c:0.1299135255623827); 240s 240s 240s 3). Outgroup at taxon #3 240s a). Transition rate test. P-Value = 0.9291732773304646 240s Log Likelihood = -921.37570190709; 240s Tree threeTaxaTree=(a:0.08354358737958395,b:0.07588180027038632,c:0.1740455829900139); 240s 240s b). Transversion rate test. P-Value = 0.5919879178907992 240s Log Likelihood = -921.515376857668; 240s Tree threeTaxaTree=(a:0.08115157531975309,b:0.07834973653854679,c:0.1740031943295483); 240s 240s c). Both rates test. P-Value = 0.8615417084585719 240s Log Likelihood = -921.520783442837; 240s Tree threeTaxaTree=(a:0.0797427566582293,b:0.0797427566582293,c:0.1740977267630993); 240s 240s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78444360128; 240s Tree fourTaxaTree1=((1:0.1138487045809995,2:0.1110122567337608)Node1:0.1041027812434805,3:0.3524784637033474,4:0.3311404591602357); 240s Tree fourTaxaTree2=((1:0.08605976045998506,2:0.09356337741977526)Node1:0.08032197435213155,3:0.385891426880159,4:0.3896179485372721); 240s 240s 240s 1). Relative ratio constraint on transitions; the P-value is:0.5738682609440525 240s Log Likelihood = -2541.23688168788; 240s Global Parameters: 240s R=0.8578541215383632; 240s 240s Tree fourTaxaTree1=((1:0.1087003096719766,2:0.09421907847385359)Node1:0.1116157058852775,3:0.3552439545342539,4:0.3552086892345077); 240s Tree fourTaxaTree2=((1:0.09037887537627746,2:0.1092097124826926)Node1:0.07302488882756823,3:0.3839571532719285,4:0.3656425327601758); 240s + for i in *.bf 240s + '[' -f HKY85relratio.bf ']' 240s + hyphy HKY85relratio.bf 240s 240s 240s 2). Relative ratio constraint on transversions; the P-value is:0.5738472550933933 240s Log Likelihood = -2541.23694349417; 240s Global Parameters: 240s R=0.8589603715892914; 240s 240s Tree fourTaxaTree1=((1:0.1086716868936693,2:0.09419409914174939)Node1:0.1116642054312137,3:0.3552401464319628,4:0.3551648291482664); 240s Tree fourTaxaTree2=((1:0.0903996047664344,2:0.1092661814701359)Node1:0.07317145803537307,3:0.3840622417334454,4:0.365787126691511); 240s 240s 240s 3). Relative ratio constraint on both rates; the P-value is:0.6565946568680778 240s Log Likelihood = -2543.19088078469; 240s Global Parameters: 240s R=0.9967217644791697; 240s 240s Tree fourTaxaTree1=((1:0.1004739282458528,2:0.1007148559674787)Node1:0.09256041076636634,3:0.371366834319677,4:0.3582398552835915); 240s Tree fourTaxaTree2=((1:0.1003279354876104,2:0.1007274698667217)Node1:0.09287222080919806,3:0.3698843409350728,4:0.3577786811818548); 240s + for i in *.bf 240s + '[' -f HKY85shared.bf ']' 240s + hyphy HKY85shared.bf 240s Log Likelihood = -1165.70301189119; 240s Global Parameters: 240s R=2.970526764066976; 240s 240s Tree givenTree=(256:0.01209242198680888,(822:0.0296096904559618,159:0.004652667075133809)Node2:0.003524577020351321,((113:0.02180310396607724,9939:0.07941957445876549)Node6:0.004909965762467951,(6760:0.07148879859256838,((317:0.03799252826569335,6767:0.07150930163009102)Node12:0.01178345155565053,((135:0.02022927441043865,(529:0.03405040226389042,105r:0.01304701782214643)Node18:0.02630176779799248)Node16:0.005817033318540698,(719:0.02973913484560455,136:0.008132528929219894)Node21:0.04877233126703942)Node15:0.01555697816688831)Node11:0.01396228515205485)Node9:0.02325904580437163)Node5:0.02145408623083264); 240s + for i in *.bf 240s + '[' -f JC69.bf ']' 240s + hyphy JC69.bf 241s Log Likelihood = -1230.82014326801; 241s 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); 241s + for i in *.bf 241s + '[' -f K2P.bf ']' 241s + hyphy K2P.bf 241s Log Likelihood = -1198.26189205175; 241s Tree givenTree=(256:0.0117668465165985,(822:0.0292653940914878,159:0.004288526200384838)Node2:0.003666060737393463,((113:0.0236716381754644,9939:0.07263577424220546)Node6:0.003382417881682191,(6760:0.06224097903728203,((317:0.04072458677499916,6767:0.06833986513863637)Node12:0.01244235776566587,((135:0.02259380423047821,(529:0.03395470049514703,105r:0.01240299777923351)Node18:0.02142194109121085)Node16:0.004488574407829232,(719:0.02882049068762725,136:0.008836870553622599)Node21:0.05083308484288266)Node15:0.01733397884713602)Node11:0.01112113549461396)Node9:0.02821428231043235)Node5:0.02369793290158257); 241s + for i in *.bf 241s + '[' -f K2Pshared.bf ']' 241s + hyphy K2Pshared.bf 241s Log Likelihood = -1210.49419565614; 241s Global Parameters: 241s R=2.61677690422922; 241s 241s 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); 241s + for i in *.bf 241s + '[' -f MatrixIndexing.bf ']' 241s + hyphy MatrixIndexing.bf 241s 241s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 241s { 241s {0.4118495649685733, 0.9569477792729036, 0.2139791709403459, 0.4114878998164758, 0.2456643551694379, 0.725101936078887} 241s {0.9237197623410541, 0.3649236898321946, 0.6454612344143589, 0.1145433185423127, 0.3242764191991362, 0.7317400557761407} 241s {0.543465406760449, 0.3179960742867542, 0.2850180715986104, 0.6063667790979069, 0.8249767014814953, 0.459668644578119} 241s {0.8813475083749154, 0.5778831643000905, 0.8817155295707554, 0.4050975980714656, 0.8838055787803153, 0.4607285543951971} 241s {0.4074985909758831, 0.2290808184140084, 0.7047783538477445, 0.5796319312834255, 0.5588327915311867, 0.7965912688049933} 241s } 241s 241s 2). Accessing a second-row third-column element and a random element. 241s 241s matrix[1][2]=0.6454612344143589 241s matrix[4][2]=0.7047783538477445 241s 241s 3). Accessing the fourth row. 241s 241s matrix[3][-1]= 241s { 241s {0.8813475083749154, 0.5778831643000905, 0.8817155295707554, 0.4050975980714656, 0.8838055787803153, 0.4607285543951971} 241s } 241s 241s 4). Accessing the first column. 241s 241s matrix[-1][0]= 241s { 241s {0.4118495649685733} 241s {0.9237197623410541} 241s {0.543465406760449} 241s {0.8813475083749154} 241s {0.4074985909758831} 241s } 241s 241s 5). Populating a matrix template (below the diagonal). 241s 241s { 241s {0, 0, 0, 0, 0, 0} 241s {1, 0, 0, 0, 0, 0} 241s {1, 1, 0, 0, 0, 0} 241s {1, 1, 1, 0, 0, 0} 241s {1, 1, 1, 1, 0, 0} 241s } 241s 241s 6). Extracting (by row) matrix elements using the template. 241s 241s { 241s {0.9237197623410541, 0.543465406760449, 0.3179960742867542, 0.8813475083749154, 0.5778831643000905, 0.8817155295707554, 0.4074985909758831, 0.2290808184140084, 0.7047783538477445, 0.5796319312834255} 241s } 241s 241s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 241s 241s matrix[{{1,1}}][{{3,2}}]= 241s { 241s {0.3649236898321946, 0.6454612344143589} 241s {0.3179960742867542, 0.2850180715986104} 241s {0.5778831643000905, 0.8817155295707554} 241s } 241s 241s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 241s 241s 241s { 241s {0.1696200641648031, 1.915749052255342, 1.045787085596318, 1.169322291695374, 1.060350975400816, 1.52577281770535} 241s {0.8532581993394135, 0.1331692994007438, 1.416620205131708, 1.013120171822686, 1.105155196048614, 1.53544350922727} 241s {0.2953546483453002, 0.1011215032617869, 0.08123530113779058, 1.36768067079357, 1.680586557987288, 1.211295262808285} 241s {0.7767734305186715, 0.3339489515814854, 0.7774222750862376, 0.1641040639632707, 1.781112301083208, 1.212270800835088} 241s {0.1660551016473301, 0.05247802136523191, 0.4967125280523365, 0.3359731757633537, 0.3122940888905388, 1.634557649536349} 241s } 241s + for i in *.bf 241s + '[' -f MolecularClockF81.bf ']' 241s + hyphy MolecularClockF81.bf 241s 241s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124421372; 241s 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); 241s 241s 241s 1). Global Molecular Clock; the P-value is:0 241s Log Likelihood = -11927.6152937212; 241s Tree theTree=(HVRNASS:0.02157256601612202,(RICRSS3:0.1233391270223043,((ZMSUCS1:0.05658065876351052,(OSRSS1A:0.04751101925662449,(TASUCSYN1:0.01824591719415406,HVSSYNMR:0.01824591719415406)Internal1:0.02926510206247043)Node9:0.009069639506886022)Node7:0.05762932787233832,(MZESUS1:0.07014502507047848,ORRSS2:0.07014502507047848)Internal2:0.04406496156537035)Node6:0.009129140386455448)Node4:0.0271554254219784,TAAJ153:0.1504945524442827); 241s 241s 241s 2). Molecular Clock starting at Internal1; the P-value is:0.1603793692668972 241s Log Likelihood = -11476.6977648554; 241s Tree theTree=(HVRNASS:0.02574463805399199,(RICRSS3:0.05630537714760154,((ZMSUCS1:0.07170662802894455,(OSRSS1A:0.06051700985579202,(TASUCSYN1:0.02411838163024049,HVSSYNMR:0.02411838163024049)Internal1:0.0518064371902121)Node9:0.02017647165128062)Node7:0.1580963984079214,(MZESUS1:0.07663695130644277,ORRSS2:0.05441168181520002)Internal2:0.02507734912974911)Node6:0.03252990709623189)Node4:0.05896343352631034,TAAJ153:0.01372808144991367); 241s 241s 241s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.01610191699969754 241s Log Likelihood = -11479.841259083; 241s 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); 241s + for i in *.bf 241s + '[' -f MolecularClockHKY85.bf ']' 241s + hyphy MolecularClockHKY85.bf 241s 241s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013283038; 241s 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); 241s 241s 241s 1). Global Molecular Clock on transition rates; the P-value is:0 241s Log Likelihood = -11434.7016033505; 241s 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); 241s 241s 241s 2). Global Molecular Clock on transversion rates; the P-value is:0 241s Log Likelihood = -11497.3782378614; 241s Tree theTree=(HVRNASS:0.02484203947298438,(RICRSS3:0.09397047508063444,((ZMSUCS1:0.06899532712237967,(OSRSS1A:0.05468071241477943,(TASUCSYN1:0.02277218833670913,HVSSYNMR:0.02034632951245292)Node11:0.04374488950975081)Node9:0.01674196535254953)Node7:0.09971736090270263,(MZESUS1:0.07446775530660792,ORRSS2:0.06134915824606269)Node14:0.03386699677794925)Node6:0.02080023539102577)Node4:0.05008131208856946,TAAJ153:0.07305847922015964); 241s 241s 241s 3). Global Molecular Clock on both rates; the P-value is:0 241s Log Likelihood = -11703.6261633936; 241s 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); 241s + for i in *.bf 241s + '[' -f Non-Rev.bf ']' 241s + hyphy Non-Rev.bf 242s Log Likelihood = -1152.7840407854; 242s Global Parameters: 242s GC=0.2693046893024039; 242s CG=0.1876161406731733; 242s GA=1.914699961722618; 242s CT=1.257156910192686; 242s GT=0.08715584073736923; 242s CA=0.9188783234416088; 242s AT=0.430903249174395; 242s AG=1.588538395343721; 242s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2564761117242166; 242s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.037427167253087; 242s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7949653914439003; 242s 242s Tree givenTree=(256:0.01343329228953684,(822:0.02847332834061019,159:0.0061120875250895)Node2:0.003449110961865998,((113:0.02186727429503996,9939:0.07932596720468554)Node6:0.004988833181775348,(6760:0.0732428699190027,((317:0.04007320673383701,6767:0.06982635443703028)Node12:0.01160662973807407,((135:0.02156255115083465,(529:0.03497226362965428,105r:0.0142176142962887)Node18:0.02378491269227611)Node16:0.005244314230208867,(719:0.02863997443092517,136:0.009565568804298864)Node21:0.04927814704156475)Node15:0.01636355941103615)Node11:0.01274336511525732)Node9:0.02193780268728399)Node5:0.02028832048383466); 242s + for i in *.bf 242s + '[' -f PBootstrapHetRates.bf ']' 242s + hyphy PBootstrapHetRates.bf 242s 242s ----ORIGINAL DATA---- 242s Log Likelihood = -1127.31560536389; 242s Global Parameters: 242s alpha=0.318903661364874; 242s kappa=0.3236251153932033; 242s 242s Tree givenTree=(256:0.01258515195286014,(822:0.03175356558495591,159:0.004692747342476685)Node2:0.003777499490449313,((113:0.02291471891534015,9939:0.09712474689339325)Node6:0.001964058262546234,(6760:0.08715359252891673,((317:0.04570220836308511,6767:0.08106974545339699)Node12:0.007409621819652962,((135:0.018636646919929,(529:0.0369383857434715,105r:0.01499292845477245)Node18:0.03033508405649344)Node16:0.007147322073341072,(719:0.03339504194476876,136:0.007167255439850933)Node21:0.05751745057914805)Node15:0.01788805604870618)Node11:0.01884118206937395)Node9:0.02369235179374087)Node5:0.02500575626841894); 242s 242s Using the seed: 242s 1710611193 242s Category variable name: TRUE 242s Site Rate 242s 0 0.00000 242s 1 0.00001 242s 2 0.00002 242s 3 0.00004 242s 4 0.00005 242s 5 0.00005 242s 6 0.00006 242s 7 0.00008 242s 8 0.00010 242s 9 0.00013 242s 10+ for i in *.bf 242s + '[' -f REV.bf ']' 242s + hyphy REV.bf 242s 0.00013 242s 11 0.00017 242s 12 0.00040 242s 13 0.00043 242s 14 0.00052 242s 15 0.00065 242s 16 0.00081 242s 17 0.00081 242s 18 0.00087 242s 19 0.00092 242s 20 0.00095 242s 21 0.00105 242s 22 0.00106 242s 23 0.00126 242s 24 0.00130 242s 25 0.00154 242s 26 0.00163 242s 27 0.00170 242s 28 0.00181 242s 29 0.00188 242s 30 0.00196 242s 31 0.00229 242s 32 0.00250 242s 33 0.00264 242s 34 0.00264 242s 35 0.00311 242s 36 0.00335 242s 37 0.00341 242s 38 0.00356 242s 39 0.00363 242s 40 0.00394 242s 41 0.00431 242s 42 0.00450 242s 43 0.00455 242s 44 0.00478 242s 45 0.00480 242s 46 0.00510 242s 47 0.00516 242s 48 0.00537 242s 49 0.00591 242s 50 0.00630 242s 51 0.00664 242s 52 0.00739 242s 53 0.00800 242s 54 0.00879 242s 55 0.00915 242s 56 0.00922 242s 57 0.01010 242s 58 0.01122 242s 59 0.01127 242s 60 0.01150 242s 61 0.01192 242s 62 0.01288 242s 63 0.01418 242s 64 0.01520 242s 65 0.01640 242s 66 0.01671 242s 67 0.01756 242s 68 0.01798 242s 69 0.01825 242s 70 0.01878 242s 71 0.02046 242s 72 0.02098 242s 73 0.02115 242s 74 0.02263 242s 75 0.02345 242s 76 0.02411 242s 77 0.02652 242s 78 0.02673 242s 79 0.02692 242s 80 0.02795 242s 81 0.03535 242s 82 0.03551 242s 83 0.03604 242s 84 0.04009 242s 85 0.04219 242s 86 0.04432 242s 87 0.04518 242s 88 0.04590 242s 89 0.04824 242s 90 0.04832 242s 91 0.04928 242s 92 0.04997 242s 93 0.05534 242s 94 0.06005 242s 95 0.06128 242s 96 0.06309 242s 97 0.06438 242s 98 0.06533 242s 99 0.07694 242s 100 0.07714 242s 101 0.09076 242s 102 0.09229 242s 103 0.09546 242s 104 0.09668 242s 105 0.09857 242s 106 0.10044 242s 107 0.10667 242s 108 0.11174 242s 109 0.11718 242s 110 0.11984 242s 111 0.12022 242s 112 0.13145 242s 113 0.13510 242s 114 0.13627 242s 115 0.13680 242s 116 0.14164 242s 117 0.14290 242s 118 0.14865 242s 119 0.15308 242s 120 0.15825 242s 121 0.17097 242s 122 0.17848 242s 123 0.17904 242s 124 0.18712 242s 125 0.19263 242s 126 0.20190 242s 127 0.20309 242s 128 0.21476 242s 129 0.21937 242s 130 0.22605 242s 131 0.23055 242s 132 0.23799 242s 133 0.23977 242s 134 0.24016 242s 135 0.25167 242s 136 0.26557 242s 137 0.26624 242s 138 0.27251 242s 139 0.27804 242s 140 0.28220 242s 141 0.28454 242s 142 0.29905 242s 143 0.30649 242s 144 0.31304 242s 145 0.31609 242s 146 0.31979 242s 147 0.34235 242s 148 0.34416 242s 149 0.34454 242s 150 0.35178 242s 151 0.36098 242s 152 0.38040 242s 153 0.38047 242s 154 0.39344 242s 155 0.40967 242s 156 0.41361 242s 157 0.41759 242s 158 0.44527 242s 159 0.46185 242s 160 0.46720 242s 161 0.47235 242s 162 0.47265 242s 163 0.47741 242s 164 0.52928 242s 165 0.54366 242s 166 0.55997 242s 167 0.57877 242s 168 0.57935 242s 169 0.58441 242s 170 0.60829 242s 171 0.61191 242s 172 0.61269 242s 173 0.63181 242s 174 0.63591 242s 175 0.64803 242s 176 0.65500 242s 177 0.69054 242s 178 0.69872 242s 179 0.70342 242s 180 0.71822 242s 181 0.73405 242s 182 0.74199 242s 183 0.74688 242s 184 0.76849 242s 185 0.77103 242s 186 0.77295 242s 187 0.78174 242s 188 0.82928 242s 189 0.84543 242s 190 0.84856 242s 191 0.87775 242s 192 0.87894 242s 193 0.93282 242s 194 0.95625 242s 195 0.97752 242s 196 0.98457 242s 197 1.00106 242s 198 1.00583 242s 199 1.01596 242s 200 1.05993 242s 201 1.06619 242s 202 1.07656 242s 203 1.10040 242s 204 1.16501 242s 205 1.21764 242s 206 1.22465 242s 207 1.23029 242s 208 1.24550 242s 209 1.24718 242s 210 1.28187 242s 211 1.28365 242s 212 1.29542 242s 213 1.31315 242s 214 1.31799 242s 215 1.33152 242s 216 1.34264 242s 217 1.34297 242s 218 1.34705 242s 219 1.37021 242s 220 1.46237 242s 221 1.48206 242s 222 1.48327 242s 223 1.55856 242s 224 1.59210 242s 225 1.60612 242s 226 1.61650 242s 227 1.70879 242s 228 1.73508 242s 229 1.73630 242s 230 1.85854 242s 231 1.87618 242s 232 1.89401 242s 233 1.99307 242s 234 2.00119 242s 235 2.00501 242s 236 2.05201 242s 237 2.06099 242s 238 2.08139 242s 239 2.09246 242s 240 2.09442 242s 241 2.18135 242s 242 2.21774 242s 243 2.27311 242s 244 2.32526 242s 245 2.36024 242s 246 2.41944 242s 247 2.43802 242s 248 2.52024 242s 249 3.13517 242s 250 3.25648 242s 251 3.27908 242s 252 3.31336 242s 253 3.37231 242s 254 3.53774 242s 255 3.56760 242s 256 3.64844 242s 257 3.81430 242s 258 4.00897 242s 259 4.12165 242s 260 4.48356 242s 261 4.50865 242s 262 4.53897 242s 263 4.55186 242s 264 4.89681 242s 265 5.04349 242s 266 5.09707 242s 267 5.54636 242s 268 6.77676 242s 269 7.60320 242s 270 7.62143 242s 271 8.66244 242s 272 11.43809 242s 242s Mean = 0.9005845456434853 242s Var = 2.370094456582559 (1/alpha) = 3.135743238945911 242s Log Likelihood = -1100.00325192676; 242s Tree givenTree=(256:0.02246871958920071,(822:0.01867826392010883,159:0.01469054619642481)Node2:0.003780037041493445,((113:0.01829386361698467,9939:0.07804102019026828)Node6:0.007456157729891971,(6760:0.07113581697010701,((317:0.0371908451117874,6767:0.07206937237146221)Node12:0.01019126092445315,((135:0.02036489328864084,(529:0.03424008693126637,105r:0.01130058987905245)Node18:0.02851169007030497)Node16:0.006571243076489387,(719:0.02830813236724508,136:0.009595583712718415)Node21:0.04404095929135449)Node15:0.01655093024567787)Node11:0.01315865370683736)Node9:0.02915628572885135)Node5:0.009980421685718468); 242s + for i in *.bf 242s + '[' -f REVshared.bf ']' 242s + hyphy REVshared.bf 242s Log Likelihood = -1156.62540457054; 242s Global Parameters: 242s AT=0.3620864498928175; 242s GT=0.4597052870130426; 242s CG=0.2460538484483357; 242s AG=1.843831882122668; 242s CT=1.197638246713696; 242s 242s Tree givenTree=(256:0.01208251220644581,(822:0.029737488493712,159:0.004672259626667204)Node2:0.003488371623634371,((113:0.02208107701492746,9939:0.07975700593153943)Node6:0.004709009765687309,(6760:0.07205505045490256,((317:0.03911304112716218,6767:0.0710717819219864)Node12:0.01083325224437629,((135:0.02050380402747335,(529:0.03438702674090106,105r:0.01467793485721706)Node18:0.02467636231794451)Node16:0.005560945661843388,(719:0.02873587733291043,136:0.009469209764284033)Node21:0.04910009406359832)Node15:0.01584220722126514)Node11:0.0142658080884724)Node9:0.02297074317769743)Node5:0.02144991115727102); 242s + for i in *.bf 242s + '[' -f ReplicateConstraint1.bf ']' 242s + hyphy ReplicateConstraint1.bf 242s 1).Unconstrained HKY85 242s 242s Log Likelihood = -1152.88; 242s 242s Independent Parameters List 242s 242s Parameter 1 : hivTree.317.trvs 242s Parameter 2 : hivTree.317.trst 242s Parameter 3 : hivTree.6767.trvs 242s Parameter 4 : hivTree.6767.trst 242s Parameter 5 : hivTree.Node2.trvs 242s Parameter 6 : hivTree.Node2.trst 242s Parameter 7 : hivTree.135.trvs 242s Parameter 8 : hivTree.135.trst 242s Parameter 9 : hivTree.529.trvs 242s Parameter 10 : hivTree.529.trst 242s Parameter 11 : hivTree.105r.trvs 242s Parameter 12 : hivTree.105r.trst 242s Parameter 13 : hivTree.Node8.trvs 242s Parameter 14 : hivTree.Node8.trst 242s Parameter 15 : hivTree.iNode1.trvs 242s Parameter 16 : hivTree.iNode1.trst 242s Parameter 17 : hivTree.719.trvs 242s Parameter 18 : hivTree.719.trst 242s Parameter 19 : hivTree.136.trvs 242s Parameter 20 : hivTree.136.trst 242s Parameter 21 : hivTree.Node11.trvs 242s Parameter 22 : hivTree.Node11.trst 242s Parameter 23 : hivTree.Node5.trvs 242s Parameter 24 : hivTree.Node5.trst 242s Parameter 25 : hivTree.Node1.trvs 242s Parameter 26 : hivTree.Node1.trst 242s Parameter 27 : hivTree.6760.trvs 242s Parameter 28 : hivTree.6760.trst 242s Parameter 29 : hivTree.113.trvs 242s Parameter 30 : hivTree.113.trst 242s Parameter 31 : hivTree.9939.trvs 242s Parameter 32 : hivTree.9939.trst 242s Parameter 33 : hivTree.Node16.trvs 242s Parameter 34 : hivTree.Node16.trst 242s Parameter 35 : hivTree.256.trvs 242s Parameter 36 : hivTree.256.trst 242s Parameter 37 : hivTree.822.trvs 242s Parameter 38 : hivTree.822.trst 242s Parameter 39 : hivTree.159.trvs 242s Parameter 40 : hivTree.159.trst 242s Parameter 41 : hivTree.Node21.trvs 242s Parameter 42 : hivTree.Node21.trst 242s Parameter 43 : hivTree.iNode2.trvs 242s Parameter 44 : hivTree.iNode2.trst 242s Parameter 45 : hivTree.Node15.trvs 242s Parameter 46 : hivTree.Node15.trst 242s 242s 2).HKY85 constrained to F81 242s 242s Log Likelihood = -1187.55; 242s 242s Independent Parameters List 242s 242s Parameter 1 : hivTree.317.trvs 242s Parameter 2 : hivTree.6767.trvs 242s Parameter 3 : hivTree.Node2.trvs 242s Parameter 4 : hivTree.135.trvs 242s Parameter 5 : hivTree.529.trvs 242s Parameter 6 : hivTree.105r.trvs 242s Parameter 7 : hivTree.Node8.trvs 242s Parameter 8 : hivTree.iNode1.trvs 242s Parameter 9 : hivTree.719.trvs 242s Parameter 10 : hivTree.136.trvs 242s Parameter 11 : hivTree.Node11.trvs 242s Parameter 12 : hivTree.Node5.trvs 242s Parameter 13 : hivTree.Node1.trvs 242s Parameter 14 : hivTree.6760.trvs 242s Parameter 15 : hivTree.113.trvs 242s Parameter 16 : hivTree.9939.trvs 242s Parameter 17 : hivTree.Node16.trvs 242s Parameter 18 : hivTree.256.trvs 242s Parameter 19 : hivTree.822.trvs 242s Parameter 20 : hivTree.159.trvs 242s Parameter 21 : hivTree.Node21.trvs 242s Parameter 22 : hivTree.iNode2.trvs 242s Parameter 23 : hivTree.Node15.trvs 242s 242s Constrained Parameters List 242s 242s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 242s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 242s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 242s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 242s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 242s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 242s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 242s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 242s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 242s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 242s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 242s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 242s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 242s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 242s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 242s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 242s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 242s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 242s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 242s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 242s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 242s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 242s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 242s 242s 3).HKY85 constrained to F81 on internal branches 242s 242s Log Likelihood = -1167.99; 242s 242s Independent Parameters List 242s 242s Parameter 1 : hivTree.Node2.trvs 242s Parameter 2 : hivTree.Node8.trvs 242s Parameter 3 : hivTree.iNode1.trvs 242s Parameter 4 : hivTree.Node11.trvs 242s Parameter 5 : hivTree.Node5.trvs 242s Parameter 6 : hivTree.Node1.trvs 242s Parameter 7 : hivTree.Node16.trvs 242s Parameter 8 : hivTree.Node21.trvs 242s Parameter 9 : hivTree.iNode2.trvs 242s Parameter 10 : hivTree.Node15.trvs 242s Parameter 11 : hivTree.317.trst 242s Parameter 12 : hivTree.317.trvs 242s Parameter 13 : hivTree.6767.trvs 242s Parameter 14 : hivTree.6767.trst 242s Parameter 15 : hivTree.135.trst 242s Parameter 16 : hivTree.135.trvs 242s Parameter 17 : hivTree.529.trvs 242s Parameter 18 : hivTree.529.trst 242s Parameter 19 : hivTree.105r.trst 242s Parameter 20 : hivTree.105r.trvs 242s Parameter 21 : hivTree.719.trvs 242s Parameter 22 : hivTree.719.trst 242s Parameter 23 : hivTree.136.trvs 242s Parameter 24 : hivTree.136.trst 242s Parameter 25 : hivTree.6760.trvs 242s Parameter 26 : hivTree.6760.trst 242s Parameter 27 : hivTree.113.trvs 242s Parameter 28 : hivTree.113.trst 242s Parameter 29 : hivTree.9939.trst 242s Parameter 30 : hivTree.9939.trvs 242s Parameter 31 : hivTree.256.trvs 242s Parameter 32 : hivTree.256.trst 242s Parameter 33 : hivTree.822.trvs 242s Parameter 34 : hivTree.822.trst 242s Parameter 35 : hivTree.159.trst 242s Parameter 36 : hivTree.159.trvs 242s 242s Constrained Parameters List 242s 242s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 242s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 242s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 242s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 242s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 242s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 242s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 242s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 242s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 242s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 242s 242s 4).HKY85 with shared ratio. 242s 242s Log Likelihood = -1165.7; 242s 242s Independent Parameters List 242s 242s Parameter 1 : R 242s Parameter 2 : hivTree.317.trst 242s Parameter 3 : hivTree.6767.trst 242s Parameter 4 : hivTree.Node2.trst 242s Parameter 5 : hivTree.135.trst 242s Parameter 6 : hivTree.529.trst 242s Parameter 7 : hivTree.105r.trst 242s Parameter 8 : hivTree.Node8.trst 242s Parameter 9 : hivTree.iNode1.trst 242s Parameter 10 : hivTree.719.trst 242s Parameter 11 : hivTree.136.trst 242s Parameter 12 : hivTree.Node11.trst 242s Parameter 13 : hivTree.Node5.trst 242s Parameter 14 : hivTree.Node1.trst 242s Parameter 15 : hivTree.6760.trst 242s Parameter 16 : hivTree.113.trst 242s Parameter 17 : hivTree.9939.trst 242s Parameter 18 : hivTree.Node16.trst 242s Parameter 19 : hivTree.256.trst 242s Parameter 20 : hivTree.822.trst 242s Parameter 21 : hivTree.159.trst 242s Parameter 22 : hivTree.Node21.trst 242s Parameter 23 : hivTree.iNode2.trst 242s Parameter 24 : hivTree.Node15.trst 242s 242s Constrained Parameters List 242s 242s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 242s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 242s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 242s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 242s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 242s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 242s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 242s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 242s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 242s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 242s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 242s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 242s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 242s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 242s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 242s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 242s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 242s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 242s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 242s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 242s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 242s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 242s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 242s + '[' -f ReplicateConstraint2.bf ']' 242s + hyphy ReplicateConstraint2.bf 243s 1).Unconstrained HKY85 243s 243s Log Likelihood = -1152.88; 243s 243s Independent Parameters List 243s 243s Parameter 1 : hivTree.317.trvs 243s Parameter 2 : hivTree.317.trst 243s Parameter 3 : hivTree.6767.trvs 243s Parameter 4 : hivTree.6767.trst 243s Parameter 5 : hivTree.Node2.trvs 243s Parameter 6 : hivTree.Node2.trst 243s Parameter 7 : hivTree.135.trvs 243s Parameter 8 : hivTree.135.trst 243s Parameter 9 : hivTree.529.trvs 243s Parameter 10 : hivTree.529.trst 243s Parameter 11 : hivTree.105r.trvs 243s Parameter 12 : hivTree.105r.trst 243s Parameter 13 : hivTree.Node8.trvs 243s Parameter 14 : hivTree.Node8.trst 243s Parameter 15 : hivTree.iNode1.trvs 243s Parameter 16 : hivTree.iNode1.trst 243s Parameter 17 : hivTree.719.trvs 243s Parameter 18 : hivTree.719.trst 243s Parameter 19 : hivTree.136.trvs 243s Parameter 20 : hivTree.136.trst 243s Parameter 21 : hivTree.Node11.trvs 243s Parameter 22 : hivTree.Node11.trst 243s Parameter 23 : hivTree.Node5.trvs 243s Parameter 24 : hivTree.Node5.trst 243s Parameter 25 : hivTree.Node1.trvs 243s Parameter 26 : hivTree.Node1.trst 243s Parameter 27 : hivTree.6760.trvs 243s Parameter 28 : hivTree.6760.trst 243s Parameter 29 : hivTree.113.trvs 243s Parameter 30 : hivTree.113.trst 243s Parameter 31 : hivTree.9939.trvs 243s Parameter 32 : hivTree.9939.trst 243s Parameter 33 : hivTree.Node16.trvs 243s Parameter 34 : hivTree.Node16.trst 243s Parameter 35 : hivTree.256.trvs 243s Parameter 36 : hivTree.256.trst 243s Parameter 37 : hivTree.822.trvs 243s Parameter 38 : hivTree.822.trst 243s Parameter 39 : hivTree.159.trvs 243s Parameter 40 : hivTree.159.trst 243s Parameter 41 : hivTree.Node21.trvs 243s Parameter 42 : hivTree.Node21.trst 243s Parameter 43 : hivTree.iNode2.trvs 243s Parameter 44 : hivTree.iNode2.trst 243s Parameter 45 : hivTree.Node15.trvs 243s Parameter 46 : hivTree.Node15.trst 243s 243s 2).HKY85 constrained to F81 on the "iNode1" subtree 243s 243s Log Likelihood = -1157.82; 243s 243s Independent Parameters List 243s 243s Parameter 1 : hivTree.135.trvs 243s Parameter 2 : hivTree.529.trvs 243s Parameter 3 : hivTree.105r.trvs 243s Parameter 4 : hivTree.Node8.trvs 243s Parameter 5 : hivTree.317.trvs 243s Parameter 6 : hivTree.317.trst 243s Parameter 7 : hivTree.6767.trst 243s Parameter 8 : hivTree.6767.trvs 243s Parameter 9 : hivTree.Node2.trst 243s Parameter 10 : hivTree.Node2.trvs 243s Parameter 11 : hivTree.iNode1.trvs 243s Parameter 12 : hivTree.iNode1.trst 243s Parameter 13 : hivTree.719.trvs 243s Parameter 14 : hivTree.719.trst 243s Parameter 15 : hivTree.136.trvs 243s Parameter 16 : hivTree.136.trst 243s Parameter 17 : hivTree.Node11.trvs 243s Parameter 18 : hivTree.Node11.trst 243s Parameter 19 : hivTree.Node5.trvs 243s Parameter 20 : hivTree.Node5.trst 243s Parameter 21 : hivTree.Node1.trvs 243s Parameter 22 : hivTree.Node1.trst 243s Parameter 23 : hivTree.6760.trvs 243s Parameter 24 : hivTree.6760.trst 243s Parameter 25 : hivTree.113.trvs 243s Parameter 26 : hivTree.113.trst 243s Parameter 27 : hivTree.9939.trvs 243s Parameter 28 : hivTree.9939.trst 243s Parameter 29 : hivTree.Node16.trvs 243s Parameter 30 : hivTree.Node16.trst 243s Parameter 31 : hivTree.256.trvs 243s Parameter 32 : hivTree.256.trst 243s Parameter 33 : hivTree.822.trvs 243s Parameter 34 : hivTree.822.trst 243s Parameter 35 : hivTree.159.trvs 243s Parameter 36 : hivTree.159.trst 243s Parameter 37 : hivTree.Node21.trvs 243s Parameter 38 : hivTree.Node21.trst 243s Parameter 39 : hivTree.iNode2.trvs 243s Parameter 40 : hivTree.iNode2.trst 243s Parameter 41 : hivTree.Node15.trvs 243s Parameter 42 : hivTree.Node15.trst 243s 243s Constrained Parameters List 243s 243s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 243s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 243s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 243s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 243s 243s 3).HKY85 constrained to F81 on the "iNode1" branch 243s 243s Log Likelihood = -1152.88; 243s 243s Independent Parameters List 243s 243s Parameter 1 : hivTree.317.trvs 243s Parameter 2 : hivTree.317.trst 243s Parameter 3 : hivTree.6767.trvs 243s Parameter 4 : hivTree.6767.trst 243s Parameter 5 : hivTree.Node2.trvs 243s Parameter 6 : hivTree.Node2.trst 243s Parameter 7 : hivTree.135.trvs 243s Parameter 8 : hivTree.135.trst 243s Parameter 9 : hivTree.529.trvs 243s Parameter 10 : hivTree.529.trst 243s Parameter 11 : hivTree.105r.trvs 243s Parameter 12 : hivTree.105r.trst 243s Parameter 13 : hivTree.Node8.trvs 243s Parameter 14 : hivTree.Node8.trst 243s Parameter 15 : hivTree.iNode1.trvs 243s Parameter 16 : hivTree.iNode1.trst 243s Parameter 17 : hivTree.719.trvs 243s Parameter 18 : hivTree.719.trst 243s Parameter 19 : hivTree.136.trvs 243s Parameter 20 : hivTree.136.trst 243s Parameter 21 : hivTree.Node11.trvs 243s Parameter 22 : hivTree.Node11.trst 243s Parameter 23 : hivTree.Node5.trvs 243s Parameter 24 : hivTree.Node5.trst 243s Parameter 25 : hivTree.Node1.trvs 243s Parameter 26 : hivTree.Node1.trst 243s Parameter 27 : hivTree.6760.trvs 243s Parameter 28 : hivTree.6760.trst 243s Parameter 29 : hivTree.113.trvs 243s Parameter 30 : hivTree.113.trst 243s Parameter 31 : hivTree.9939.trvs 243s Parameter 32 : hivTree.9939.trst 243s Parameter 33 : hivTree.Node16.trvs 243s Parameter 34 : hivTree.Node16.trst 243s Parameter 35 : hivTree.256.trvs 243s Parameter 36 : hivTree.256.trst 243s Parameter 37 : hivTree.822.trvs 243s Parameter 38 : hivTree.822.trst 243s Parameter 39 : hivTree.159.trvs 243s Parameter 40 : hivTree.159.trst 243s Parameter 41 : hivTree.Node21.trvs 243s Parameter 42 : hivTree.Node21.trst 243s Parameter 43 : hivTree.iNode2.trvs 243s Parameter 44 : hivTree.iNode2.trst 243s Parameter 45 : hivTree.Node15.trvs 243s Parameter 46 : hivTree.Node15.trst 243s 243s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 243s 243s Log Likelihood = -1152.88; 243s 243s Independent Parameters List 243s 243s Parameter 1 : hivTree.317.trvs 243s Parameter 2 : hivTree.317.trst 243s Parameter 3 : hivTree.6767.trvs 243s Parameter 4 : hivTree.6767.trst 243s Parameter 5 : hivTree.Node2.trvs 243s Parameter 6 : hivTree.Node2.trst 243s Parameter 7 : hivTree.135.trvs 243s Parameter 8 : hivTree.135.trst 243s Parameter 9 : hivTree.529.trvs 243s Parameter 10 : hivTree.529.trst 243s Parameter 11 : hivTree.105r.trvs 243s Parameter 12 : hivTree.105r.trst 243s Parameter 13 : hivTree.Node8.trvs 243s Parameter 14 : hivTree.Node8.trst 243s Parameter 15 : hivTree.iNode1.trvs 243s Parameter 16 : hivTree.iNode1.trst 243s Parameter 17 : hivTree.719.trvs 243s Parameter 18 : hivTree.719.trst 243s Parameter 19 : hivTree.136.trvs 243s Parameter 20 : hivTree.136.trst 243s Parameter 21 : hivTree.Node11.trvs 243s Parameter 22 : hivTree.Node11.trst 243s Parameter 23 : hivTree.Node5.trvs 243s Parameter 24 : hivTree.Node5.trst 243s Parameter 25 : hivTree.Node1.trvs 243s Parameter 26 : hivTree.Node1.trst 243s Parameter 27 : hivTree.6760.trvs 243s Parameter 28 : hivTree.6760.trst 243s Parameter 29 : hivTree.113.trvs 243s Parameter 30 : hivTree.113.trst 243s Parameter 31 : hivTree.9939.trvs 243s Parameter 32 : hivTree.9939.trst 243s Parameter 33 : hivTree.Node16.trvs 243s Parameter 34 : hivTree.Node16.trst 243s Parameter 35 : hivTree.256.trvs 243s Parameter 36 : hivTree.256.trst 243s Parameter 37 : hivTree.822.trvs 243s Parameter 38 : hivTree.822.trst 243s Parameter 39 : hivTree.159.trvs 243s Parameter 40 : hivTree.159.trst 243s Parameter 41 : hivTree.Node21.trvs 243s Parameter 42 : hivTree.Node21.trst 243s Parameter 43 : hivTree.iNode2.trvs 243s Parameter 44 : hivTree.iNode2.trst 243s Parameter 45 : hivTree.Node15.trvs 243s Parameter 46 : hivTree.Node15.trst 243s 243s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 243s 243s Log Likelihood = -1152.88; 243s 243s Independent Parameters List 243s 243s Parameter 1 : hivTree.317.trvs 243s Parameter 2 : hivTree.317.trst 243s Parameter 3 : hivTree.6767.trvs 243s Parameter 4 : hivTree.6767.trst 243s Parameter 5 : hivTree.Node2.trvs 243s Parameter 6 : hivTree.Node2.trst 243s Parameter 7 : hivTree.135.trvs 243s Parameter 8 : hivTree.135.trst 243s Parameter 9 : hivTree.529.trvs 243s Parameter 10 : hivTree.529.trst 243s Parameter 11 : hivTree.105r.trvs 243s Parameter 12 : hivTree.105r.trst 243s Parameter 13 : hivTree.Node8.trvs 243s Parameter 14 : hivTree.Node8.trst 243s Parameter 15 : hivTree.iNode1.trvs 243s Parameter 16 : hivTree.iNode1.trst 243s Parameter 17 : hivTree.719.trvs 243s Parameter 18 : hivTree.719.trst 243s Parameter 19 : hivTree.136.trvs 243s Parameter 20 : hivTree.136.trst 243s Parameter 21 : hivTree.Node11.trvs 243s Parameter 22 : hivTree.Node11.trst 243s Parameter 23 : hivTree.Node5.trvs 243s Parameter 24 : hivTree.Node5.trst 243s Parameter 25 : hivTree.Node1.trvs 243s Parameter 26 : hivTree.Node1.trst 243s Parameter 27 : hivTree.6760.trvs 243s Parameter 28 : hivTree.6760.trst 243s Parameter 29 : hivTree.113.trvs 243s Parameter 30 : hivTree.113.trst 243s Parameter 31 : hivTree.9939.trvs 243s Parameter 32 : hivTree.9939.trst 243s Parameter 33 : hivTree.Node16.trvs 243s Parameter 34 : hivTree.Node16.trst 243s Parameter 35 : hivTree.256.trvs 243s Parameter 36 : hivTree.256.trst 243s Parameter 37 : hivTree.822.trvs 243s Parameter 38 : hivTree.822.trst 243s Parameter 39 : hivTree.159.trvs 243s Parameter 40 : hivTree.159.trst 243s Parameter 41 : hivTree.Node21.trvs 243s Parameter 42 : hivTree.Node21.trst 243s Parameter 43 : hivTree.iNode2.trvs 243s Parameter 44 : hivTree.iNode2.trst 243s Parameter 45 : hivTree.Node15.trvs 243s Parameter 46 : hivTree.Node15.trst 243s 243s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 243s 243s Log Likelihood = -1157.82; 243s 243s Independent Parameters List 243s 243s Parameter 1 : hivTree.135.trst 243s Parameter 2 : hivTree.529.trst 243s Parameter 3 : hivTree.105r.trst 243s Parameter 4 : hivTree.Node8.trst 243s Parameter 5 : hivTree.317.trvs 243s Parameter 6 : hivTree.317.trst 243s Parameter 7 : hivTree.6767.trst 243s Parameter 8 : hivTree.6767.trvs 243s Parameter 9 : hivTree.Node2.trst 243s Parameter 10 : hivTree.Node2.trvs 243s Parameter 11 : hivTree.iNode1.trvs 243s Parameter 12 : hivTree.iNode1.trst 243s Parameter 13 : hivTree.719.trvs 243s Parameter 14 : hivTree.719.trst 243s Parameter 15 : hivTree.136.trvs 243s Parameter 16 : hivTree.136.trst 243s Parameter 17 : hivTree.Node11.trvs 243s Parameter 18 : hivTree.Node11.trst 243s Parameter 19 : hivTree.Node5.trvs 243s Parameter 20 : hivTree.Node5.trst 243s Parameter 21 : hivTree.Node1.trvs 243s Parameter 22 : hivTree.Node1.trst 243s Parameter 23 : hivTree.6760.trvs 243s Parameter 24 : hivTree.6760.trst 243s Parameter 25 : hivTree.113.trvs 243s Parameter 26 : hivTree.113.trst 243s Parameter 27 : hivTree.9939.trvs 243s Parameter 28 : hivTree.9939.trst 243s Parameter 29 : hivTree.Node16.trvs 243s Parameter 30 : hivTree.Node16.trst 243s Parameter 31 : hivTree.256.trvs 243s Parameter 32 : hivTree.256.trst 243s Parameter 33 : hivTree.822.trvs 243s Parameter 34 : hivTree.822.trst 243s Parameter 35 : hivTree.159.trvs 243s Parameter 36 : hivTree.159.trst 243s Parameter 37 : hivTree.Node21.trvs 243s Parameter 38 : hivTree.Node21.trst 243s Parameter 39 : hivTree.iNode2.trvs 243s Parameter 40 : hivTree.iNode2.trst 243s Parameter 41 : hivTree.Node15.trvs 243s Parameter 42 : hivTree.Node15.trst 243s 243s Constrained Parameters List 243s 243s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 243s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 243s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 243s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 243s + '[' -f aa.bf ']' 243s + hyphy aa.bf 243s Log Likelihood = -1134.73158903811; 243s 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); 243s + for i in *.bf 243s + '[' -f definitions2.bf ']' 243s + hyphy definitions2.bf 243s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 243s 243s Sample by MEAN: 243s 243s Sample mean = 0.5 (sample variance = 0.2450374540764348) 243s 243s Rate[0]= 0.06847689 (weight=0.2500000) 243s Rate[1]= 0.23837593 (weight=0.2500000) 243s Rate[2]= 0.50000000 (weight=0.2500000) 243s Rate[3]= 1.19314718 (weight=0.2500000) 243s ------------------------------------------------ 243s 243s Sample by MEDIAN: 243s 243s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 243s 243s Rate[0]= 0.06676570 (weight=0.2500000) 243s Rate[1]= 0.23500181 (weight=0.2500000) 243s Rate[2]= 0.49041463 (weight=0.2500000) 243s Rate[3]= 1.03972077 (weight=0.2500000) 243s ------------------------------------------------ 243s 243s Sample by SCALED_MEDIAN: 243s 243s Sample mean = 0.5 (sample variance = 0.2154404122636025) 243s 243s Rate[0]= 0.07289218 (weight=0.2500000) 243s Rate[1]= 0.25656580 (weight=0.2500000) 243s Rate[2]= 0.53541552 (weight=0.2500000) 243s Rate[3]= 1.13512650 (weight=0.2500000) 243s ------------------------------------------------ 243s 243s Sample by MEAN (numerical averaging): 243s 243s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 243s 243s Rate[0]= 0.06846096 (weight=0.2500000) 243s Rate[1]= 0.23834015 (weight=0.2500000) 243s Rate[2]= 0.49996411 (weight=0.2500000) 243s Rate[3]= 1.19314889 (weight=0.2500000) 243s ------------------------------------------------ 243s 243s Sample by MEAN (numerical CDF and averaging): 243s 243s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 243s 243s Rate[0]= 0.06849282 (weight=0.2500000) 243s Rate[1]= 0.23835613 (weight=0.2500000) 243s Rate[2]= 0.49994751 (weight=0.2500000) 243s Rate[3]= 1.19311765 (weight=0.2500000) 243s ------------------------------------------------ 243s 2). Equiprobable rates sampled from Exponential with lambda = 2 243s 243s Sample by MEDIAN (3 rate classes): 243s 243s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 243s 243s Rate[0]= 0.09116078 (weight=0.3333333) 243s Rate[1]= 0.34657359 (weight=0.3333333) 243s Rate[2]= 0.89587973 (weight=0.3333333) 243s ------------------------------------------------ 243s 243s Sample by MEDIAN (9 rate classes): 243s 243s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 243s 243s Rate[0]= 0.02857921 (weight=0.1111111) 243s Rate[1]= 0.09116078 (weight=0.1111111) 243s Rate[2]= 0.16271120 (weight=0.1111111) 243s Rate[3]= 0.24623824 (weight=0.1111111) 243s Rate[4]= 0.34657359 (weight=0.1111111) 243s Rate[5]= 0.47223080 (weight=0.1111111) 243s Rate[6]= 0.64046692 (weight=0.1111111) 243s Rate[7]= 0.89587973 (weight=0.1111111) 243s Rate[8]= 1.44518588 (weight=0.1111111) 243s ------------------------------------------------ 243s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 243s 243s Sample by MEAN (10 rate classes): 243s 243s Sample mean = 1 (sample variance = 0.1057310289486733) 243s 243s Rate[0]= 0.52447499 (weight=0.1000000) 243s Rate[1]= 0.67866972 (weight=0.1000000) 243s Rate[2]= 0.77209919 (weight=0.1000000) 243s Rate[3]= 0.85214884 (weight=0.1000000) 243s Rate[4]= 0.92850815 (weight=0.1000000) 243s Rate[5]= 1.00664500 (weight=0.1000000) 243s Rate[6]= 1.09192933 (weight=0.1000000) 243s Rate[7]= 1.19267960 (weight=0.1000000) 243s Rate[8]= 1.32858029 (weight=0.1000000) 243s Rate[9]= 1.62426489 (weight=0.1000000) 243s ------------------------------------------------ 243s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 243s 243s Sample by MEAN (10 rate classes): 243s 243s Sample mean = 2 (sample variance = 0.04259071282256012) 243s 243s Rate[0]= 1.66431246 (weight=0.1000000) 243s Rate[1]= 1.79212822 (weight=0.1000000) 243s Rate[2]= 1.86123411 (weight=0.1000000) 243s Rate[3]= 1.91722052 (weight=0.1000000) 243s Rate[4]= 1.96832799 (weight=0.1000000) 243s Rate[5]= 2.01862937 (weight=0.1000000) 243s Rate[6]= 2.07152664 (weight=0.1000000) 243s Rate[7]= 2.13166629 (weight=0.1000000) 243s Rate[8]= 2.20930216 (weight=0.1000000) 243s Rate[9]= 2.36565224 (weight=0.1000000) 243s ------------------------------------------------ 243s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 243s 243s Sample by MEAN (8 rate classes): 243s 243s Sample mean = 0.5 (sample variance = 0.09375000225643569) 243s 243s Rate[0]= 0.06250000 (weight=0.1250000) 243s Rate[1]= 0.18750000 (weight=0.1250000) 243s Rate[2]= 0.31250001 (weight=0.1250000) 243s Rate[3]= 0.43750001 (weight=0.1250000) 243s Rate[4]= 0.56249993 (weight=0.1250000) 243s Rate[5]= 0.68750001 (weight=0.1250000) 243s Rate[6]= 0.81250002 (weight=0.1250000) 243s Rate[7]= 0.93750002 (weight=0.1250000) 243s ------------------------------------------------ 243s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 243s 243s Sample by MEAN (8 rate classes): 243s 243s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 243s 243s Rate[0]= 2.17658588 (weight=0.1250000) 243s Rate[1]= 2.55230783 (weight=0.1250000) 243s Rate[2]= 2.75432532 (weight=0.1250000) 243s Rate[3]= 2.92101185 (weight=0.1250000) 243s Rate[4]= 3.07898815 (weight=0.1250000) 243s Rate[5]= 3.24567468 (weight=0.1250000) 243s Rate[6]= 3.44769217 (weight=0.1250000) 243s Rate[7]= 3.82341415 (weight=0.1250000) 243s ------------------------------------------------ 243s + for i in *.bf 243s + '[' -f definitions3.bf ']' 243s + hyphy definitions3.bf 243s 243s 243s Sample mean = 1 (sample variance = 0.9920002887656187) 243s 243s Rate[0]= 0.05175536 (weight=0.1000000) 243s Rate[1]= 0.16309623 (weight=0.1000000) 243s Rate[2]= 0.28842380 (weight=0.1000000) 243s Rate[3]= 0.43177086 (weight=0.1000000) 243s Rate[4]= 0.59921784 (weight=0.1000000) 243s Rate[5]= 0.80057298 (weight=0.1000000) 243s Rate[6]= 1.05324451 (weight=0.1000000)+ for i in *.bf 243s + '[' -f displayFunction.bf ']' 243s + hyphy displayFunction.bf 243s + for i in *.bf 243s + '[' -f profile_test.bf ']' 243s + hyphy profile_test.bf 243s 243s Rate[7]= 1.39304259 (weight=0.1000000) 243s Rate[8]= 1.91629073 (weight=0.1000000) 243s Rate[9]= 3.30258509 (weight=0.1000000) 243s ------------------------------------------------ 243s 243s Total run time (seconds) : 0.000000 243s Total number of steps : 1500005 243s 243s 1 : s=0; 243s Call count: 1 243s Time (seconds): 1.5e-11+ for i in *.bf 243s + '[' -f shared.bf ']' 243s + hyphy shared.bf 243s 243s 2 : m={5,1}; 243s Call count: 1 243s Time (seconds): 1.9e-11 243s 3 : k=0; 243s Call count: 1 243s Time (seconds): 2e-12 243s 4 : Branch under condition 'k<250000' 243s to 243s s=s+k; 243s else 243s #profilePAUSE, ; 243s Call count: 250001 243s Time (seconds): 3.609600000001502e-08 243s 5 : s=s+k; 243s Call count: 250000 243s Time (seconds): 4.060500000001948e-08 243s 6 : t=Random(0,5); 243s Call count: 250000 243s Time (seconds): 4.096900000001944e-08 243s 7 : m[t]=m[t]+1; 243s Call count: 250000 243s Time (seconds): 1.037050000000808e-07 243s 8 : k=k+1; 243s Call count: 250000 243s Time (seconds): 4.565400000002456e-08 243s 9 : Go to step 4 243s Call count: 250000 243s Time (seconds): 1.143199999999811e-08 243s 10 : #profilePAUSE, ; 243s Call count: 1 243s Time (seconds): 2e-12 243s + rm -f '*messages.log*' '*errors.log*' 243s autopkgtest [17:04:29]: test run-unit-tests: -----------------------] 244s autopkgtest [17:04:30]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 244s run-unit-tests PASS 244s autopkgtest [17:04:30]: @@@@@@@@@@@@@@@@@@@@ summary 244s run-unit-tests PASS 269s Creating nova instance adt-noble-s390x-hyphy-20240316-170026-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240315.img (UUID 72478735-497c-4832-870c-30bdd7312d7f)...