0s autopkgtest [08:09:56]: starting date and time: 2024-03-25 08:09:56+0000 0s autopkgtest [08:09:56]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [08:09:56]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h3upf_p4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl,src:orthanc-python --apt-upgrade hyphy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2 orthanc-python/4.1+ds-2build3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-12.secgroup --name adt-noble-arm64-hyphy-20240325-075553-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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://us.ports.ubuntu.com/ubuntu-ports/ 129s autopkgtest [08:12:05]: testbed dpkg architecture: arm64 130s autopkgtest [08:12:06]: testbed apt version: 2.7.12 130s autopkgtest [08:12:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 131s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 131s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3987 kB] 132s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.8 kB] 132s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 132s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 132s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 132s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 132s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 132s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 132s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 132s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB] 132s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 138s Fetched 9851 kB in 3s (3388 kB/s) 138s Reading package lists... 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 143s Calculating upgrade... 144s The following packages will be REMOVED: 144s libssl3 144s The following NEW packages will be installed: 144s libssl3t64 144s The following packages have been kept back: 144s curl 144s The following packages will be upgraded: 144s openssl 144s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 144s Need to get 2777 kB of archives. 144s After this operation, 139 kB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 145s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 146s Fetched 2777 kB in 1s (3938 kB/s) 146s (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 ... 75911 files and directories currently installed.) 146s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 146s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 146s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 146s wget depends on libssl3 (>= 3.0.0). 146s u-boot-tools depends on libssl3 (>= 3.0.0). 146s tnftp depends on libssl3 (>= 3.0.0). 146s tcpdump depends on libssl3 (>= 3.0.0). 146s systemd-resolved depends on libssl3 (>= 3.0.0). 146s systemd depends on libssl3 (>= 3.0.0). 146s sudo depends on libssl3 (>= 3.0.0). 146s sbsigntool depends on libssl3 (>= 3.0.0). 146s rsync depends on libssl3 (>= 3.0.0). 146s python3-cryptography depends on libssl3 (>= 3.0.0). 146s openssh-server depends on libssl3 (>= 3.0.10). 146s openssh-client depends on libssl3 (>= 3.0.10). 146s mtd-utils depends on libssl3 (>= 3.0.0). 146s mokutil depends on libssl3 (>= 3.0.0). 146s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 146s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 146s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 146s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 146s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 146s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 146s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 146s libnvme1 depends on libssl3 (>= 3.0.0). 146s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 146s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 146s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 146s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 146s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 146s kmod depends on libssl3 (>= 3.0.0). 146s dhcpcd-base depends on libssl3 (>= 3.0.0). 146s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 146s 146s (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 ... 75911 files and directories currently installed.) 146s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 146s Selecting previously unselected package libssl3t64:arm64. 146s (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 ... 75900 files and directories currently installed.) 146s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 146s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 147s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 147s Setting up openssl (3.0.13-0ubuntu2) ... 147s Processing triggers for man-db (2.12.0-3) ... 147s Processing triggers for libc-bin (2.39-0ubuntu6) ... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 150s sh: Attempting to set up Debian/Ubuntu apt sources automatically 150s sh: Distribution appears to be Ubuntu 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 154s eatmydata is already the newest version (131-1). 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 155s dbus is already the newest version (1.14.10-4ubuntu1). 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 157s rng-tools-debian is already the newest version (2.4). 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s The following packages will be REMOVED: 158s cloud-init* python3-configobj* python3-debconf* 159s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 159s After this operation, 3256 kB disk space will be freed. 159s (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 ... 75913 files and directories currently installed.) 159s Removing cloud-init (24.1.2-0ubuntu1) ... 160s Removing python3-configobj (5.0.8-3) ... 160s Removing python3-debconf (1.5.86) ... 160s Processing triggers for man-db (2.12.0-3) ... 161s (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 ... 75524 files and directories currently installed.) 161s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 162s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 162s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 162s invoke-rc.d: policy-rc.d denied execution of try-restart. 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s linux-generic is already the newest version (6.8.0-11.11+1). 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 165s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 165s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 170s Reading package lists... 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 171s Calculating upgrade... 172s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s autopkgtest [08:12:49]: rebooting testbed after setup commands that affected boot 327s autopkgtest [08:15:23]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 330s autopkgtest [08:15:26]: @@@@@@@@@@@@@@@@@@@@ apt-source hyphy 334s Get:1 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (dsc) [2423 B] 334s Get:2 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (tar) [2613 kB] 334s Get:3 http://ftpmaster.internal/ubuntu noble/universe hyphy 2.5.59+dfsg-1 (diff) [17.0 kB] 334s gpgv: Signature made Sat Jan 13 16:06:18 2024 UTC 334s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 334s gpgv: issuer "emollier@debian.org" 334s gpgv: Can't check signature: No public key 334s dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.59+dfsg-1.dsc: no acceptable signature found 335s autopkgtest [08:15:31]: testing package hyphy version 2.5.59+dfsg-1 335s autopkgtest [08:15:31]: build not needed 336s autopkgtest [08:15:32]: test run-unit-tests: preparing testbed 341s Reading package lists... 341s Building dependency tree... 341s Reading state information... 342s Starting pkgProblemResolver with broken count: 0 342s Starting 2 pkgProblemResolver with broken count: 0 342s Done 343s The following additional packages will be installed: 343s hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 libamdhip64-5 libatomic1 343s libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libgomp1 343s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 343s libmunge2 libopenmpi3 libpciaccess0 libpmix2 librdmacm1t64 libucx0 343s libxnvctrl0 ocl-icd-libopencl1 343s Suggested packages: 343s opencl-icd 343s The following NEW packages will be installed: 343s autopkgtest-satdep hyphy-common hyphy-mpi hyphy-pt libamd-comgr2 343s libamdhip64-5 libatomic1 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 343s libgomp1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libllvm17 343s libmunge2 libopenmpi3 libpciaccess0 libpmix2 librdmacm1t64 libucx0 343s libxnvctrl0 ocl-icd-libopencl1 343s 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. 343s Need to get 53.5 MB/53.5 MB of archives. 343s After this operation, 233 MB of additional disk space will be used. 343s Get:1 /tmp/autopkgtest.DRxwj6/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 343s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 hyphy-common all 2.5.59+dfsg-1 [624 kB] 344s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 344s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 344s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 344s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 344s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3build1 [541 kB] 344s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 344s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 344s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 344s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 344s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 344s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 344s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 344s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 345s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 345s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 345s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 345s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 345s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 345s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 345s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 345s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 hyphy-mpi arm64 2.5.59+dfsg-1 [1199 kB] 345s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 hyphy-pt arm64 2.5.59+dfsg-1 [1162 kB] 346s Fetched 53.5 MB in 2s (26.1 MB/s) 346s Selecting previously unselected package hyphy-common. 346s (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 ... 75469 files and directories currently installed.) 346s Preparing to unpack .../00-hyphy-common_2.5.59+dfsg-1_all.deb ... 346s Unpacking hyphy-common (2.5.59+dfsg-1) ... 346s Selecting previously unselected package libgomp1:arm64. 346s Preparing to unpack .../01-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 346s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 346s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 346s Preparing to unpack .../02-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 346s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 347s Selecting previously unselected package libatomic1:arm64. 347s Preparing to unpack .../03-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 347s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 347s Selecting previously unselected package librdmacm1t64:arm64. 347s Preparing to unpack .../04-librdmacm1t64_50.0-2_arm64.deb ... 347s Unpacking librdmacm1t64:arm64 (50.0-2) ... 347s Selecting previously unselected package libfabric1:arm64. 347s Preparing to unpack .../05-libfabric1_1.17.0-3build1_arm64.deb ... 347s Unpacking libfabric1:arm64 (1.17.0-3build1) ... 347s Selecting previously unselected package libhwloc15:arm64. 347s Preparing to unpack .../06-libhwloc15_2.10.0-1_arm64.deb ... 347s Unpacking libhwloc15:arm64 (2.10.0-1) ... 347s Selecting previously unselected package libmunge2:arm64. 347s Preparing to unpack .../07-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 347s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 347s Selecting previously unselected package libpciaccess0:arm64. 347s Preparing to unpack .../08-libpciaccess0_0.17-3_arm64.deb ... 347s Unpacking libpciaccess0:arm64 (0.17-3) ... 347s Selecting previously unselected package libxnvctrl0:arm64. 347s Preparing to unpack .../09-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 347s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 347s Selecting previously unselected package ocl-icd-libopencl1:arm64. 347s Preparing to unpack .../10-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 347s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 347s Selecting previously unselected package libhwloc-plugins:arm64. 347s Preparing to unpack .../11-libhwloc-plugins_2.10.0-1_arm64.deb ... 347s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 347s Selecting previously unselected package libpmix2:arm64. 347s Preparing to unpack .../12-libpmix2_5.0.1-4_arm64.deb ... 347s Unpacking libpmix2:arm64 (5.0.1-4) ... 347s Selecting previously unselected package libllvm17:arm64. 347s Preparing to unpack .../13-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 347s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 348s Selecting previously unselected package libamd-comgr2:arm64. 348s Preparing to unpack .../14-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 348s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 349s Selecting previously unselected package libdrm-amdgpu1:arm64. 349s Preparing to unpack .../15-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 349s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 349s Selecting previously unselected package libhsakmt1:arm64. 349s Preparing to unpack .../16-libhsakmt1_5.7.0-1_arm64.deb ... 349s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 349s Selecting previously unselected package libhsa-runtime64-1. 349s Preparing to unpack .../17-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 349s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 349s Selecting previously unselected package libamdhip64-5. 349s Preparing to unpack .../18-libamdhip64-5_5.2.3-12_arm64.deb ... 349s Unpacking libamdhip64-5 (5.2.3-12) ... 349s Selecting previously unselected package libucx0:arm64. 349s Preparing to unpack .../19-libucx0_1.16.0+ds-4_arm64.deb ... 349s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 349s Selecting previously unselected package libopenmpi3:arm64. 349s Preparing to unpack .../20-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 349s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 350s Selecting previously unselected package hyphy-mpi. 350s Preparing to unpack .../21-hyphy-mpi_2.5.59+dfsg-1_arm64.deb ... 350s Unpacking hyphy-mpi (2.5.59+dfsg-1) ... 350s Selecting previously unselected package hyphy-pt. 350s Preparing to unpack .../22-hyphy-pt_2.5.59+dfsg-1_arm64.deb ... 350s Unpacking hyphy-pt (2.5.59+dfsg-1) ... 350s Selecting previously unselected package autopkgtest-satdep. 350s Preparing to unpack .../23-1-autopkgtest-satdep.deb ... 350s Unpacking autopkgtest-satdep (0) ... 350s Setting up libpciaccess0:arm64 (0.17-3) ... 350s Setting up hyphy-common (2.5.59+dfsg-1) ... 350s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 350s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 350s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 350s Setting up libhwloc15:arm64 (2.10.0-1) ... 350s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 350s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 350s Setting up librdmacm1t64:arm64 (50.0-2) ... 350s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 350s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 350s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 350s Setting up libfabric1:arm64 (1.17.0-3build1) ... 350s Setting up hyphy-pt (2.5.59+dfsg-1) ... 350s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 350s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 350s Setting up libhsakmt1:arm64 (5.7.0-1) ... 350s Setting up libpmix2:arm64 (5.0.1-4) ... 350s Setting up libhsa-runtime64-1 (5.7.1-1) ... 350s Setting up libamdhip64-5 (5.2.3-12) ... 350s Setting up libucx0:arm64 (1.16.0+ds-4) ... 350s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 350s Setting up hyphy-mpi (2.5.59+dfsg-1) ... 350s Setting up autopkgtest-satdep (0) ... 350s Processing triggers for man-db (2.12.0-3) ... 351s Processing triggers for libc-bin (2.39-0ubuntu6) ... 356s (Reading database ... 76374 files and directories currently installed.) 356s Removing autopkgtest-satdep (0) ... 357s autopkgtest [08:15:53]: test run-unit-tests: [----------------------- 358s + for i in *.bf 358s + '[' -f ExonIntron.bf ']' 358s + hyphy ExonIntron.bf 359s Log Likelihood = -1113.34523093823; 359s Tree exon1Tree=(BLYMUB2:0,(RICRMA630:0.04134922377013523,(ZMUBIS27F:0,(ZMU29160:0.05439434205555755,ZMU29161:0.0397099920707908)Node8:0.01201941603219406)Node6:0)Node4:0.024593255793118,BLYMUB1:0.01185775856148526); 359s Tree exon2Tree=(BLYMUB2:0.03542711161011008,(RICRMA630:0.02935212298046051,(ZMUBIS27F:0.0754561862717683,(ZMU29160:0.09103007688546581,ZMU29161:0.02595054789089673)Node8:0.01157422438148664)Node6:0.04928335134660832)Node4:0.0293070179401226,BLYMUB1:0.02204339668689216); 359s Tree intronTree=(BLYMUB2:0.03120148427034726,(RICRMA630:0.04155588440025249,(ZMUBIS27F:0.02044499908430787,(ZMU29160:0.02069042212081659,ZMU29161:0.01019776647832744)Node8:0.02068976996248074)Node6:0)Node4:0,BLYMUB1:0.01036597515885792); 359s + for i in *.bf 359s + '[' -f F81.bf ']' 359s + hyphy F81.bf 359s Log Likelihood = -1187.54702793755; 359s Tree givenTree=(256:0.01194350383198776,(822:0.02944830535067936,159:0.004470566641478981)Node2:0.003648416798768103,((113:0.02244746421090052,9939:0.07632907795011984)Node6:0.005077663434270926,(6760:0.06903113887339882,((317:0.03751818003606587,6767:0.07086144053643872)Node12:0.01229344910542729,((135:0.0204561966689408,(529:0.03338016202897984,105r:0.01322045242403323)Node18:0.02586876285451697)Node16:0.005414274244521212,(719:0.02965902532867767,136:0.00823423126564937)Node21:0.04882998609564283)Node15:0.01525962444960303)Node11:0.01379933321924546)Node9:0.02422268145877303)Node5:0.02148378325227054); 359s + for i in *.bf 359s + '[' -f F81relrate.bf ']' 359s + hyphy F81relrate.bf 359s 359s 0).UNCONSTRAINED MODEL:Log Likelihood = -944.00100141847; 359s Tree threeTaxaTree=(a:0.08501458078571071,b:0.0733761302676995,c:0.1653894108755128); 359s 359s 359s 1). With the outgroup at taxon #1, the P-value is:0.002155106158012732 359s Log Likelihood = -948.707253867895; 359s Tree threeTaxaTree=(a:0.08228741139559752,b:0.1194507598364935,c:0.1194507598364935); 359s 359s 359s 2). With the outgroup at taxon #2, the P-value is:0.008353404406027276 359s Log Likelihood = -947.479050125031; 359s Tree threeTaxaTree=(a:0.1250762650865298,b:0.07125949231018089,c:0.1250762650865298); 359s 359s 359s 3). With the outgroup at taxon #3, the P-value is:0.6669137051109912 359s Log Likelihood = -944.093618166809; 359s Tree threeTaxaTree=(a:0.07922730021537434,b:0.07922730021537434,c:0.1653339858408152); 359s 359s 0). UNCONSTRAINED MODEL:Log Likelihood = -2574.6305958295; 359s Tree fourTaxaTree1=((1:0.1129104492125219,2:0.1073439047614921)Node1:0.09978717865825038,3:0.3469443599499342,4:0.3219019510192432); 359s Tree fourTaxaTree2=((1:0.08585820917628031,2:0.09338078540397989)Node1:0.0736417066106991,3:0.3933121047170701,4:0.3801923094565385); 359s + for i in *.bf 359s + '[' -f F81relratio.bf ']' 359s + hyphy F81relratio.bf 359s 359s 359s 1). Relative ratio constraint; the P-value is:0.6933531573039489 359s Log Likelihood = -2575.74610909373; 359s Global Parameters: 359s R=1.007290880092107; 359s 359s Tree fourTaxaTree1=((1:0.0994836464016693,2:0.09943037069217289)Node1:0.0869682969122717,3:0.3687236014963378,4:0.3489177341828117); 359s Tree fourTaxaTree2=((1:0.1000737390781421,2:0.100020147360868)Node1:0.08748415411040895,3:0.3709107056562232,4:0.3509873587601161); 359s + for i in *.bf 359s + '[' -f HKY85.bf ']' 359s + hyphy HKY85.bf 360s Log Likelihood = -1152.88077759984; 360s Tree givenTree=(256:0.01162288667782179,(822:0.02979925771976042,159:0.004015138877223606)Node2:0.003749807242919053,((113:0.02130516453029382,9939:0.0778595684461199)Node6:0.004320575954985553,(6760:0.07315569451374035,((317:0.03809378462441171,6767:0.07101548352042635)Node12:0.006276166945365902,((135:0.01788116181775997,(529:0.0325778241649983,105r:0.01514141560707552)Node18:0.02833952512606345)Node16:0.007921523942608337,(719:0.02987633065012513,136:0.008041687755300973)Node21:0.0485931478377624)Node15:0.01599220240534575)Node11:0.01658008402363219)Node9:0.0266563505744944)Node5:0.02296365216628453); 360s + for i in *.bf 360s + '[' -f HKY852blocks.bf ']' 360s + hyphy HKY852blocks.bf 360s 360s ----- RESULTS ----- 360s Log Likelihood = -6801.91483914271; 360s Tree actinTree1=(ZMU60513:0,ZMU60514:0.01050213079878777,((((((ZMU60511:0.0103964390210716,ZMU60510:0.02378493210091168)Node8:0.08350026384022306,OSRAC2:0.1885441289425745)Node7:0.05846032966993056,(OSRAC1:0.01535047106336434,SVSOAC1:0.07341796996529404)Node12:0.07285957830769609)Node6:0,((OSRAC3:0.07326281403030475,ZMU60507:0.06501886193980418)Node16:0.07966506413955368,ZMU60509:0.12889876402029)Node15:0.001337061339439503)Node5:0.08259949396484567,(MZEACT1G:0.1142070205924238,OSRAC7:0.03425239723740178)Node20:0)Node4:0.105904092604038,ZMU60508:0.01701208383807174)Node3:0.05972259836120912); 360s Tree actinTree2=(ZMU60513:0.01013433247873647,ZMU60514:0.02362266936808758,((((((ZMU60511:0.03959926850963617,ZMU60510:0.02870478512134468)Node8:0.04599109182442013,OSRAC2:0.1281540501826964)Node7:0.02274865176629471,(OSRAC1:0.04039890987490254,SVSOAC1:0.0553286130063774)Node12:0.0905395571679606)Node6:0.02100488746729546,((OSRAC3:0.1082126627070749,ZMU60507:0.07345368472804116)Node16:0.05601401247636992,ZMU60509:0.1117304891545221)Node15:0.02915321876146179)Node5:0.04980904638864664,(MZEACT1G:0.1070193486175715,OSRAC7:0.09559226343698206)Node20:0.02269013920069791)Node4:0.04831903334853681,ZMU60508:0.02346472825105576)Node3:0.05650090551461232); 360s + for i in *.bf 360s + '[' -f HKY852blocks2models.bf ']' 360s + hyphy HKY852blocks2models.bf 360s 360s ----- RESULTS ----- 360s Log Likelihood = -6049.33430509219; 360s Tree actinTree1=(ZMU60513:0.01368065835946704,ZMU60514:0.06662560144432099,((((((ZMU60511:0.1014698393343548,ZMU60510:0.08941869435591956)Node8:0.2110383153534773,OSRAC2:0.3684369266868493)Node7:0.06393319699898629,(OSRAC1:0.04344267527694522,SVSOAC1:0.2445300038759274)Node12:0.4077968913614998)Node6:0.1004066359203368,((OSRAC3:0.1861632105151208,ZMU60507:0.3287949285775706)Node16:0.1592030395019906,ZMU60509:0.4442382581177137)Node15:0.04671926403427797)Node5:0.1895203615491486,(MZEACT1G:0.3244981794276043,OSRAC7:0.2477753232924249)Node20:0.009414964421613197)Node4:0.2663190361503114,ZMU60508:0.01033901940751635)Node3:0.2230500126676203); 360s Tree actinTree2=(ZMU60513:0.004498640605527752,ZMU60514:0.004482898757018348,((((((ZMU60511:0.004483072442852635,ZMU60510:0.005993388586689664)Node8:0.004874092480403656,OSRAC2:0.04744636325973004)Node7:0.003178294515027827,(OSRAC1:0.01209268208445469,SVSOAC1:0.007445167231502748)Node12:0.02729855311737739)Node6:0,((OSRAC3:0.04642967638294117,ZMU60507:0.009175845755993344)Node16:0.01045215429481289,ZMU60509:0.0244781963857302)Node15:0)Node5:0.01926914288035394,(MZEACT1G:0.03379329078628768,OSRAC7:0.03062841308654933)Node20:0.006213356233780941)Node4:0.007801168753207949,ZMU60508:0.004487784516264148)Node3:0.015116075995397); 360s + for i in *.bf 360s + '[' -f HKY85relrate.bf ']' 360s + hyphy HKY85relrate.bf 360s 360s 0).UNCONSTRAINED MODEL:Log Likelihood = -921.371751632041; 360s Tree threeTaxaTree=(a:0.08473003191111293,b:0.07473137624491773,c:0.1740645452720764); 360s 360s 360s 1). Outgroup at taxon #1 360s a). Transition rate test. P-Value = 0.02098226517412549 360s Log Likelihood = -924.03588402071; 360s Tree threeTaxaTree=(a:0.08099122821686185,b:0.1064970285402011,c:0.1431287318444799); 360s 360s b). Transversion rate test. P-Value = 0.03655174810897788 360s Log Likelihood = -923.557339860284; 360s Tree threeTaxaTree=(a:0.08438586068793587,b:0.09108496737387296,c:0.157793239649387); 360s 360s c). Both rates test. P-Value = 0.006323998283663035 360s Log Likelihood = -926.435155263128; 360s Tree threeTaxaTree=(a:0.08054168133397031,b:0.1248197487342514,c:0.1248197487342514); 360s 360s 360s 2). Outgroup at taxon #2 360s a). Transition rate test. P-Value = 0.02758028957244585 360s Log Likelihood = -923.798808189913; 360s Tree threeTaxaTree=(a:0.1157945381968907,b:0.07102316558833002,c:0.1442792954664215); 360s 360s b). Transversion rate test. P-Value = 0.1106456954879589 360s Log Likelihood = -922.644238895678; 360s Tree threeTaxaTree=(a:0.09762132950835234,b:0.07463526436014642,c:0.160897156664404); 360s 360s c). Both rates test. P-Value = 0.0219950008118095 360s Log Likelihood = -925.188691719365; 360s Tree threeTaxaTree=(a:0.1299135243067527,b:0.07078650482744393,c:0.1299135243067527); 360s 360s 360s 3). Outgroup at taxon #3 360s a). Transition rate test. P-Value = + for i in *.bf 360s + '[' -f HKY85relratio.bf ']' 360s + hyphy HKY85relratio.bf 360s 0.9291732747688928 360s Log Likelihood = -921.375701906994; 360s Tree threeTaxaTree=(a:0.08354359190419325,b:0.07588179938172648,c:0.1740455814250527); 360s 360s b). Transversion rate test. P-Value = 0.5919879226055667 360s Log Likelihood = -921.515376853629; 360s Tree threeTaxaTree=(a:0.08115158798052034,b:0.07834975239261983,c:0.1740032070467013); 360s 360s c). Both rates test. P-Value = 0.8615417053068671 360s Log Likelihood = -921.520783446112; 360s Tree threeTaxaTree=(a:0.07974274672476114,b:0.07974274672476114,c:0.174097726933251); 360s 360s 0). UNCONSTRAINED MODEL:Log Likelihood = -2539.78444360881; 360s Tree fourTaxaTree1=((1:0.1138486705938774,2:0.1110122462972651)Node1:0.104102842106571,3:0.3524784878138216,4:0.3311404413991695); 360s Tree fourTaxaTree2=((1:0.0860597386392196,2:0.09356343941933419)Node1:0.08032201490231416,3:0.3858914607428712,4:0.3896179276135943); 360s 360s 360s 1). Relative ratio constraint on transitions; the P-value is:0.5738662884098752 360s Log Likelihood = -2541.23688749921; 360s Global Parameters: 360s R=0.8575284325133654; 360s 360s Tree fourTaxaTree1=((1:0.1086649864354847,2:0.09424031379397739)Node1:0.111620122827603,3:0.3553976425639594,4:0.3553083906830451); 360s Tree fourTaxaTree2=((1:0.09036354678634317,2:0.1091988683375492)Node1:0.07301594252847129,3:0.3837981988164835,4:0.3656297801660289); 360s 360s 360s 2). Relative ratio constraint on transversions; the P-value is:0.5738627516274089 360s Log Likelihood = -2541.23689790555; 360s Global Parameters: 360s R=0.85825951450135; 360s 360s Tree fourTaxaTree1=((1:0.1086625191715241,2:0.09426238845211039)Node1:0.1116480307060316,3:0.3552777897755875,4:0.3552083160672975); 360s Tree fourTaxaTree2=((1:0.09039762776903866,2:0.1092537393704408)Node1:0.07309817242646641,3:0.3840137782019722,4:0.3657793455039087); 360s 360s 360s 3). Relative ratio constraint on both rates; the P-value is:0.6565969025918279 360s Log Likelihood = -2543.19086999415; 360s Global Parameters: 360s R=0.9964954639800966; 360s 360s Tree fourTaxaTree1=((1:0.1004904775311104,2:0.1007304508148404)Node1:0.09257492961864017,3:0.3715249546720786,4:0.3582649192759509); 360s Tree fourTaxaTree2=((1:0.1003215762759256,2:0.1007202855739472)Node1:0.09286598060944462,3:0.3699568886876284,4:0.357722170418195); 360s + for i in *.bf 360s + '[' -f HKY85shared.bf ']' 360s + hyphy HKY85shared.bf 360s Log Likelihood = -1165.70301127147; 360s Global Parameters: 360s R=2.970524885533917; 360s 360s Tree givenTree=(256:0.01208775338325542,(822:0.02960968859585506,159:0.004651897379088246)Node2:0.003524577290327657,((113:0.0218031141251108,9939:0.0794195761547906)Node6:0.004908086009945949,(6760:0.07148879456878611,((317:0.03799252030357465,6767:0.07150930824234027)Node12:0.01178345206858378,((135:0.02022927720301946,(529:0.03405040173466748,105r:0.01304699573961813)Node18:0.02630176613069551)Node16:0.005817017418013274,(719:0.02973913964285991,136:0.008132530317728802)Node21:0.04877233392933042)Node15:0.01555697405185011)Node11:0.01396228297512418)Node9:0.02325904761636235)Node5:0.02146761028962216); 360s + for i in *.bf 360s + '[' -f JC69.bf ']' 360s + hyphy JC69.bf 360s Log Likelihood = -1227.45123451939; 360s Tree givenTree=(256:0.01208132378741086,(822:0.02897031120684837,159:0.004654690199997344)Node2:0.003646466641669312,((113:0.02417961708467097,9939:0.07265778198907162)Node6:0.005829014238445143,(6760:0.06388799683505494,((317:0.04027387637637774,6767:0.06819735681028999)Node12:0.01441604714363964,((135:0.0242734433643081,(529:0.03328072256381603,105r:0.01296055910155082)Node18:0.01988332856887562)Node16:0.003612544702306865,(719:0.02786537888441625,136:0.009982165852536065)Node21:0.05116795319458452)Node15:0.01668528231338159)Node11:0.008473522540836919)Node9:0.02634101151157303)Node5:0.02075182753820698); 360s + for i in *.bf 360s + '[' -f K2P.bf ']' 360s + hyphy K2P.bf 360s Log Likelihood = -1198.26189231186; 360s Tree givenTree=(256:0.01176910305654432,(822:0.02927352642982053,159:0.004287897193840723)Node2:0.003666638179085252,((113:0.02368483463279736,9939:0.07265294425600895)Node6:0.003381518624634053,(6760:0.06223538160532885,((317:0.0407374314051176,6767:0.06835321688034353)Node12:0.01245065810213201,((135:0.02259928814936616,(529:0.03395729246298833,105r:0.01240107392534691)Node18:0.02141967588130321)Node16:0.00449235792631839,(719:0.02880184618664692,136:0.008841875309372457)Node21:0.05084948701327376)Node15:0.01732969308569131)Node11:0.01112009431307714)Node9:0.02820939857869801)Node5:0.02370247369599254); 360s + for i in *.bf 360s + '[' -f K2Pshared.bf ']' 360s + hyphy K2Pshared.bf 361s Log Likelihood = -1210.49426595799; 361s Global Parameters: 361s R=2.615269647870584; 361s 361s Tree givenTree=(256:0.01222199849007476,(822:0.02897035218554136,159:0.00477714541146832)Node2:0.003545897261880193,((113:0.02375458958827501,9939:0.0749091377084513)Node6:0.005890435198643676,(6760:0.0649295420105835,((317:0.0397090245869384,6767:0.06948376439991623)Node12:0.01423214146310314,((135:0.02390228433170875,(529:0.03396509897647851,105r:0.01262329197452233)Node18:0.02071313860718839)Node16:0.003967941189956443,(719:0.02813193832889056,136:0.009506313249870686)Node21:0.05080798320925575)Node15:0.01659426317214061)Node11:0.008794881328943547)Node9:0.0262605646979837)Node5:0.02011433136081846); 361s + for i in *.bf 361s + '[' -f MatrixIndexing.bf ']' 361s + hyphy MatrixIndexing.bf 361s 361s 1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1]. 361s { 361s {0.3600914884265725, 0.758089963756057, 0.795124349136633, 0.278902115132404, 0.3962955047367829, 0.0117456426405687} 361s {0.8577798772272142, 0.7481084141759454, 0.388009913821707, 0.2432854846686324, 0.8931202217687667, 0.02762399963746406} 361s {0.3868112795489866, 0.3323023154708329, 0.6835718556967498, 0.823507501702641, 0.8582943812614061, 0.2404198677373165} 361s {0.1662853612020345, 0.4947495275397668, 0.6633935642110634, 0.6478056923131937, 0.6761398300705803, 0.7008913840867792} 361s {0.4401736588776516, 0.8835823514693375, 0.7928215884121185, 0.6017646038908895, 0.276062482100926, 0.7972422430285351} 361s }+ for i in *.bf 361s 361s 361s 2). Accessing a second-row third-column element and a random element. 361s 361s matrix[1][2]=0.388009913821707 361s matrix[1][0]=0.8577798772272142 361s 361s 3). Accessing the fourth row. 361s 361s matrix[3][-1]= 361s { 361s {0.1662853612020345, 0.4947495275397668, 0.6633935642110634, 0.6478056923131937, 0.6761398300705803, 0.7008913840867792} 361s } 361s 361s 4). Accessing the first column. 361s 361s matrix[-1][0]= 361s { 361s {0.3600914884265725} 361s {0.8577798772272142} 361s {0.3868112795489866} 361s {0.1662853612020345} 361s {0.4401736588776516} 361s } 361s 361s 5). Populating a matrix template (below the diagonal). 361s 361s { 361s {0, 0, 0, 0, 0, 0} 361s {1, 0, 0, 0, 0, 0} 361s {1, 1, 0, 0, 0, 0} 361s {1, 1, 1, 0, 0, 0} 361s {1, 1, 1, 1, 0, 0} 361s } 361s 361s 6). Extracting (by row) matrix elements using the template. 361s 361s { 361s {0.8577798772272142, 0.3868112795489866, 0.3323023154708329, 0.1662853612020345, 0.4947495275397668, 0.6633935642110634, 0.4401736588776516, 0.8835823514693375, 0.7928215884121185, 0.6017646038908895} 361s } 361s 361s 7). Extracting a submatrix: top left corner at (1,1) - bottom right corner at (3,2). 361s 361s matrix[{{1,1}}][{{3,2}}]= 361s { 361s {0.7481084141759454, 0.388009913821707} 361s {0.3323023154708329, 0.6835718556967498} 361s {0.4947495275397668, 0.6633935642110634} 361s } 361s 361s 8). Returning a matrix in which all elements are squared and above diagonal elements are further increased by 1. 361s 361s 361s { 361s {0.1296658800372644, 1.57470039314766, 1.632222730589954, 1.077786389825329, 1.157050127074581, 1.00013796012104} 361s {0.7357863177759346, 0.5596661993608479, 1.150551693223929, 1.059187827050451, 1.797663730532291, 1.000763085355971} 361s {0.1496229659863243, 0.110424828867277, 0.4672704819006982, 1.678164605360525, 1.7366692449049, 1.057801712802829} 361s {0.02765082135009108, 0.2447770950008224, 0.4400910210366584, 0.4196522149933762, 1.457165069807873, 1.491248732287081} 361s {0.1937528499697392, 0.7807177718280839, 0.6285660710523145, 0.3621206384959591, 0.07621049402372408, 1.63559519406917} 361s } 361s + '[' -f MolecularClockF81.bf ']' 361s + hyphy MolecularClockF81.bf 361s 361s 0).UNCONSTRAINED MODEL:Log Likelihood = -11475.7124455898; 361s Tree theTree=(HVRNASS:0.02574343818698083,(RICRSS3:0.05627616267647488,((ZMSUCS1:0.07160732998770968,(OSRSS1A:0.0605882871342691,(TASUCSYN1:0.02788189879694929,HVSSYNMR:0.02037311730942106)Internal1:0.05182863735260022)Node9:0.02015511134557432)Node7:0.1581453919621747,(MZESUS1:0.0766455265177465,ORRSS2:0.05437554665156652)Internal2:0.02506690253273259)Node6:0.03254407420921539)Node4:0.05900645921387682,TAAJ153:0.0137240823557105); 361s 361s 361s 1). Global Molecular Clock; the P-value is:0 361s Log Likelihood = -11927.6152937369; 361s Tree theTree=(HVRNASS:0.02157256105224451,(RICRSS3:0.1233391624335933,((ZMSUCS1:0.05658068351739532,(OSRSS1A:0.04751103199830189,(TASUCSYN1:0.01824592668340718,HVSSYNMR:0.01824592668340718)Internal1:0.02926510531489471)Node9:0.009069651519093433)Node7:0.05762932995774125,(MZESUS1:0.07014505382594971,ORRSS2:0.07014505382594971)Internal2:0.04406495964918684)Node6:0.009129148958456767)Node4:0.0271554279855623,TAAJ153:0.1504945904191556); 361s 361s 361s 2). Molecular Clock starting at Internal1; the P-value is:0.1603800996417838 361s Log Likelihood = -11476.6977648658; 361s Tree theTree=(HVRNASS:0.02574463877872497,(RICRSS3:0.05630537922293165,((ZMSUCS1:0.07170663228293392,(OSRSS1A:0.06051692341998914,(TASUCSYN1:0.0241183626915089,HVSSYNMR:0.0241183626915089)Internal1:0.05180646849531016)Node9:0.02017647183178858)Node7:0.1580963980052938,(MZESUS1:0.07663695353693974,ORRSS2:0.05441168358245108)Internal2:0.02507735229076212)Node6:0.03252990279147008)Node4:0.05896342842216468,TAAJ153:0.01372807420946328); 361s 361s 361s 3). Molecular Clock starting at Internal1 and Internal2; the P-value is:0.0161019722752217 361s Log Likelihood = -11479.8412591028; 361s Tree theTree=(HVRNASS:0.02577199027361876,(RICRSS3:0.0565088634272685,((ZMSUCS1:0.07148106086700545,(OSRSS1A:0.06062414834514016,(TASUCSYN1:0.02412281644248133,HVSSYNMR:0.02412281644248133)Internal1:0.0516691688196029)Node9:0.02036313732843775)Node7:0.1580479219859107,(MZESUS1:0.06553054265699038,ORRSS2:0.06553054265699038)Internal2:0.0250209971949034)Node6:0.0323579537198934)Node4:0.05873963393381004,TAAJ153:0.01369897052902781); 361s + for i in *.bf 361s + '[' -f MolecularClockHKY85.bf ']' 361s + hyphy MolecularClockHKY85.bf 361s 361s 0).UNCONSTRAINED MODEL:Log Likelihood = -11243.8013196361; 361s Tree theTree=(HVRNASS:0.02587907737396311,(RICRSS3:0.0572894124085676,((ZMSUCS1:0.07272709601044716,(OSRSS1A:0.06095570992118214,(TASUCSYN1:0.02742497968105604,HVSSYNMR:0.02082031616288811)Node11:0.05283536750873715)Node9:0.02050572458204564)Node7:0.1590163318162333,(MZESUS1:0.0776144692251914,ORRSS2:0.05414212880562341)Node14:0.02601315280911412)Node6:0.03166660548063902)Node4:0.06041546479717889,TAAJ153:0.01384412085712321); 361s 361s 361s 1). Global Molecular Clock on transition rates; the P-value is:0 361s Log Likelihood = -11434.7016033383; 361s Tree theTree=(HVRNASS:0.02319733761553288,(RICRSS3:0.08334085055188765,((ZMSUCS1:0.06367266227632011,(OSRSS1A:0.05485169643806629,(TASUCSYN1:0.0232551460867506,HVSSYNMR:0.01890604954545845)Node11:0.04016831567262675)Node9:0.01328538420556341)Node7:0.1273995940933478,(MZESUS1:0.07240244266209002,ORRSS2:0.06226503778212443)Node14:0.03460943298177104)Node6:0.02068820627130245)Node4:0.03899425489109949,TAAJ153:0.08890804672536808); 362s 362s 362s 2). Global Molecular Clock on transversion rates; the P-value is:0 362s Log Likelihood = -11497.3782386367; 362s Tree theTree=(HVRNASS:0.02484528756261216,(RICRSS3:0.09397660711566694,((ZMSUCS1:0.06900744557579687,(OSRSS1A:0.05468497070692049,(TASUCSYN1:0.0227716508779853,HVSSYNMR:0.02034233073929944)Node11:0.04373646643512617)Node9:0.01673694266275387)Node7:0.09971901063820572,(MZESUS1:0.07447177543760836,ORRSS2:0.06134376047192384)Node14:0.03386900175600831)Node6:0.02079418106193919)Node4:0.05008072898660467,TAAJ153:0.07306008055237165); 362s 362s 362s 3). Global Molecular Clock on both rates; the P-value is:0 362s Log Likelihood = -11703.6261452004; 362s Tree theTree=(HVRNASS:0.02209626591814473,(RICRSS3:0.1239907399586609,((ZMSUCS1:0.05799737347185272,(OSRSS1A:0.04854802437863659,(TASUCSYN1:0.01832984801726247,HVSSYNMR:0.01832984801726247)Node11:0.03021817636137412)Node9:0.009449349093216129)Node7:0.05733994328761582,(MZESUS1:0.07024387052667865,ORRSS2:0.07024387052667865)Node14:0.04509344623278988)Node6:0.008653423199192328)Node4:0.02801466046190713,TAAJ153:0.152005400420568); 362s + for i in *.bf 362s + '[' -f Non-Rev.bf ']' 362s + hyphy Non-Rev.bf 362s Log Likelihood = -1152.78710751755; 362s Global Parameters: 362s GC=0.2673717629043678; 362s CG=0.1879725041961234; 362s GA=1.906997212510186; 362s CT=1.25432124957511; 362s GT=0.08659420371435869; 362s CA=0.9169624508171991; 362s AT=0.4294566060975135; 362s AG=1.579582298763264; 362s TA=AT+(1-CA)*0.6401468788249693+(AG-GA)*0.6940024479804162 = 0.2553860823864982; 362s TC=CT+(CA-1)*2.009791921664627+(CG-GC)*0.6940024479804162 = 1.032329774121336; 362s TG=GT+(GA-AG)*2.009791921664627+(GC-CG)*0.6401468788249693 = 0.7954572400385406; 362s 362s Tree givenTree=(256:0.01344571870725272,(822:0.02845783395472617,159:0.006115915198300314)Node2:0.003449135470006578,((113:0.02187809547969332,9939:0.07931816392912154)Node6:0.004992457654194302,(6760:0.07327161875810702,((317:0.04010320766143192,6767:0.0698204766147643)Node12:0.01161137628902245,((135:0.02156673769261042,(529:0.03496780719460366,105r:0.01422580887377339)Node18:0.02377215572369166)Node16:0.0052399578773703,(719:0.02863612630376735,136:0.009571233923960042)Node21:0.04927895375848007)Node15:0.0163659383710647)Node11:0.01272182237795112)Node9:0.02192935195035267)Node5:0.02027787334193628); 362s + for i in *.bf 362s + '[' -f PBootstrapHetRates.bf ']' 362s + hyphy PBootstrapHetRates.bf 363s 363s ----ORIGINAL DATA---- 363s Log Likelihood = -1127.31560726467; 363s Global Parameters: 363s alpha=0.3189019521637245; 363s kappa=0.323634843422934; 363s 363s Tree givenTree=(256:0.01258500542706293,(822:0.03175318657470722,159:0.004691996269708359)Node2:0.003777657874653248,((113:0.02291425151829138,9939:0.09712404277422883)Node6:0.001963873996793157,(6760:0.08715253670421785,((317:0.04570163939234655,6767:0.08106912982648756)Node12:0.007409764477276542,((135:0.01863677865921079,(529:0.03693823573662843,105r:0.01499278826225312)Node18:0.03033449865114696)Node16:0.007147086743127492,(719:0.03339487747583827,136:0.007167238341417949)Node21:0.05751756487654235)Node15:0.01788782180184505)Node11:0.0188402524940454)Node9:0.02369234296522092)Node5:0.02500545734330536); 363s 363s Using the seed: 363s 1711356062 363s Category variable name: TRUE 363s Site Rate 363s 0 0.00000 363s 1 0.00000 363s 2 0.00000 363s 3 0.00000 363s 4 0.00000 363s 5 0.00001 363s 6 0.00001 363s 7 0.00001 363s 8 0.00008 363s 9 0.00011 363s 10 0.00016 363s 11 0.00019 363s 12 0.00020 363s 13 0.00024 363s 14 0.00029 363s 15 0.00030 363s 16 0.00032 363s 17 0.00052 363s 18 0.00073 363s 19 0.00076 363s 20 0.00084 363s 21 0.00108 363s 22 0.00116 363s 23 0.00176 363s 24 0.00235 363s 25 0.00278 363s 26 0.00383 363s 27 0.00391 363s 28 0.00424 363s 29 0.00425 363s 30 0.00479 363s 31 0.00501 363s 32 0.00535 363s 33 0.00649 363s 34 0.00695 363s 35 0.00764 363s 36 0.00793 363s 37 0.00816 363s 38 0.00910 363s 39 0.00945 363s 40 0.01036 363s 41 0.01066 363s 42 0.01117 363s 43 0.01143 363s 44 0.01242 363s 45 0.01296 363s 46 0.01380 363s 47 0.01472 363s 48 0.01559 363s 49 0.01795 363s 50 0.01961 363s 51 0.02410 363s 52 0.02726 363s 53 0.03190 363s 54 0.03516 363s 55 0.03602 363s 56 0.03643 363s 57 0.03676 363s 58 0.03875 363s 59 0.04310 363s 60 0.04691 363s 61 0.04704 363s 62 0.04967 363s 63 0.05872 363s 64 0.06114 363s 65 0.06182 363s 66 0.06344 363s 67 0.06384 363s 68 0.06740 363s 69 0.07141 363s 70 0.07221 363s 71 0.07987 363s 72 0.08181 363s 73 0.09047 363s 74 0.09075 363s 75 0.09149 363s 76 0.09166 363s 77 0.09217 363s 78 0.09678 363s 79 0.09710 363s 80 0.09971 363s 81 0.09997 363s 82 0.10047 363s 83 0.10279 363s 84 0.10905 363s 85 0.10935 363s 86 0.11306 363s 87 0.11322 363s 88 0.11706 363s 89 0.12188 363s 90 0.12384 363s 91 0.12405 363s 92 0.12548 363s 93 0.12796 363s 94 0.13182 363s 95 0.13202 363s 96 0.13458 363s 97 0.13466 363s 98 0.14304 363s 99 0.14326 363s 100 0.14791 363s 101 0.15166 363s 102 0.16115 363s 103 0.16476 363s 104 0.16807 363s 105 0.17085 363s 106 0.17330 363s 107 0.17816 363s 108 0.17958 363s 109 0.17981 363s 110 0.18129 363s 111 0.18439 363s 112 0.19616 363s 113 0.21587 363s 114 0.22638 363s 115 0.24463 363s 116 0.25437 363s 117 0.25810 363s 118 0.26161 363s 119 0.28733 363s 120 0.28759 363s 121 0.29495 363s 122 0.29834 363s 123 0.30062 363s 124 0.31229 363s 125 0.31360 363s 126 0.32882 363s 127 0.33040 363s 128 0.33064 363s 129 0.33141 363s 130 0.34266 363s 131 0.34484 363s 132 0.36365 363s 133 0.36922 363s 134 0.37267 363s 135 0.37831 363s 136 0.38681 363s 137 0.39141 363s 138 0.40515 363s 139 0.41266 363s 140 0.42276 363s 141 0.43803 363s 142 0.44913 363s + for i in *.bf 363s + '[' -f REV.bf ']' 363s + hyphy REV.bf 363s 143 0.46380 363s 144 0.47417 363s 145 0.48137 363s 146 0.51024 363s 147 0.55051 363s 148 0.56581 363s 149 0.56945 363s 150 0.57117 363s 151 0.57188 363s 152 0.59693 363s 153 0.59810 363s 154 0.60077 363s 155 0.60692 363s 156 0.61403 363s 157 0.61888 363s 158 0.64943 363s 159 0.66209 363s 160 0.66593 363s 161 0.68475 363s 162 0.68524 363s 163 0.70345 363s 164 0.71681 363s 165 0.73652 363s 166 0.73893 363s 167 0.76460 363s 168 0.77629 363s 169 0.77788 363s 170 0.80317 363s 171 0.82047 363s 172 0.82700 363s 173 0.83035 363s 174 0.83865 363s 175 0.86093 363s 176 0.87296 363s 177 0.89379 363s 178 0.89789 363s 179 0.90790 363s 180 0.91670 363s 181 0.92393 363s 182 0.94740 363s 183 0.94771 363s 184 0.94969 363s 185 0.95503 363s 186 1.00131 363s 187 1.00304 363s 188 1.05452 363s 189 1.09481 363s 190 1.09590 363s 191 1.10521 363s 192 1.11048 363s 193 1.11161 363s 194 1.14314 363s 195 1.17751 363s 196 1.20152 363s 197 1.20296 363s 198 1.21133 363s 199 1.24621 363s 200 1.27424 363s 201 1.28738 363s 202 1.30472 363s 203 1.32501 363s 204 1.34293 363s 205 1.36044 363s 206 1.37805 363s 207 1.39872 363s 208 1.45771 363s 209 1.46235 363s 210 1.50230 363s 211 1.51267 363s 212 1.58186 363s 213 1.66472 363s 214 1.68394 363s 215 1.69273 363s 216 1.70779 363s 217 1.71572 363s 218 1.74990 363s 219 1.76583 363s 220 1.79541 363s 221 1.86115 363s 222 1.87792 363s 223 1.88821 363s 224 1.89319 363s 225 1.94410 363s 226 2.04969 363s 227 2.05807 363s 228 2.06104 363s 229 2.13636 363s 230 2.16256 363s 231 2.27934 363s 232 2.28933 363s 233 2.38198 363s 234 2.38296 363s 235 2.43277 363s 236 2.47541 363s 237 2.51459 363s 238 2.55124 363s 239 2.57421 363s 240 2.58873 363s 241 2.66460 363s 242 2.82798 363s 243 2.85551 363s 244 2.87092 363s 245 2.96413 363s 246 2.97658 363s 247 2.97940 363s 248 3.00122 363s 249 3.13886 363s 250 3.24849 363s 251 3.31007 363s 252 3.33180 363s 253 3.40230 363s 254 3.48672 363s 255 3.51744 363s 256 3.57394 363s 257 3.57921 363s 258 3.63250 363s 259 3.63331 363s 260 3.79685 363s 261 3.88327 363s 262 3.95977 363s 263 3.98205 363s 264 4.09155 363s 265 4.54145 363s 266 4.62569 363s 267 5.05611 363s 268 5.13088 363s 269 5.21859 363s 270 6.06400 363s 271 7.17678 363s 272 11.26392 363s 363s Mean = 0.9879035639635538 363s Var = 1.984872258019616 (1/alpha) = 3.135760045415461 363s Log Likelihood = -1100.00325192825; 363s Tree givenTree=(256:0.02246875114337755,(822:0.01867823122043897,159:0.01469059913175439)Node2:0.003780035603908842,((113:0.01829385606031696,9939:0.07804100019464809)Node6:0.007456159322626059,(6760:0.07113582386827495,((317:0.03719085130056347,6767:0.07206936945595187)Node12:0.01019125089869471,((135:0.02036489400110258,(529:0.03424008585662204,105r:0.01130059017016288)Node18:0.0285116839730642)Node16:0.006571188750754679,(719:0.02830813536460677,136:0.009595572687636146)Node21:0.04404096153060984)Node15:0.01655093511589027)Node11:0.01315864559716088)Node9:0.02915629967554301)Node5:0.009980424315425578); 363s + for i in *.bf 363s + '[' -f REVshared.bf ']' 363s + hyphy REVshared.bf 363s Log Likelihood = -1156.62548891656; 363s Global Parameters: 363s AT=0.3618422195106666; 363s GT=0.4591848014349445; 363s CG=0.2458226660545487; 363s AG=1.842836886938053; 363s CT=1.196790957516014; 363s 363s Tree givenTree=(256:0.0120849443891866,(822:0.02974480620049809,159:0.004669448660303607)Node2:0.003489904910174796,((113:0.02207977238258231,9939:0.07977360902457309)Node6:0.004706047666819394,(6760:0.07205077737979429,((317:0.0390946747526612,6767:0.07105937428611539)Node12:0.01083776419000808,((135:0.02050612528374597,(529:0.03436945795905898,105r:0.01468004972546612)Node18:0.02466827485670234)Node16:0.00555941424528441,(719:0.02873374717341659,136:0.009464694805887797)Node21:0.04909369045408175)Node15:0.01584715826584453)Node11:0.01425933999551002)Node9:0.02296161961066105)Node5:0.02145184527825768); 363s + for i in *.bf 363s + '[' -f ReplicateConstraint1.bf ']' 363s + hyphy ReplicateConstraint1.bf 363s 1).Unconstrained HKY85 363s 363s Log Likelihood = -1152.88; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.317.trvs 363s Parameter 2 : hivTree.317.trst 363s Parameter 3 : hivTree.6767.trvs 363s Parameter 4 : hivTree.6767.trst 363s Parameter 5 : hivTree.Node2.trvs 363s Parameter 6 : hivTree.Node2.trst 363s Parameter 7 : hivTree.135.trvs 363s Parameter 8 : hivTree.135.trst 363s Parameter 9 : hivTree.529.trvs 363s Parameter 10 : hivTree.529.trst 363s Parameter 11 : hivTree.105r.trvs 363s Parameter 12 : hivTree.105r.trst 363s Parameter 13 : hivTree.Node8.trvs 363s Parameter 14 : hivTree.Node8.trst 363s Parameter 15 : hivTree.iNode1.trvs 363s Parameter 16 : hivTree.iNode1.trst 363s Parameter 17 : hivTree.719.trvs 363s Parameter 18 : hivTree.719.trst 363s Parameter 19 : hivTree.136.trvs 363s Parameter 20 : hivTree.136.trst 363s Parameter 21 : hivTree.Node11.trvs 363s Parameter 22 : hivTree.Node11.trst 363s Parameter 23 : hivTree.Node5.trvs 363s Parameter 24 : hivTree.Node5.trst 363s Parameter 25 : hivTree.Node1.trvs 363s Parameter 26 : hivTree.Node1.trst 363s Parameter 27 : hivTree.6760.trvs 363s Parameter 28 : hivTree.6760.trst 363s Parameter 29 : hivTree.113.trvs 363s Parameter 30 : hivTree.113.trst 363s Parameter 31 : hivTree.9939.trvs 363s Parameter 32 : hivTree.9939.trst 363s Parameter 33 : hivTree.Node16.trvs 363s Parameter 34 : hivTree.Node16.trst 363s Parameter 35 : hivTree.256.trvs 363s Parameter 36 : hivTree.256.trst 363s Parameter 37 : hivTree.822.trvs 363s Parameter 38 : hivTree.822.trst 363s Parameter 39 : hivTree.159.trvs 363s Parameter 40 : hivTree.159.trst 363s Parameter 41 : hivTree.Node21.trvs 363s Parameter 42 : hivTree.Node21.trst 363s Parameter 43 : hivTree.iNode2.trvs 363s Parameter 44 : hivTree.iNode2.trst 363s Parameter 45 : hivTree.Node15.trvs 363s Parameter 46 : hivTree.Node15.trst 363s 363s 2).HKY85 constrained to F81 363s 363s Log Likelihood = -1187.55; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.317.trvs 363s Parameter 2 : hivTree.6767.trvs 363s Parameter 3 : hivTree.Node2.trvs 363s Parameter 4 : hivTree.135.trvs 363s Parameter 5 : hivTree.529.trvs 363s Parameter 6 : hivTree.105r.trvs 363s Parameter 7 : hivTree.Node8.trvs 363s Parameter 8 : hivTree.iNode1.trvs 363s Parameter 9 : hivTree.719.trvs 363s Parameter 10 : hivTree.136.trvs 363s Parameter 11 : hivTree.Node11.trvs 363s Parameter 12 : hivTree.Node5.trvs 363s Parameter 13 : hivTree.Node1.trvs 363s Parameter 14 : hivTree.6760.trvs 363s Parameter 15 : hivTree.113.trvs 363s Parameter 16 : hivTree.9939.trvs 363s Parameter 17 : hivTree.Node16.trvs 363s Parameter 18 : hivTree.256.trvs 363s Parameter 19 : hivTree.822.trvs 363s Parameter 20 : hivTree.159.trvs 363s Parameter 21 : hivTree.Node21.trvs 363s Parameter 22 : hivTree.iNode2.trvs 363s Parameter 23 : hivTree.Node15.trvs 363s 363s Constrained Parameters List 363s 363s Parameter 1 : hivTree.317.trst = hivTree.317.trvs 363s Parameter 2 : hivTree.6767.trst = hivTree.6767.trvs 363s Parameter 3 : hivTree.Node2.trst = hivTree.Node2.trvs 363s Parameter 4 : hivTree.135.trst = hivTree.135.trvs 363s Parameter 5 : hivTree.529.trst = hivTree.529.trvs 363s Parameter 6 : hivTree.105r.trst = hivTree.105r.trvs 363s Parameter 7 : hivTree.Node8.trst = hivTree.Node8.trvs 363s Parameter 8 : hivTree.iNode1.trst = hivTree.iNode1.trvs 363s Parameter 9 : hivTree.719.trst = hivTree.719.trvs 363s Parameter 10 : hivTree.136.trst = hivTree.136.trvs 363s Parameter 11 : hivTree.Node11.trst = hivTree.Node11.trvs 363s Parameter 12 : hivTree.Node5.trst = hivTree.Node5.trvs 363s Parameter 13 : hivTree.Node1.trst = hivTree.Node1.trvs 363s Parameter 14 : hivTree.6760.trst = hivTree.6760.trvs 363s Parameter 15 : hivTree.113.trst = hivTree.113.trvs 363s Parameter 16 : hivTree.9939.trst = hivTree.9939.trvs 363s Parameter 17 : hivTree.Node16.trst = hivTree.Node16.trvs 363s Parameter 18 : hivTree.256.trst = hivTree.256.trvs 363s Parameter 19 : hivTree.822.trst = hivTree.822.trvs 363s Parameter 20 : hivTree.159.trst = hivTree.159.trvs 363s Parameter 21 : hivTree.Node21.trst = hivTree.Node21.trvs 363s Parameter 22 : hivTree.iNode2.trst = hivTree.iNode2.trvs 363s Parameter 23 : hivTree.Node15.trst = hivTree.Node15.trvs 363s 363s 3).HKY85 constrained to F81 on internal branches 363s 363s Log Likelihood = -1167.99; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.Node2.trvs 363s Parameter 2 : hivTree.Node8.trvs 363s Parameter 3 : hivTree.iNode1.trvs 363s Parameter 4 : hivTree.Node11.trvs 363s Parameter 5 : hivTree.Node5.trvs 363s Parameter 6 : hivTree.Node1.trvs 363s Parameter 7 : hivTree.Node16.trvs 363s Parameter 8 : hivTree.Node21.trvs 363s Parameter 9 : hivTree.iNode2.trvs 363s Parameter 10 : hivTree.Node15.trvs 363s Parameter 11 : hivTree.317.trst 363s Parameter 12 : hivTree.317.trvs 363s Parameter 13 : hivTree.6767.trvs 363s Parameter 14 : hivTree.6767.trst 363s Parameter 15 : hivTree.135.trst 363s Parameter 16 : hivTree.135.trvs 363s Parameter 17 : hivTree.529.trvs 363s Parameter 18 : hivTree.529.trst 363s Parameter 19 : hivTree.105r.trst 363s Parameter 20 : hivTree.105r.trvs 363s Parameter 21 : hivTree.719.trvs 363s Parameter 22 : hivTree.719.trst 363s Parameter 23 : hivTree.136.trvs 363s Parameter 24 : hivTree.136.trst 363s Parameter 25 : hivTree.6760.trvs 363s Parameter 26 : hivTree.6760.trst 363s Parameter 27 : hivTree.113.trvs 363s Parameter 28 : hivTree.113.trst 363s Parameter 29 : hivTree.9939.trst 363s Parameter 30 : hivTree.9939.trvs 363s Parameter 31 : hivTree.256.trvs 363s Parameter 32 : hivTree.256.trst 363s Parameter 33 : hivTree.822.trvs 363s Parameter 34 : hivTree.822.trst 363s Parameter 35 : hivTree.159.trst 363s Parameter 36 : hivTree.159.trvs 363s 363s Constrained Parameters List 363s 363s Parameter 1 : hivTree.Node2.trst = hivTree.Node2.trvs 363s Parameter 2 : hivTree.Node8.trst = hivTree.Node8.trvs 363s Parameter 3 : hivTree.iNode1.trst = hivTree.iNode1.trvs 363s Parameter 4 : hivTree.Node11.trst = hivTree.Node11.trvs 363s Parameter 5 : hivTree.Node5.trst = hivTree.Node5.trvs 363s Parameter 6 : hivTree.Node1.trst = hivTree.Node1.trvs 363s Parameter 7 : hivTree.Node16.trst = hivTree.Node16.trvs 363s Parameter 8 : hivTree.Node21.trst = hivTree.Node21.trvs 363s Parameter 9 : hivTree.iNode2.trst = hivTree.iNode2.trvs 363s Parameter 10 : hivTree.Node15.trst = hivTree.Node15.trvs 363s 363s 4).HKY85 with shared ratio. 363s 363s Log Likelihood = -1165.7; 363s 363s Independent Parameters List 363s 363s Parameter 1 : R 363s Parameter 2 : hivTree.317.trst 363s Parameter 3 : hivTree.6767.trst 363s Parameter 4 : hivTree.Node2.trst 363s Parameter 5 : hivTree.135.trst 363s Parameter 6 : hivTree.529.trst 363s Parameter 7 : hivTree.105r.trst 363s Parameter 8 : hivTree.Node8.trst 363s Parameter 9 : hivTree.iNode1.trst 363s Parameter 10 : hivTree.719.trst 363s Parameter 11 : hivTree.136.trst 363s Parameter 12 : hivTree.Node11.trst 363s Parameter 13 : hivTree.Node5.trst 363s Parameter 14 : hivTree.Node1.trst 363s Parameter 15 : hivTree.6760.trst 363s Parameter 16 : hivTree.113.trst 363s Parameter 17 : hivTree.9939.trst 363s Parameter 18 : hivTree.Node16.trst 363s Parameter 19 : hivTree.256.trst 363s Parameter 20 : hivTree.822.trst 363s Parameter 21 : hivTree.159.trst 363s Parameter 22 : hivTree.Node21.trst 363s Parameter 23 : hivTree.iNode2.trst 363s Parameter 24 : hivTree.Node15.trst 363s 363s Constrained Parameters List 363s 363s Parameter 1 : hivTree.317.trvs = R*hivTree.317.trst 363s Parameter 2 : hivTree.6767.trvs = R*hivTree.6767.trst 363s Parameter 3 : hivTree.Node2.trvs = R*hivTree.Node2.trst 363s Parameter 4 : hivTree.135.trvs = R*hivTree.135.trst 363s Parameter 5 : hivTree.529.trvs = R*hivTree.529.trst 363s Parameter 6 : hivTree.105r.trvs = R*hivTree.105r.trst 363s Parameter 7 : hivTree.Node8.trvs = R*hivTree.Node8.trst 363s Parameter 8 : hivTree.iNode1.trvs = R*hivTree.iNode1.trst 363s Parameter 9 : hivTree.719.trvs = R*hivTree.719.trst 363s Parameter 10 : hivTree.136.trvs = R*hivTree.136.trst 363s Parameter 11 : hivTree.Node11.trvs = R*hivTree.Node11.trst 363s Parameter 12 : hivTree.Node5.trvs = R*hivTree.Node5.trst 363s Parameter 13 : hivTree.Node1.trvs = R*hivTree.Node1.trst 363s Parameter 14 : hivTree.6760.trvs = R*hivTree.6760.trst 363s Parameter 15 : hivTree.113.trvs = R*hivTree.113.trst 363s Parameter 16 : hivTree.9939.trvs = R*hivTree.9939.trst 363s Parameter 17 : hivTree.Node16.trvs = R*hivTree.Node16.trst 363s Parameter 18 : hivTree.256.trvs = R*hivTree.256.trst 363s Parameter 19 : hivTree.822.trvs = R*hivTree.822.trst 363s Parameter 20 : hivTree.159.trvs = R*hivTree.159.trst 363s Parameter 21 : hivTree.Node21.trvs = R*hivTree.Node21.trst 363s Parameter 22 : hivTree.iNode2.trvs = R*hivTree.iNode2.trst 363s Parameter 23 : hivTree.Node15.trvs = R*hivTree.Node15.trst+ for i in *.bf 363s + '[' -f ReplicateConstraint2.bf ']' 363s + hyphy ReplicateConstraint2.bf 363s 1).Unconstrained HKY85 363s 363s Log Likelihood = -1152.88; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.317.trvs 363s Parameter 2 : hivTree.317.trst 363s Parameter 3 : hivTree.6767.trvs 363s Parameter 4 : hivTree.6767.trst 363s Parameter 5 : hivTree.Node2.trvs 363s Parameter 6 : hivTree.Node2.trst 363s Parameter 7 : hivTree.135.trvs 363s Parameter 8 : hivTree.135.trst 363s Parameter 9 : hivTree.529.trvs 363s Parameter 10 : hivTree.529.trst 363s Parameter 11 : hivTree.105r.trvs 363s Parameter 12 : hivTree.105r.trst 363s Parameter 13 : hivTree.Node8.trvs 363s Parameter 14 : hivTree.Node8.trst 363s Parameter 15 : hivTree.iNode1.trvs 363s Parameter 16 : hivTree.iNode1.trst 363s Parameter 17 : hivTree.719.trvs 363s Parameter 18 : hivTree.719.trst 363s Parameter 19 : hivTree.136.trvs 363s Parameter 20 : hivTree.136.trst 363s Parameter 21 : hivTree.Node11.trvs 363s Parameter 22 : hivTree.Node11.trst 363s Parameter 23 : hivTree.Node5.trvs 363s Parameter 24 : hivTree.Node5.trst 363s Parameter 25 : hivTree.Node1.trvs 363s Parameter 26 : hivTree.Node1.trst 363s Parameter 27 : hivTree.6760.trvs 363s Parameter 28 : hivTree.6760.trst 363s Parameter 29 : hivTree.113.trvs 363s Parameter 30 : hivTree.113.trst 363s Parameter 31 : hivTree.9939.trvs 363s Parameter 32 : hivTree.9939.trst 363s Parameter 33 : hivTree.Node16.trvs 363s Parameter 34 : hivTree.Node16.trst 363s Parameter 35 : hivTree.256.trvs 363s Parameter 36 : hivTree.256.trst 363s Parameter 37 : hivTree.822.trvs 363s Parameter 38 : hivTree.822.trst 363s Parameter 39 : hivTree.159.trvs 363s Parameter 40 : hivTree.159.trst 363s Parameter 41 : hivTree.Node21.trvs 363s Parameter 42 : hivTree.Node21.trst 363s Parameter 43 : hivTree.iNode2.trvs 363s Parameter 44 : hivTree.iNode2.trst 363s Parameter 45 : hivTree.Node15.trvs 363s Parameter 46 : hivTree.Node15.trst 363s 363s 2).HKY85 constrained to F81 on the "iNode1" subtree 363s 363s Log Likelihood = -1157.82; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.135.trvs 363s Parameter 2 : hivTree.529.trvs 363s Parameter 3 : hivTree.105r.trvs 363s Parameter 4 : hivTree.Node8.trvs 363s Parameter 5 : hivTree.317.trvs 363s Parameter 6 : hivTree.317.trst 363s Parameter 7 : hivTree.6767.trst 363s Parameter 8 : hivTree.6767.trvs 363s Parameter 9 : hivTree.Node2.trst 363s Parameter 10 : hivTree.Node2.trvs 363s Parameter 11 : hivTree.iNode1.trvs 363s Parameter 12 : hivTree.iNode1.trst 363s Parameter 13 : hivTree.719.trvs 363s Parameter 14 : hivTree.719.trst 363s Parameter 15 : hivTree.136.trvs 363s Parameter 16 : hivTree.136.trst 363s Parameter 17 : hivTree.Node11.trvs 363s Parameter 18 : hivTree.Node11.trst 363s Parameter 19 : hivTree.Node5.trvs 363s Parameter 20 : hivTree.Node5.trst 363s Parameter 21 : hivTree.Node1.trvs 363s Parameter 22 : hivTree.Node1.trst 363s Parameter 23 : hivTree.6760.trvs 363s Parameter 24 : hivTree.6760.trst 363s Parameter 25 : hivTree.113.trvs 363s Parameter 26 : hivTree.113.trst 363s Parameter 27 : hivTree.9939.trvs 363s Parameter 28 : hivTree.9939.trst 363s Parameter 29 : hivTree.Node16.trvs 363s Parameter 30 : hivTree.Node16.trst 363s Parameter 31 : hivTree.256.trvs 363s Parameter 32 : hivTree.256.trst 363s Parameter 33 : hivTree.822.trvs 363s Parameter 34 : hivTree.822.trst 363s Parameter 35 : hivTree.159.trvs 363s Parameter 36 : hivTree.159.trst 363s Parameter 37 : hivTree.Node21.trvs 363s Parameter 38 : hivTree.Node21.trst 363s Parameter 39 : hivTree.iNode2.trvs 363s Parameter 40 : hivTree.iNode2.trst 363s Parameter 41 : hivTree.Node15.trvs 363s Parameter 42 : hivTree.Node15.trst 363s 363s Constrained Parameters List 363s 363s Parameter 1 : hivTree.135.trst = hivTree.135.trvs 363s Parameter 2 : hivTree.529.trst = hivTree.529.trvs 363s Parameter 3 : hivTree.105r.trst = hivTree.105r.trvs 363s Parameter 4 : hivTree.Node8.trst = hivTree.Node8.trvs 363s 363s 3).HKY85 constrained to F81 on the "iNode1" branch 363s 363s Log Likelihood = -1152.88; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.317.trvs 363s Parameter 2 : hivTree.317.trst 363s Parameter 3 : hivTree.6767.trvs 363s Parameter 4 : hivTree.6767.trst 363s Parameter 5 : hivTree.Node2.trvs 363s Parameter 6 : hivTree.Node2.trst 363s Parameter 7 : hivTree.135.trvs 363s Parameter 8 : hivTree.135.trst 363s Parameter 9 : hivTree.529.trvs 363s Parameter 10 : hivTree.529.trst 363s Parameter 11 : hivTree.105r.trvs 363s Parameter 12 : hivTree.105r.trst 363s Parameter 13 : hivTree.Node8.trvs 363s Parameter 14 : hivTree.Node8.trst 363s Parameter 15 : hivTree.iNode1.trvs 363s Parameter 16 : hivTree.iNode1.trst 363s Parameter 17 : hivTree.719.trvs 363s Parameter 18 : hivTree.719.trst 363s Parameter 19 : hivTree.136.trvs 363s Parameter 20 : hivTree.136.trst 363s Parameter 21 : hivTree.Node11.trvs 363s Parameter 22 : hivTree.Node11.trst 363s Parameter 23 : hivTree.Node5.trvs 363s Parameter 24 : hivTree.Node5.trst 363s Parameter 25 : hivTree.Node1.trvs 363s Parameter 26 : hivTree.Node1.trst 363s Parameter 27 : hivTree.6760.trvs 363s Parameter 28 : hivTree.6760.trst 363s Parameter 29 : hivTree.113.trvs 363s Parameter 30 : hivTree.113.trst 363s Parameter 31 : hivTree.9939.trvs 363s Parameter 32 : hivTree.9939.trst 363s Parameter 33 : hivTree.Node16.trvs 363s Parameter 34 : hivTree.Node16.trst 363s Parameter 35 : hivTree.256.trvs 363s Parameter 36 : hivTree.256.trst 363s Parameter 37 : hivTree.822.trvs 363s Parameter 38 : hivTree.822.trst 363s Parameter 39 : hivTree.159.trvs 363s Parameter 40 : hivTree.159.trst 363s Parameter 41 : hivTree.Node21.trvs 363s Parameter 42 : hivTree.Node21.trst 363s Parameter 43 : hivTree.iNode2.trvs 363s Parameter 44 : hivTree.iNode2.trst 363s Parameter 45 : hivTree.Node15.trvs 363s Parameter 46 : hivTree.Node15.trst 363s 363s 4).HKY85 with "iNode1" subtree constrained equal to "iNode2" subtree 363s 363s Log Likelihood = -1152.88; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.317.trvs 363s Parameter 2 : hivTree.317.trst 363s Parameter 3 : hivTree.6767.trvs 363s Parameter 4 : hivTree.6767.trst 363s Parameter 5 : hivTree.Node2.trvs 363s Parameter 6 : hivTree.Node2.trst 363s Parameter 7 : hivTree.135.trvs 363s Parameter 8 : hivTree.135.trst 363s Parameter 9 : hivTree.529.trvs 363s Parameter 10 : hivTree.529.trst 363s Parameter 11 : hivTree.105r.trvs 363s Parameter 12 : hivTree.105r.trst 363s Parameter 13 : hivTree.Node8.trvs 363s Parameter 14 : hivTree.Node8.trst 363s Parameter 15 : hivTree.iNode1.trvs 363s Parameter 16 : hivTree.iNode1.trst 363s Parameter 17 : hivTree.719.trvs 363s Parameter 18 : hivTree.719.trst 363s Parameter 19 : hivTree.136.trvs 363s Parameter 20 : hivTree.136.trst 363s Parameter 21 : hivTree.Node11.trvs 363s Parameter 22 : hivTree.Node11.trst 363s Parameter 23 : hivTree.Node5.trvs 363s Parameter 24 : hivTree.Node5.trst 363s Parameter 25 : hivTree.Node1.trvs 363s Parameter 26 : hivTree.Node1.trst 363s Parameter 27 : hivTree.6760.trvs 363s Parameter 28 : hivTree.6760.trst 363s Parameter 29 : hivTree.113.trvs 363s Parameter 30 : hivTree.113.trst 363s Parameter 31 : hivTree.9939.trvs 363s Parameter 32 : hivTree.9939.trst 363s Parameter 33 : hivTree.Node16.trvs 363s Parameter 34 : hivTree.Node16.trst 363s Parameter 35 : hivTree.256.trvs 363s Parameter 36 : hivTree.256.trst 363s Parameter 37 : hivTree.822.trvs 363s Parameter 38 : hivTree.822.trst 363s Parameter 39 : hivTree.159.trvs 363s Parameter 40 : hivTree.159.trst 363s Parameter 41 : hivTree.Node21.trvs 363s Parameter 42 : hivTree.Node21.trst 363s Parameter 43 : hivTree.iNode2.trvs 363s Parameter 44 : hivTree.iNode2.trst 363s Parameter 45 : hivTree.Node15.trvs 363s Parameter 46 : hivTree.Node15.trst 363s 363s 5).HKY85 with "iNode1" subtree constrained proportional to "iNode2" subtree 363s 363s Log Likelihood = -1152.88; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.317.trvs 363s Parameter 2 : hivTree.317.trst 363s Parameter 3 : hivTree.6767.trvs 363s Parameter 4 : hivTree.6767.trst 363s Parameter 5 : hivTree.Node2.trvs 363s Parameter 6 : hivTree.Node2.trst 363s Parameter 7 : hivTree.135.trvs 363s Parameter 8 : hivTree.135.trst 363s Parameter 9 : hivTree.529.trvs 363s Parameter 10 : hivTree.529.trst 363s Parameter 11 : hivTree.105r.trvs 363s Parameter 12 : hivTree.105r.trst 363s Parameter 13 : hivTree.Node8.trvs 363s Parameter 14 : hivTree.Node8.trst 363s Parameter 15 : hivTree.iNode1.trvs 363s Parameter 16 : hivTree.iNode1.trst 363s Parameter 17 : hivTree.719.trvs 363s Parameter 18 : hivTree.719.trst 363s Parameter 19 : hivTree.136.trvs 363s Parameter 20 : hivTree.136.trst 363s Parameter 21 : hivTree.Node11.trvs 363s Parameter 22 : hivTree.Node11.trst 363s Parameter 23 : hivTree.Node5.trvs 363s Parameter 24 : hivTree.Node5.trst 363s Parameter 25 : hivTree.Node1.trvs 363s Parameter 26 : hivTree.Node1.trst 363s Parameter 27 : hivTree.6760.trvs 363s Parameter 28 : hivTree.6760.trst 363s Parameter 29 : hivTree.113.trvs 363s Parameter 30 : hivTree.113.trst 363s Parameter 31 : hivTree.9939.trvs 363s Parameter 32 : hivTree.9939.trst 363s Parameter 33 : hivTree.Node16.trvs 363s Parameter 34 : hivTree.Node16.trst 363s Parameter 35 : hivTree.256.trvs 363s Parameter 36 : hivTree.256.trst 363s Parameter 37 : hivTree.822.trvs 363s Parameter 38 : hivTree.822.trst 363s Parameter 39 : hivTree.159.trvs 363s Parameter 40 : hivTree.159.trst 363s Parameter 41 : hivTree.Node21.trvs 363s Parameter 42 : hivTree.Node21.trst 363s Parameter 43 : hivTree.iNode2.trvs 363s Parameter 44 : hivTree.iNode2.trst 363s Parameter 45 : hivTree.Node15.trvs 363s Parameter 46 : hivTree.Node15.trst 363s 363s 5).HKY85 with "iNode1" subtree constrained to the average of those in the "iNode2" subtree 363s 363s Log Likelihood = -1157.82; 363s 363s Independent Parameters List 363s 363s Parameter 1 : hivTree.135.trst 363s Parameter 2 : hivTree.529.trst 363s Parameter 3 : hivTree.105r.trst 363s Parameter 4 : hivTree.Node8.trst 363s Parameter 5 : hivTree.317.trvs 363s Parameter 6 : hivTree.317.trst 363s Parameter 7 : hivTree.6767.trst 363s Parameter 8 : hivTree.6767.trvs 363s Parameter 9 : hivTree.Node2.trst 363s Parameter 10 : hivTree.Node2.trvs 363s Parameter 11 : hivTree.iNode1.trvs 363s Parameter 12 : hivTree.iNode1.trst 363s Parameter 13 : hivTree.719.trvs 363s Parameter 14 : hivTree.719.trst 363s Parameter 15 : hivTree.136.trvs 363s Parameter 16 : hivTree.136.trst 363s Parameter 17 : hivTree.Node11.trvs 363s Parameter 18 : hivTree.Node11.trst 363s Parameter 19 : hivTree.Node5.trvs 363s Parameter 20 : hivTree.Node5.trst 363s Parameter 21 : hivTree.Node1.trvs 363s Parameter 22 : hivTree.Node1.trst 363s Parameter 23 : hivTree.6760.trvs 363s Parameter 24 : hivTree.6760.trst 363s Parameter 25 : hivTree.113.trvs 363s Parameter 26 : hivTree.113.trst 363s Parameter 27 : hivTree.9939.trvs 363s Parameter 28 : hivTree.9939.trst 363s Parameter 29 : hivTree.Node16.trvs 363s Parameter 30 : hivTree.Node16.trst 363s Parameter 31 : hivTree.256.trvs 363s Parameter 32 : hivTree.256.trst 363s Parameter 33 : hivTree.822.trvs 363s Parameter 34 : hivTree.822.trst 363s Parameter 35 : hivTree.159.trvs 363s Parameter 36 : hivTree.159.trst 363s Parameter 37 : hivTree.Node21.trvs 363s Parameter 38 : hivTree.Node21.trst 363s Parameter 39 : hivTree.iNode2.trvs 363s Parameter 40 : hivTree.iNode2.trst 363s Parameter 41 : hivTree.Node15.trvs 363s Parameter 42 : hivTree.Node15.trst 363s 363s Constrained Parameters List 363s 363s Parameter 1 : hivTree.135.trvs = hivTree.135.trst 363s Parameter 2 : hivTree.529.trvs = hivTree.529.trst 363s Parameter 3 : hivTree.105r.trvs = hivTree.105r.trst 363s Parameter 4 : hivTree.Node8.trvs = hivTree.Node8.trst+ for i in *.bf 363s + '[' -f aa.bf ']' 363s + hyphy aa.bf 364s Log Likelihood = -1134.73158903913; 364s Tree theTree=(((Langur:0.07430927355753303,Baboon:0.03832845958677486)Node2:0.02339192532927102,Human:0.05949975683358704)Node1:0.02006656431022491,Rat:0.2458809238984347,(Cow:0.2552868260837879,Horse:0.5627637212219557)Node7:0.07060308849528245); 364s + for i in *.bf 364s + '[' -f definitions2.bf ']' 364s + hyphy definitions2.bf 364s 1). 4 equiprobable rates sampled from Exponential with lambda = 2 364s 364s Sample by MEAN: 364s 364s Sample mean = 0.5 (sample variance = 0.2450374540764348) 364s 364s Rate[0]= 0.06847689 (weight=0.2500000) 364s Rate[1]= 0.23837593 (weight=0.2500000) 364s Rate[2]= 0.50000000 (weight=0.2500000) 364s Rate[3]= 1.19314718 (weight=0.2500000) 364s ------------------------------------------------ 364s 364s Sample by MEDIAN: 364s 364s Sample mean = 0.4579757270702274 (sample variance = 0.1807474106483087) 364s 364s Rate[0]= 0.06676570 (weight=0.2500000) 364s Rate[1]= 0.23500181 (weight=0.2500000) 364s Rate[2]= 0.49041463 (weight=0.2500000) 364s Rate[3]= 1.03972077 (weight=0.2500000) 364s ------------------------------------------------ 364s 364s Sample by SCALED_MEDIAN: 364s 364s Sample mean = 0.5 (sample variance = 0.2154404122636025) 364s 364s Rate[0]= 0.07289218 (weight=0.2500000) 364s Rate[1]= 0.25656580 (weight=0.2500000) 364s Rate[2]= 0.53541552 (weight=0.2500000) 364s Rate[3]= 1.13512650 (weight=0.2500000) 364s ------------------------------------------------ 364s 364s Sample by MEAN (numerical averaging): 364s 364s Sample mean = 0.4999785276721994 (sample variance = 0.2450490709657362) 364s 364s Rate[0]= 0.06846096 (weight=0.2500000) 364s Rate[1]= 0.23834015 (weight=0.2500000) 364s Rate[2]= 0.49996411 (weight=0.2500000) 364s Rate[3]= 1.19314889 (weight=0.2500000) 364s ------------------------------------------------ 364s 364s Sample by MEAN (numerical CDF and averaging): 364s 364s Sample mean = 0.4999785261159418 (sample variance = 0.2450226791380972) 364s 364s Rate[0]= 0.06849282 (weight=0.2500000) 364s Rate[1]= 0.23835613 (weight=0.2500000) 364s Rate[2]= 0.49994751 (weight=0.2500000) 364s Rate[3]= 1.19311765 (weight=0.2500000) 364s ------------------------------------------------ 364s 2). Equiprobable rates sampled from Exponential with lambda = 2 364s 364s Sample by MEDIAN (3 rate classes): 364s 364s Sample mean = 0.4445380344303255 (sample variance = 0.1690909238620303) 364s 364s Rate[0]= 0.09116078 (weight=0.3333333) 364s Rate[1]= 0.34657359 (weight=0.3333333) 364s Rate[2]= 0.89587973 (weight=0.3333333) 364s ------------------------------------------------ 364s 364s Sample by MEDIAN (9 rate classes): 364s 364s Sample mean = 0.4810029287863006 (sample variance = 0.2073045870856967) 364s 364s Rate[0]= 0.02857921 (weight=0.1111111) 364s Rate[1]= 0.09116078 (weight=0.1111111) 364s Rate[2]= 0.16271120 (weight=0.1111111) 364s Rate[3]= 0.24623824 (weight=0.1111111) 364s Rate[4]= 0.34657359 (weight=0.1111111) 364s Rate[5]= 0.47223080 (weight=0.1111111) 364s Rate[6]= 0.64046692 (weight=0.1111111) 364s Rate[7]= 0.89587973 (weight=0.1111111) 364s Rate[8]= 1.44518588 (weight=0.1111111) 364s ------------------------------------------------ 364s 3). Equiprobable rates sampled from Gamma with mean 1, variance 1/10. 364s 364s Sample by MEAN (10 rate classes): 364s 364s Sample mean = 1 (sample variance = 0.1057310289486733) 364s 364s Rate[0]= 0.52447499 (weight=0.1000000) 364s Rate[1]= 0.67866972 (weight=0.1000000) 364s Rate[2]= 0.77209919 (weight=0.1000000) 364s Rate[3]= 0.85214884 (weight=0.1000000) 364s Rate[4]= 0.92850815 (weight=0.1000000) 364s Rate[5]= 1.00664500 (weight=0.1000000) 364s Rate[6]= 1.09192933 (weight=0.1000000) 364s Rate[7]= 1.19267960 (weight=0.1000000) 364s Rate[8]= 1.32858029 (weight=0.1000000) 364s Rate[9]= 1.62426489 (weight=0.1000000) 364s ------------------------------------------------ 364s 4). Equiprobable rates sampled from Gamma with mean 2, variance 1/25. 364s 364s Sample by MEAN (10 rate classes): 364s 364s Sample mean = 2 (sample variance = 0.04259071282256012) 364s 364s Rate[0]= 1.66431246 (weight=0.1000000) 364s Rate[1]= 1.79212822 (weight=0.1000000) 364s Rate[2]= 1.86123411 (weight=0.1000000) 364s Rate[3]= 1.91722052 (weight=0.1000000) 364s Rate[4]= 1.96832799 (weight=0.1000000) 364s Rate[5]= 2.01862937 (weight=0.1000000) 364s Rate[6]= 2.07152664 (weight=0.1000000) 364s Rate[7]= 2.13166629 (weight=0.1000000) 364s Rate[8]= 2.20930216 (weight=0.1000000) 364s Rate[9]= 2.36565224 (weight=0.1000000) 364s ------------------------------------------------ 364s 5). Equiprobable rates sampled from Beta with mean 1/2 , variance 1/12. 364s 364s Sample by MEAN (8 rate classes): 364s 364s Sample mean = 0.5 (sample variance = 0.09375000225643569) 364s 364s Rate[0]= 0.06250000 (weight=0.1250000) 364s Rate[1]= 0.18750000 (weight=0.1250000) 364s Rate[2]= 0.31250001 (weight=0.1250000) 364s Rate[3]= 0.43750001 (weight=0.1250000) 364s Rate[4]= 0.56249993 (weight=0.1250000) 364s Rate[5]= 0.68750001 (weight=0.1250000) 364s Rate[6]=+ for i in *.bf 364s + '[' -f definitions3.bf ']' 364s + hyphy definitions3.bf 364s 0.81250002 (weight=0.1250000) 364s Rate[7]= 0.93750002 (weight=0.1250000) 364s ------------------------------------------------ 364s 6). Equiprobable rates sampled from Normal(>0) with mean 3 , variance 1/4. 364s 364s Sample by MEAN (8 rate classes): 364s 364s Sample mean = 3.000000003037941 (sample variance = 0.2700097975580249) 364s 364s Rate[0]= 2.17658588 (weight=0.1250000) 364s Rate[1]= 2.55230783 (weight=0.1250000) 364s Rate[2]= 2.75432532 (weight=0.1250000) 364s Rate[3]= 2.92101185 (weight=0.1250000) 364s Rate[4]= 3.07898815 (weight=0.1250000) 364s Rate[5]= 3.24567468 (weight=0.1250000) 364s Rate[6]= 3.44769217 (weight=0.1250000) 364s Rate[7]= 3.82341415 (weight=0.1250000) 364s ------------------------------------------------ 364s 364s 364s Sample mean = 1 (sample variance = 0.9920002887656187) 364s 364s Rate[0]= 0.05175536 (weight=0.1000000) 364s Rate[1]= 0.16309623 (weight=0.1000000) 364s Rate[2]= 0.28842380 (weight=0.1000000) 364s Rate[3]= 0.43177086 (weight=0.1000000) 364s Rate[4]= 0.59921784 (weight=0.1000000) 364s Rate[5]= 0.80057298 (weight=0.1000000) 364s Rate[6]= 1.05324451 (weight=0.1000000) 364s Rate[7]= 1.39304259 (weight=0.1000000) 364s Rate[8]= 1.91629073 (weight=0.1000000) 364s Rate[9]= 3.30258509 (weight=0.1000000) 364s ------------------------------------------------ 364s + for i in *.bf 364s + '[' -f displayFunction.bf ']' 364s + hyphy displayFunction.bf 364s + for i in *.bf 364s + '[' -f profile_test.bf ']' 364s + hyphy profile_test.bf 364s 364s Total run time (seconds) : 0.000000 364s Total number of steps : 1500005 364s 364s 1 : s=0; 364s Call count: 1 364s Time (seconds): 5.1e-11 364s 2 : m={5,1}; 364s Call count: 1 364s Time (seconds): 6.5e-11 364s 3 : k=0; 364s Call count: 1 364s Time (seconds): 7e-12 364s 4 : Branch under condition 'k<250000' 364s to 364s s=s+k; 364s else 364s #profilePAUSE, ; 364s Call count: 250001 364s Time (seconds): 4.970800000002875e-08 364s 5 : s=s+k; 364s Call count: 250000 364s Time (seconds): 5.57910000000348e-08 364s 6 : t=Random(0,5); 364s Call count: 250000 364s Time (seconds): 5.542100000003325e-08 364s 7 : m[t]=m[t]+1; 364s Call count: 250000 364s Time (seconds): 1.621730000001393e-07 364s 8 : k=k+1; 364s Call count: 250000 364s Time (seconds): 5.909500000003797e-08 364s 9 : Go to step 4 364s Call count: 250000 364s Time (seconds): 1.527899999999526e-08 364s 10 : #profilePAUSE, ; 364s Call count: 1 364s Time (seconds): 2e-12 364s + for i in *.bf 364s + '[' -f shared.bf ']' 364s + hyphy shared.bf 364s + rm -f '*messages.log*' '*errors.log*' 365s autopkgtest [08:16:01]: test run-unit-tests: -----------------------] 365s autopkgtest [08:16:01]: test run-unit-tests: - - - - - - - - - - results - - - - - - - - - - 365s run-unit-tests PASS 365s autopkgtest [08:16:01]: @@@@@@@@@@@@@@@@@@@@ summary 365s run-unit-tests PASS 379s Creating nova instance adt-noble-arm64-hyphy-20240325-075553-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...