0s autopkgtest [23:30:38]: starting date and time: 2025-03-15 23:30:38+0000 0s autopkgtest [23:30:38]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:30:38]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8l1iaxj9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade tree-puzzle --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-9.secgroup --name adt-plucky-amd64-tree-puzzle-20250315-233037-juju-7f2275-prod-proposed-migration-environment-15-13f3a586-6d53-46c5-8651-13105428a129 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 46s autopkgtest [23:31:24]: testbed dpkg architecture: amd64 46s autopkgtest [23:31:24]: testbed apt version: 2.9.31ubuntu1 46s autopkgtest [23:31:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 46s autopkgtest [23:31:24]: testbed release detected to be: None 46s autopkgtest [23:31:24]: updating testbed package index (apt update) 46s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 46s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 46s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 46s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 46s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 47s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 47s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 47s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 47s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 47s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 47s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 47s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 47s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 47s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 47s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 47s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 47s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 47s Fetched 1265 kB in 0s (6912 kB/s) 48s Reading package lists... 48s + lsb_release --codename --short 48s + RELEASE=plucky 48s + cat 48s + [ plucky != trusty ] 48s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 48s Reading package lists... 48s Building dependency tree... 48s Reading state information... 49s Calculating upgrade... 49s Calculating upgrade... 49s The following package was automatically installed and is no longer required: 49s libnl-genl-3-200 49s Use 'sudo apt autoremove' to remove it. 49s The following NEW packages will be installed: 49s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 49s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 49s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 49s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 49s The following packages will be upgraded: 49s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 49s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 49s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 49s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 49s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 49s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 49s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 49s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 49s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 49s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 49s linux-headers-generic linux-headers-virtual linux-image-generic 49s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 49s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 49s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 49s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 49s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 49s python3.13-minimal rsync rsyslog strace xz-utils 49s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 49s Need to get 807 MB of archives. 49s After this operation, 326 MB of additional disk space will be used. 49s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 49s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 49s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 49s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 49s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 49s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 49s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 49s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 49s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 49s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 49s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 49s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 49s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 49s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 49s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 49s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 49s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 49s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 49s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 49s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 49s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 49s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 49s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 49s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 49s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 49s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 49s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 49s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 49s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 49s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 49s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 49s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 49s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 49s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 49s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 49s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 49s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 49s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 49s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 49s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 49s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 49s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 49s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 49s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 49s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 49s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 49s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 49s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 49s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 49s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 49s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 49s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 49s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 49s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 49s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 49s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 49s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 49s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 49s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 49s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 49s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 49s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 49s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 49s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 49s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 49s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 49s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 49s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 49s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 49s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 49s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 49s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 49s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 49s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 49s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 53s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 53s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 54s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 55s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 55s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 55s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 55s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 55s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 55s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 55s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 55s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 55s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 55s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 55s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 55s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 55s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 55s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 55s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 55s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 55s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 55s Preconfiguring packages ... 55s Fetched 807 MB in 6s (134 MB/s) 56s (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 ... 109138 files and directories currently installed.) 56s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 56s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 56s Setting up ncurses-bin (6.5+20250216-2) ... 56s (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 ... 109138 files and directories currently installed.) 56s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 56s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 56s Setting up ncurses-base (6.5+20250216-2) ... 56s (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 ... 109138 files and directories currently installed.) 56s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 56s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 56s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 56s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 57s Setting up liblz4-1:amd64 (1.10.0-4) ... 57s (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 ... 109138 files and directories currently installed.) 57s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 57s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 57s Setting up liblzma5:amd64 (5.6.4-1) ... 57s (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 ... 109138 files and directories currently installed.) 57s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 57s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 57s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 57s (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 ... 109138 files and directories currently installed.) 57s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 57s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 57s Setting up apt (2.9.33) ... 58s (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 ... 109138 files and directories currently installed.) 58s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 58s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 58s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 58s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 58s Setting up python3-minimal (3.13.2-2) ... 58s (Reading database ... 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 74s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 74s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 74s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 74s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 74s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 74s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 74s Setting up media-types (13.0.0) ... 74s Installing new version of config file /etc/mime.types ... 74s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 74s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 74s Setting up pci.ids (0.0~2025.03.09-1) ... 74s Setting up apt-utils (2.9.33) ... 74s Setting up libdebuginfod-common (0.192-4) ... 74s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 74s Setting up bpftool (7.6.0+6.14.0-10.10) ... 74s Setting up libestr0:amd64 (0.1.11-2) ... 74s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 74s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 74s Setting up dosfstools (4.2-1.2) ... 74s Setting up rsyslog (8.2412.0-2ubuntu2) ... 74s info: The user `syslog' is already a member of `adm'. 75s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 75s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 75s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 75s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 75s Setting up linux-headers-generic (6.14.0-10.10) ... 75s Setting up libjemalloc2:amd64 (5.3.0-3) ... 75s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 75s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 75s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 75s Installing new version of config file /etc/apparmor.d/openvpn ... 76s Reloading AppArmor profiles 78s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 78s No schema files found: doing nothing. 78s Setting up libglib2.0-data (2.84.0-1) ... 78s Setting up libncurses6:amd64 (6.5+20250216-2) ... 78s Setting up strace (6.13+ds-1ubuntu1) ... 78s Setting up xz-utils (5.6.4-1) ... 78s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 78s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 80s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 80s Setting up libpci3:amd64 (1:3.13.0-2) ... 80s Setting up python-apt-common (2.9.9build1) ... 80s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 80s Setting up pnp.ids (0.393-3) ... 80s Setting up libnl-3-200:amd64 (3.7.0-1) ... 80s Setting up python3.13-minimal (3.13.2-2) ... 80s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 80s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 80s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 80s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 80s Setting up rsync (3.4.1+ds1-3) ... 81s rsync.service is a disabled or a static unit not running, not starting it. 81s Setting up python3.13-gdbm (3.13.2-2) ... 81s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 81s Setting up ncurses-term (6.5+20250216-2) ... 81s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 81s Setting up libpython3.13:amd64 (3.13.2-2) ... 81s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 81s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 81s Setting up linux-headers-virtual (6.14.0-10.10) ... 81s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 81s Setting up python3.13 (3.13.2-2) ... 82s Setting up htop (3.4.0-2) ... 82s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 84s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 84s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 84s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 84s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 84s Setting up libfwupd3:amd64 (2.0.6-4) ... 84s Setting up python3 (3.13.2-2) ... 85s Setting up python3-markupsafe (2.1.5-1build4) ... 85s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 87s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 87s Setting up hwdata (0.393-3) ... 87s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 87s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 87s Setting up linux-perf (6.14.0-10.10) ... 87s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 87s Setting up python3-gi (3.50.0-4build1) ... 87s Setting up pciutils (1:3.13.0-2) ... 87s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 87s Setting up curl (8.12.1-3ubuntu1) ... 87s Setting up linux-image-virtual (6.14.0-10.10) ... 87s Setting up linux-tools-common (6.14.0-10.10) ... 87s Setting up fwupd (2.0.6-4) ... 88s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 88s fwupd.service is a disabled or a static unit not running, not starting it. 88s Setting up python3-systemd (235-1build6) ... 88s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 88s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 88s Setting up linux-image-generic (6.14.0-10.10) ... 88s Setting up python3-dbus (1.3.2-5build5) ... 88s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 88s Setting up linux-generic (6.14.0-10.10) ... 88s Setting up python3-apt (2.9.9build1) ... 88s Setting up python3-yaml (6.0.2-1build2) ... 88s Setting up python3-lazr.uri (1.0.6-6) ... 88s Setting up binutils (2.44-3ubuntu1) ... 88s Setting up cloud-init-base (25.1-0ubuntu3) ... 90s Setting up linux-virtual (6.14.0-10.10) ... 90s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 90s Setting up cloud-init (25.1-0ubuntu3) ... 90s Processing triggers for systemd (257.3-1ubuntu3) ... 90s Processing triggers for man-db (2.13.0-1) ... 92s Processing triggers for dbus (1.16.2-1ubuntu1) ... 92s Processing triggers for libc-bin (2.41-1ubuntu1) ... 92s Processing triggers for initramfs-tools (0.146ubuntu1) ... 92s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 92s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 102s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 102s /etc/kernel/postinst.d/initramfs-tools: 102s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 102s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 113s /etc/kernel/postinst.d/zz-update-grub: 113s Sourcing file `/etc/default/grub' 113s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 113s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 113s Generating grub configuration file ... 113s Found linux image: /boot/vmlinuz-6.14.0-10-generic 113s Found initrd image: /boot/initrd.img-6.14.0-10-generic 113s Found linux image: /boot/vmlinuz-6.12.0-16-generic 113s Found initrd image: /boot/initrd.img-6.12.0-16-generic 113s Found linux image: /boot/vmlinuz-6.11.0-8-generic 114s Found initrd image: /boot/initrd.img-6.11.0-8-generic 114s Warning: os-prober will not be executed to detect other bootable partitions. 114s Systems on them will not be added to the GRUB boot configuration. 114s Check GRUB_DISABLE_OS_PROBER documentation entry. 114s Adding boot menu entry for UEFI Firmware Settings ... 114s done 114s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 114s + /usr/lib/apt/apt-helper analyze-pattern ?true 114s + uname -r 114s + sed s/\./\\./g 114s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.* 114s + apt list ?obsolete 114s + tail -n+2 114s + cut -d/ -f1 114s + grep -v ^linux-.*6\.12\.0-16-generic.* 115s + obsolete_pkgs=linux-headers-6.11.0-8-generic 115s linux-headers-6.11.0-8 115s linux-headers-6.12.0-16 115s linux-image-6.11.0-8-generic 115s linux-modules-6.11.0-8-generic 115s linux-tools-6.11.0-8-generic 115s linux-tools-6.11.0-8 115s linux-tools-6.12.0-16 115s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-headers-6.12.0-16 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 linux-tools-6.12.0-16 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Solving dependencies... 116s The following packages will be REMOVED: 116s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 116s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 116s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 116s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 116s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 116s linux-tools-6.12.0-16-generic* 116s 0 upgraded, 0 newly installed, 15 to remove and 5 not upgraded. 116s After this operation, 371 MB disk space will be freed. 117s (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 ... 148643 files and directories currently installed.) 117s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 117s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 117s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 117s Removing libpython3.12t64:amd64 (3.12.9-1) ... 117s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 117s Removing libnsl2:amd64 (1.3.0-3build3) ... 117s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 117s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 117s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 120s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 120s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 122s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 122s /etc/kernel/postrm.d/initramfs-tools: 122s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 123s /etc/kernel/postrm.d/zz-update-grub: 123s Sourcing file `/etc/default/grub' 123s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 123s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 123s Generating grub configuration file ... 123s Found linux image: /boot/vmlinuz-6.14.0-10-generic 123s Found initrd image: /boot/initrd.img-6.14.0-10-generic 123s Found linux image: /boot/vmlinuz-6.12.0-16-generic 123s Found initrd image: /boot/initrd.img-6.12.0-16-generic 123s Warning: os-prober will not be executed to detect other bootable partitions. 123s Systems on them will not be added to the GRUB boot configuration. 123s Check GRUB_DISABLE_OS_PROBER documentation entry. 123s Adding boot menu entry for UEFI Firmware Settings ... 123s done 123s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 123s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 123s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 123s Processing triggers for libc-bin (2.41-1ubuntu1) ... 123s (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 ... 84830 files and directories currently installed.) 123s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 123s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 123s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 124s + grep -q trusty /etc/lsb-release 124s + [ ! -d /usr/share/doc/unattended-upgrades ] 124s + [ ! -d /usr/share/doc/lxd ] 124s + [ ! -d /usr/share/doc/lxd-client ] 124s + [ ! -d /usr/share/doc/snapd ] 124s + type iptables 124s + cat 124s + chmod 755 /etc/rc.local 124s + . /etc/rc.local 124s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 124s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 124s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 124s + uname -m 124s + [ x86_64 = ppc64le ] 124s + [ -d /run/systemd/system ] 124s + systemd-detect-virt --quiet --vm 124s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 124s + cat 124s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 124s + echo COMPRESS=lz4 124s autopkgtest [23:32:42]: upgrading testbed (apt dist-upgrade and autopurge) 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 125s Entering ResolveByKeep 125s 125s Calculating upgrade... 126s The following packages will be upgraded: 126s libc-bin libc-dev-bin libc6 libc6-dev locales 126s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Need to get 10.5 MB of archives. 126s After this operation, 1024 B of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 126s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 126s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 126s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 126s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 126s Preconfiguring packages ... 126s Fetched 10.5 MB in 0s (67.6 MB/s) 126s (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 ... 84827 files and directories currently installed.) 126s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 126s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 126s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 126s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 126s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 127s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 127s Setting up libc6:amd64 (2.41-1ubuntu2) ... 127s (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 ... 84827 files and directories currently installed.) 127s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 127s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 127s Setting up libc-bin (2.41-1ubuntu2) ... 127s (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 ... 84827 files and directories currently installed.) 127s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 127s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 127s Setting up locales (2.41-1ubuntu2) ... 128s Generating locales (this might take a while)... 129s en_US.UTF-8... done 129s Generation complete. 129s Setting up libc-dev-bin (2.41-1ubuntu2) ... 129s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 129s Processing triggers for man-db (2.13.0-1) ... 130s Processing triggers for systemd (257.3-1ubuntu3) ... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s Starting pkgProblemResolver with broken count: 0 132s Starting 2 pkgProblemResolver with broken count: 0 132s Done 132s Solving dependencies... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s autopkgtest [23:32:50]: rebooting testbed after setup commands that affected boot 136s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 148s autopkgtest [23:33:06]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 148s autopkgtest [23:33:06]: @@@@@@@@@@@@@@@@@@@@ apt-source tree-puzzle 150s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (dsc) [2235 B] 150s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (tar) [591 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (diff) [32.4 kB] 150s gpgv: Signature made Sat Nov 30 06:14:46 2024 UTC 150s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 150s gpgv: Can't check signature: No public key 150s dpkg-source: warning: cannot verify inline signature for ./tree-puzzle_5.3~rc16+dfsg-12build1.dsc: no acceptable signature found 150s autopkgtest [23:33:08]: testing package tree-puzzle version 5.3~rc16+dfsg-12build1 150s autopkgtest [23:33:08]: build not needed 152s autopkgtest [23:33:10]: test run-unit-test: preparing testbed 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Starting pkgProblemResolver with broken count: 0 153s Starting 2 pkgProblemResolver with broken count: 0 153s Done 153s The following NEW packages will be installed: 153s libamd-comgr2 libamdhip64-5 libevent-pthreads-2.1-7t64 libfabric1 libgomp1 153s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 153s libibumad3 libllvm17t64 libmunge2 libopenmpi40 libpciaccess0 libpmix2t64 153s libpsm-infinipath1 libpsm2-2 librdmacm1t64 libsprng2 libucx0 libxnvctrl0 153s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common tree-ppuzzle 153s tree-puzzle tree-puzzle-doc 153s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 58.0 MB of archives. 153s After this operation, 238 MB of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-21 [26.0 MB] 154s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 154s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 154s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 154s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 154s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 154s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 154s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 154s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 55.0-1ubuntu1 [71.5 kB] 154s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 154s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 154s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 154s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 154s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 154s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 154s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 154s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 154s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-5 [714 kB] 154s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 55.0-1ubuntu1 [29.7 kB] 154s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 55.0-1ubuntu1 [42.7 kB] 154s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.18.1+ds-2 [1293 kB] 154s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 154s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsprng2 amd64 2.0a-16 [92.2 kB] 154s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-common all 5.0.7-1 [97.9 kB] 154s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-bin amd64 5.0.7-1 [192 kB] 154s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 mpi-default-bin amd64 1.18 [2510 B] 154s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 tree-ppuzzle amd64 5.3~rc16+dfsg-12build1 [202 kB] 154s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 tree-puzzle amd64 5.3~rc16+dfsg-12build1 [182 kB] 154s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 tree-puzzle-doc all 5.3~rc16+dfsg-12build1 [409 kB] 154s Fetched 58.0 MB in 1s (84.4 MB/s) 154s Selecting previously unselected package libllvm17t64:amd64. 155s (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 ... 84827 files and directories currently installed.) 155s Preparing to unpack .../00-libllvm17t64_1%3a17.0.6-21_amd64.deb ... 155s Unpacking libllvm17t64:amd64 (1:17.0.6-21) ... 155s Selecting previously unselected package libamd-comgr2:amd64. 155s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 155s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 155s Selecting previously unselected package libhsakmt1:amd64. 155s Preparing to unpack .../02-libhsakmt1_5.7.0-1build1_amd64.deb ... 155s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 156s Selecting previously unselected package libhsa-runtime64-1. 156s Preparing to unpack .../03-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 156s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 156s Selecting previously unselected package libamdhip64-5. 156s Preparing to unpack .../04-libamdhip64-5_5.7.1-5_amd64.deb ... 156s Unpacking libamdhip64-5 (5.7.1-5) ... 156s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 156s Preparing to unpack .../05-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 156s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 156s Selecting previously unselected package libpsm-infinipath1. 156s Preparing to unpack .../06-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 156s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 156s Selecting 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.../12-libmunge2_0.5.16-1_amd64.deb ... 156s Unpacking libmunge2:amd64 (0.5.16-1) ... 156s Selecting previously unselected package libpciaccess0:amd64. 156s Preparing to unpack .../13-libpciaccess0_0.17-3build1_amd64.deb ... 156s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 156s Selecting previously unselected package libxnvctrl0:amd64. 156s Preparing to unpack .../14-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 156s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 156s Selecting previously unselected package ocl-icd-libopencl1:amd64. 156s Preparing to unpack .../15-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 156s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 156s Selecting previously unselected package libhwloc-plugins:amd64. 156s Preparing to unpack .../16-libhwloc-plugins_2.12.0-1_amd64.deb ... 156s Unpacking libhwloc-plugins:amd64 (2.12.0-1) ... 156s Selecting previously unselected package libpmix2t64:amd64. 156s Preparing to unpack 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unselected package openmpi-common. 156s Preparing to unpack .../23-openmpi-common_5.0.7-1_all.deb ... 156s Unpacking openmpi-common (5.0.7-1) ... 156s Selecting previously unselected package openmpi-bin. 156s Preparing to unpack .../24-openmpi-bin_5.0.7-1_amd64.deb ... 156s Unpacking openmpi-bin (5.0.7-1) ... 156s Selecting previously unselected package mpi-default-bin. 156s Preparing to unpack .../25-mpi-default-bin_1.18_amd64.deb ... 156s Unpacking mpi-default-bin (1.18) ... 156s Selecting previously unselected package tree-ppuzzle. 156s Preparing to unpack .../26-tree-ppuzzle_5.3~rc16+dfsg-12build1_amd64.deb ... 156s Unpacking tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 156s Selecting previously unselected package tree-puzzle. 156s Preparing to unpack .../27-tree-puzzle_5.3~rc16+dfsg-12build1_amd64.deb ... 156s Unpacking tree-puzzle (5.3~rc16+dfsg-12build1) ... 157s Selecting previously unselected package tree-puzzle-doc. 157s Preparing to unpack .../28-tree-puzzle-doc_5.3~rc16+dfsg-12build1_all.deb ... 157s Unpacking tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 157s Setting up libpciaccess0:amd64 (0.17-3build1) ... 157s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 157s Setting up libibumad3:amd64 (55.0-1ubuntu1) ... 157s Setting up libibmad5:amd64 (55.0-1ubuntu1) ... 157s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 157s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 157s Setting up libmunge2:amd64 (0.5.16-1) ... 157s Setting up libllvm17t64:amd64 (1:17.0.6-21) ... 157s Setting up libhwloc15:amd64 (2.12.0-1) ... 157s Setting up tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 157s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 157s Setting up libpsm2-2 (11.2.185-2.1) ... 157s Setting up openmpi-common (5.0.7-1) ... 157s Setting up librdmacm1t64:amd64 (55.0-1ubuntu1) ... 157s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 157s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 157s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 157s Setting up libsprng2 (2.0a-16) ... 157s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 157s Setting up libfabric1:amd64 (1.17.0-3.1) ... 157s Setting up tree-puzzle (5.3~rc16+dfsg-12build1) ... 157s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 157s Setting up libpmix2t64:amd64 (5.0.6-5) ... 157s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 157s Setting up libamdhip64-5 (5.7.1-5) ... 157s Setting up libucx0:amd64 (1.18.1+ds-2) ... 157s Setting up libopenmpi40:amd64 (5.0.7-1) ... 157s Setting up openmpi-bin (5.0.7-1) ... 157s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 157s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 157s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 157s Setting up mpi-default-bin (1.18) ... 157s Setting up tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 157s Processing triggers for man-db (2.13.0-1) ... 157s Processing triggers for libc-bin (2.41-1ubuntu2) ... 158s autopkgtest [23:33:16]: test run-unit-test: [----------------------- 158s .: 158s EF.3trees 158s EF.phy 158s atp6.a 158s globin.a 158s globin.ctrees 158s globin.trees 158s marswolf.ctrees 158s marswolf.n 158s marswolf.trees 158s primates.b 158s primates.ctrees 158s primates.trees 158s tests 158s 158s ./tests: 158s build-puzzle.log 158s build-puzzle.trs 158s build-remark.log 158s build-remark.trs 158s check-cons-pure-prot 158s check-lm-pure-prot 158s check-qp-clock 158s check-qp-hky-clock-nucl 158s check-qp-hky-rhet-clock-nucl 158s check-qp-hky-rhet-nucl 158s check-qp-jtt-prot 158s check-qp-jtt-rhet-clock-prot 158s check-qp-jtt-rhet-prot 158s check-qp-mtrev-prot 158s check-qp-pure-bin 158s check-qp-pure-nucl 158s check-qp-pure-prot 158s check-qp-tn-nucl 158s check-qp-vt-prot 158s check-qp-wag-prot 158s check-ut-pure-prot 158s cons-pure-prot.ctrees 158s cons-pure-prot.log 158s cons-pure-prot.param 158s cons-pure-prot.prot 158s cons-pure-prot.test 158s cons-pure-prot.trs 158s generate-scripts.sh 158s lm-pure-prot.log 158s lm-pure-prot.param 158s lm-pure-prot.prot 158s lm-pure-prot.test 158s lm-pure-prot.trs 158s qp-clock.log 158s qp-clock.nucl 158s qp-clock.param 158s qp-clock.test 158s qp-clock.trs 158s qp-hky-clock-nucl.log 158s qp-hky-clock-nucl.nucl 158s qp-hky-clock-nucl.param 158s qp-hky-clock-nucl.test 158s qp-hky-clock-nucl.trs 158s qp-hky-rhet-clock-nucl.log 158s qp-hky-rhet-clock-nucl.nucl 158s qp-hky-rhet-clock-nucl.param 158s qp-hky-rhet-clock-nucl.test 158s qp-hky-rhet-clock-nucl.trs 158s qp-hky-rhet-nucl.log 158s qp-hky-rhet-nucl.nucl 158s qp-hky-rhet-nucl.param 158s qp-hky-rhet-nucl.test 158s qp-hky-rhet-nucl.trs 158s qp-jtt-prot.log 158s qp-jtt-prot.param 158s qp-jtt-prot.prot 158s qp-jtt-prot.test 158s qp-jtt-prot.trs 158s qp-jtt-rhet-clock-prot.log 158s qp-jtt-rhet-clock-prot.param 158s qp-jtt-rhet-clock-prot.prot 158s qp-jtt-rhet-clock-prot.test 158s qp-jtt-rhet-clock-prot.trs 158s qp-jtt-rhet-prot.log 158s qp-jtt-rhet-prot.param 158s qp-jtt-rhet-prot.prot 158s qp-jtt-rhet-prot.test 158s qp-jtt-rhet-prot.trs 158s qp-mtrev-prot.log 158s qp-mtrev-prot.param 158s qp-mtrev-prot.prot 158s qp-mtrev-prot.test 158s qp-mtrev-prot.trs 158s qp-pure-bin.bin 158s qp-pure-bin.log 158s qp-pure-bin.param 158s qp-pure-bin.test 158s qp-pure-bin.trs 158s qp-pure-nucl.log 158s qp-pure-nucl.nucl 158s qp-pure-nucl.param 158s qp-pure-nucl.test 158s qp-pure-nucl.trs 158s qp-pure-prot.log 158s qp-pure-prot.param 158s qp-pure-prot.prot 158s qp-pure-prot.test 158s qp-pure-prot.trs 158s qp-tn-nucl.log 158s qp-tn-nucl.nucl 158s qp-tn-nucl.param 158s qp-tn-nucl.test 158s qp-tn-nucl.trs 158s qp-vt-prot.log 158s qp-vt-prot.param 158s qp-vt-prot.prot 158s qp-vt-prot.test 158s qp-vt-prot.trs 158s qp-wag-prot.log 158s qp-wag-prot.param 158s qp-wag-prot.prot 158s qp-wag-prot.test 158s qp-wag-prot.trs 158s template-test 158s test-suite.log 158s ut-pure-prot.log 158s ut-pure-prot.param 158s ut-pure-prot.prot 158s ut-pure-prot.test 158s ut-pure-prot.trees 158s ut-pure-prot.trs 158s Test 1 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-pure-bin.bin' 158s Input file: tests/qp-pure-bin.bin 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-pure-bin.bin) contains 5 sequences of length 895 158s 1. Gibbon 158s 2. Human 158s 3. Chimpanzee 158s 4. Gorilla 158s 5. Orangutan 158s (consists very likely of binary state data) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Exact maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Gibbon (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Binary states 158s m Model of substitution? Two-state model (Felsenstein 1981) 158s f Binary state frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Exact maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Gibbon (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Exact maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Gibbon (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Def.: JTT (Jones et al. 1992) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Exact maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Gibbon (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Binary states 158s m Model of substitution? Two-state model (Felsenstein 1981) 158s f Binary state frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Writing parameters to file tests/qp-pure-bin.bin.puzzle 158s Writing parameters to file tests/qp-pure-bin.bin.puzzle 158s Writing pairwise distances to file tests/qp-pure-bin.bin.dist 158s Writing parameters to file tests/qp-pure-bin.bin.puzzle 158s Writing parameters to file tests/qp-pure-bin.bin.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-pure-bin.bin.puzzle 158s Likelihood distances: tests/qp-pure-bin.bin.dist 158s Phylip tree file: tests/qp-pure-bin.bin.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 2 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-pure-nucl.nucl' 158s Input file: tests/qp-pure-nucl.nucl 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-pure-nucl.nucl) contains 8 sequences of length 116 158s 1. Thylacinus 158s 2. Sarcophilu 158s 3. Dasyurus 158s 4. Echymipera 158s 5. Trichosuru 158s 6. Phalanger 158s 7. Philander 158s 8. Bos 158s (consists very likely of nucleotides) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Optimizing missing substitution process parameters 158s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 158s Writing pairwise distances to file tests/qp-pure-nucl.nucl.dist 158s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-pure-nucl.nucl.puzzle 158s Likelihood distances: tests/qp-pure-nucl.nucl.dist 158s Phylip tree file: tests/qp-pure-nucl.nucl.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s WARNING: random seed set to 1001 for debugging! 158s Passed 158s 158s Test 3 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-tn-nucl.nucl' 158s Input file: tests/qp-tn-nucl.nucl 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-tn-nucl.nucl) contains 8 sequences of length 116 158s 1. Thylacinus 158s 2. Sarcophilu 158s 3. Dasyurus 158s 4. Echymipera 158s 5. Trichosuru 158s 6. Phalanger 158s 7. Philander 158s 8. Bos 158s (consists very likely of nucleotides) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? TN (Tamura-Nei 1993) 158s p Constrain TN model to F84 model? No 158s t Transition/transversion parameter? Estimate from data set 158s r Y/R transition parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Optimizing missing substitution process parameters 158s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 158s Writing pairwise distances to file tests/qp-tn-nucl.nucl.dist 158s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s WARNING: random seed set to 1001 for debugging! 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-tn-nucl.nucl.puzzle 158s Likelihood distances: tests/qp-tn-nucl.nucl.dist 158s Phylip tree file: tests/qp-tn-nucl.nucl.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 4 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-hky-clock-nucl.nucl' 158s Input file: tests/qp-hky-clock-nucl.nucl 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-hky-clock-nucl.nucl) contains 8 sequences of length 116 158s 1. Thylacinus 158s 2. Sarcophilu 158s 3. Dasyurus 158s 4. Echymipera 158s 5. Trichosuru 158s 6. Phalanger 158s 7. Philander 158s 8. Bos 158s (consists very likely of nucleotides) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? Yes 158s l Location of root? Best place (automatic search) 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Optimizing missing substitution process parameters 158s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 158s Writing pairwise distances to file tests/qp-hky-clock-nucl.nucl.dist 158s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s Computing maximum likelihood branch lengths (with clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-hky-clock-nucl.nucl.puzzle 158s Likelihood distances: tests/qp-hky-clock-nucl.nucl.dist 158s Phylip tree file: tests/qp-hky-clock-nucl.nucl.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 5 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-hky-rhet-nucl.nucl' 158s Input file: tests/qp-hky-rhet-nucl.nucl 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-hky-rhet-nucl.nucl) contains 8 sequences of length 116 158s 1. Thylacinus 158s 2. Sarcophilu 158s 3. Dasyurus 158s 4. Echymipera 158s 5. Trichosuru 158s 6. Phalanger 158s 7. Philander 158s 8. Bos 158s (consists very likely of nucleotides) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Gamma distributed rates 158s a Gamma distribution parameter alpha? Estimate from data set 158s c Number of Gamma rate categories? 4 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Optimizing missing substitution process parameters 158s Optimizing missing rate heterogeneity parameters 158s Optimizing missing substitution process parameters 158s Optimizing missing rate heterogeneity parameters 158s Optimizing missing substitution process parameters 158s Optimizing missing rate heterogeneity parameters 158s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 158s Writing pairwise distances to file tests/qp-hky-rhet-nucl.nucl.dist 158s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-hky-rhet-nucl.nucl.puzzle 158s Likelihood distances: tests/qp-hky-rhet-nucl.nucl.dist 158s Phylip tree file: tests/qp-hky-rhet-nucl.nucl.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 6 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-hky-rhet-clock-nucl.nucl' 158s Input file: tests/qp-hky-rhet-clock-nucl.nucl 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-hky-rhet-clock-nucl.nucl) contains 8 sequences of length 116 158s 1. Thylacinus 158s 2. Sarcophilu 158s 3. Dasyurus 158s 4. Echymipera 158s 5. Trichosuru 158s 6. Phalanger 158s 7. Philander 158s 8. Bos 158s (consists very likely of nucleotides) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? Yes 158s l Location of root? Best place (automatic search) 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? Yes 158s l Location of root? Best place (automatic search) 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Gamma distributed rates 158s a Gamma distribution parameter alpha? Estimate from data set 158s c Number of Gamma rate categories? 4 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Optimizing missing substitution process parameters 158s Optimizing missing rate heterogeneity parameters 158s Optimizing missing substitution process parameters 158s Optimizing missing rate heterogeneity parameters 158s Optimizing missing substitution process parameters 158s Optimizing missing rate heterogeneity parameters 158s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 158s Writing pairwise distances to file tests/qp-hky-rhet-clock-nucl.nucl.dist 158s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 158s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s Computing maximum likelihood branch lengths (with clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-hky-rhet-clock-nucl.nucl.puzzle 158s Likelihood distances: tests/qp-hky-rhet-clock-nucl.nucl.dist 158s Phylip tree file: tests/qp-hky-rhet-clock-nucl.nucl.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 7 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-pure-prot.prot' 158s Input file: tests/qp-pure-prot.prot 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-pure-prot.prot) contains 7 sequences of length 128 158s 1. HBB_HUMAN 158s 2. HBB_HORSE 158s 3. HBA_HUMAN 158s 4. HBA_HORSE 158s 5. MYG_PHYCA 158s 6. GLB5_PETMA 158s 7. LGB2_LUPLU 158s (consists very likely of amino acids encoded on nuclear DNA) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Writing parameters to file tests/qp-pure-prot.prot.puzzle 158s Writing parameters to file tests/qp-pure-prot.prot.puzzle 158s Writing pairwise distances to file tests/qp-pure-prot.prot.dist 158s Writing parameters to file tests/qp-pure-prot.prot.puzzle 158s Writing parameters to file tests/qp-pure-prot.prot.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-pure-prot.prot.puzzle 158s Likelihood distances: tests/qp-pure-prot.prot.dist 158s Phylip tree file: tests/qp-pure-prot.prot.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 8 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-mtrev-prot.prot' 158s Input file: tests/qp-mtrev-prot.prot 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s WARNING: random seed set to 1001 for debugging! 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-mtrev-prot.prot) contains 7 sequences of length 128 158s 1. HBB_HUMAN 158s 2. HBB_HORSE 158s 3. HBA_HUMAN 158s 4. HBA_HORSE 158s 5. MYG_PHYCA 158s 6. GLB5_PETMA 158s 7. LGB2_LUPLU 158s (consists very likely of amino acids encoded on nuclear DNA) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? JTT (Jones et al. 1992) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 158s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 158s Writing pairwise distances to file tests/qp-mtrev-prot.prot.dist 158s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 158s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-mtrev-prot.prot.puzzle 158s Likelihood distances: tests/qp-mtrev-prot.prot.dist 158s Phylip tree file: tests/qp-mtrev-prot.prot.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 9 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-vt-prot.prot' 158s Input file: tests/qp-vt-prot.prot 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-vt-prot.prot) contains 7 sequences of length 128 158s 1. HBB_HUMAN 158s 2. HBB_HORSE 158s 3. HBA_HUMAN 158s 4. HBA_HORSE 158s 5. MYG_PHYCA 158s 6. GLB5_PETMA 158s 7. LGB2_LUPLU 158s (consists very likely of amino acids encoded on nuclear DNA) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? JTT (Jones et al. 1992) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? VT (Mueller-Vingron 2000) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Writing parameters to file tests/qp-vt-prot.prot.puzzle 158s Writing parameters to file tests/qp-vt-prot.prot.puzzle 158s Writing pairwise distances to file tests/qp-vt-prot.prot.dist 158s Writing parameters to file tests/qp-vt-prot.prot.puzzle 158s Writing parameters to file tests/qp-vt-prot.prot.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-vt-prot.prot.puzzle 158s Likelihood distances: tests/qp-vt-prot.prot.dist 158s Phylip tree file: tests/qp-vt-prot.prot.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 10 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-wag-prot.prot' 158s Input file: tests/qp-wag-prot.prot 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-wag-prot.prot) contains 7 sequences of length 128 158s 1. HBB_HUMAN 158s 2. HBB_HORSE 158s 3. HBA_HUMAN 158s 4. HBA_HORSE 158s 5. MYG_PHYCA 158s 6. GLB5_PETMA 158s 7. LGB2_LUPLU 158s (consists very likely of amino acids encoded on nuclear DNA) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? JTT (Jones et al. 1992) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? VT (Mueller-Vingron 2000) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? WAG (Whelan-Goldman 2000) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Writing parameters to file tests/qp-wag-prot.prot.puzzle 158s Writing parameters to file tests/qp-wag-prot.prot.puzzle 158s Writing pairwise distances to file tests/qp-wag-prot.prot.dist 158s Writing parameters to file tests/qp-wag-prot.prot.puzzle 158s Writing parameters to file tests/qp-wag-prot.prot.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-wag-prot.prot.puzzle 158s Likelihood distances: tests/qp-wag-prot.prot.dist 158s Phylip tree file: tests/qp-wag-prot.prot.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 11 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-clock.nucl' 158s Input file: tests/qp-clock.nucl 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-clock.nucl) contains 8 sequences of length 116 158s 1. Thylacinus 158s 2. Sarcophilu 158s 3. Dasyurus 158s 4. Echymipera 158s 5. Trichosuru 158s 6. Phalanger 158s 7. Philander 158s 8. Bos 158s (consists very likely of nucleotides) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? Thylacinus (1) 158s z Compute clocklike branch lengths? Yes 158s l Location of root? Best place (automatic search) 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Optimizing missing substitution process parameters 158s Writing parameters to file tests/qp-clock.nucl.puzzle 158s Writing parameters to file tests/qp-clock.nucl.puzzle 158s Writing pairwise distances to file tests/qp-clock.nucl.dist 158s Writing parameters to file tests/qp-clock.nucl.puzzle 158s Writing parameters to file tests/qp-clock.nucl.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s Computing maximum likelihood branch lengths (with clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-clock.nucl.puzzle 158s Likelihood distances: tests/qp-clock.nucl.dist 158s Phylip tree file: tests/qp-clock.nucl.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 1.00 seconds (= 0.02 minutes = 0.00 hours) 158s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 158s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 158s Passed 158s 158s Test 12 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-jtt-prot.prot' 158s Input file: tests/qp-jtt-prot.prot 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s WARNING: random seed set to 1001 for debugging! 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-jtt-prot.prot) contains 7 sequences of length 128 158s 1. HBB_HUMAN 158s 2. HBB_HORSE 158s 3. HBA_HUMAN 158s 4. HBA_HORSE 158s 5. MYG_PHYCA 158s 6. GLB5_PETMA 158s 7. LGB2_LUPLU 158s (consists very likely of amino acids encoded on nuclear DNA) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? JTT (Jones et al. 1992) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 158s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 158s Writing pairwise distances to file tests/qp-jtt-prot.prot.dist 158s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 158s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 158s Computing quartet maximum likelihood trees 158s Computing quartet puzzling trees 158s Computing maximum likelihood branch lengths (without clock) 158s 158s All results written to disk: 158s Puzzle report file: tests/qp-jtt-prot.prot.puzzle 158s Likelihood distances: tests/qp-jtt-prot.prot.dist 158s Phylip tree file: tests/qp-jtt-prot.prot.tree 158s 158s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 158s Passed 158s 158s Test 13 158s WARNING: random seed set to 1001 for debugging! 158s 158s 158s 158s WELCOME TO TREE-PUZZLE 5.3.rc16! 158s 158s 158s 158s argv[1] = '-randseed1001' 158s argv[2] = 'tests/qp-jtt-rhet-prot.prot' 158s Input file: tests/qp-jtt-rhet-prot.prot 158s Using SPRNG -- Scalable Parallel Random Number Generator 158s RANDOM SEED: 1001 158s 158s Input data set (tests/qp-jtt-rhet-prot.prot) contains 7 sequences of length 128 158s 1. HBB_HUMAN 158s 2. HBB_HORSE 158s 3. HBA_HUMAN 158s 4. HBA_HORSE 158s 5. MYG_PHYCA 158s 6. GLB5_PETMA 158s 7. LGB2_LUPLU 158s (consists very likely of amino acids encoded on nuclear DNA) 158s 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Auto: Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Nucleotides 158s m Model of substitution? HKY (Hasegawa et al. 1985) 158s t Transition/transversion parameter? Estimate from data set 158s f Nucleotide frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? JTT (Jones et al. 1992) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Uniform rate 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s 158s 158s GENERAL OPTIONS 158s b Type of analysis? Tree reconstruction 158s k Tree search procedure? Quartet puzzling 158s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 158s n Number of puzzling steps? 1000 158s o Display as outgroup? HBB_HUMAN (1) 158s z Compute clocklike branch lengths? No 158s e Parameter estimates? Approximate (faster) 158s x Parameter estimation uses? Neighbor-joining tree 158s OUTPUT OPTIONS 158s 9 List puzzling trees/splits (NEXUS)? No 158s u List unresolved quartets? No 158s j List puzzling step trees? No 158s SUBSTITUTION PROCESS 158s d Type of sequence input data? Amino acids 158s m Model of substitution? JTT (Jones et al. 1992) 158s f Amino acid frequencies? Estimate from data set 158s RATE HETEROGENEITY 158s w Model of rate heterogeneity? Gamma distributed rates 158s a Gamma distribution parameter alpha? Estimate from data set 158s c Number of Gamma rate categories? 4 158s 158s Quit [q], confirm [y], or change [menu] settings: 158s Optimizing missing rate heterogeneity parameters 159s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 159s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 159s Writing pairwise distances to file tests/qp-jtt-rhet-prot.prot.dist 159s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 159s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 159s Computing quartet maximum likelihood trees 159s Computing quartet puzzling trees 159s Computing maximum likelihood branch lengths (without clock) 159s 159s All results written to disk: 159s Puzzle report file: tests/qp-jtt-rhet-prot.prot.puzzle 159s Likelihood distances: tests/qp-jtt-rhet-prot.prot.dist 159s Phylip tree file: tests/qp-jtt-rhet-prot.prot.tree 159s 159s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s WARNING: random seed set to 1001 for debugging! 159s Passed 159s 159s Test 14 159s 159s 159s 159s WELCOME TO TREE-PUZZLE 5.3.rc16! 159s 159s 159s 159s argv[1] = '-randseed1001' 159s argv[2] = 'tests/qp-jtt-rhet-clock-prot.prot' 159s Input file: tests/qp-jtt-rhet-clock-prot.prot 159s Using SPRNG -- Scalable Parallel Random Number Generator 159s RANDOM SEED: 1001 159s 159s Input data set (tests/qp-jtt-rhet-clock-prot.prot) contains 7 sequences of length 128 159s 1. HBB_HUMAN 159s 2. HBB_HORSE 159s 3. HBA_HUMAN 159s 4. HBA_HORSE 159s 5. MYG_PHYCA 159s 6. GLB5_PETMA 159s 7. LGB2_LUPLU 159s (consists very likely of amino acids encoded on nuclear DNA) 159s 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Auto: Amino acids 159s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Nucleotides 159s m Model of substitution? HKY (Hasegawa et al. 1985) 159s t Transition/transversion parameter? Estimate from data set 159s f Nucleotide frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Amino acids 159s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Amino acids 159s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Amino acids 159s m Model of substitution? JTT (Jones et al. 1992) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? Yes 159s l Location of root? Best place (automatic search) 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Amino acids 159s m Model of substitution? JTT (Jones et al. 1992) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? Yes 159s l Location of root? Best place (automatic search) 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Amino acids 159s m Model of substitution? JTT (Jones et al. 1992) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Gamma distributed rates 159s a Gamma distribution parameter alpha? Estimate from data set 159s c Number of Gamma rate categories? 4 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s Optimizing missing rate heterogeneity parameters 159s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 159s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 159s Writing pairwise distances to file tests/qp-jtt-rhet-clock-prot.prot.dist 159s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 159s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 159s Computing quartet maximum likelihood trees 159s Computing quartet puzzling trees 159s Computing maximum likelihood branch lengths (without clock) 159s Computing maximum likelihood branch lengths (with clock) 159s 159s All results written to disk: 159s Puzzle report file: tests/qp-jtt-rhet-clock-prot.prot.puzzle 159s Likelihood distances: tests/qp-jtt-rhet-clock-prot.prot.dist 159s Phylip tree file: tests/qp-jtt-rhet-clock-prot.prot.tree 159s 159s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s Passed 159s 159s Test 15 159s WARNING: random seed set to 1001 for debugging! 159s 159s 159s 159s WELCOME TO TREE-PUZZLE 5.3.rc16! 159s 159s 159s 159s argv[1] = '-randseed1001' 159s argv[2] = 'tests/lm-pure-prot.prot' 159s Input file: tests/lm-pure-prot.prot 159s Using SPRNG -- Scalable Parallel Random Number Generator 159s RANDOM SEED: 1001 159s 159s Input data set (tests/lm-pure-prot.prot) contains 7 sequences of length 128 159s 1. HBB_HUMAN 159s 2. HBB_HORSE 159s 3. HBA_HUMAN 159s 4. HBA_HORSE 159s 5. MYG_PHYCA 159s 6. GLB5_PETMA 159s 7. LGB2_LUPLU 159s (consists very likely of amino acids encoded on nuclear DNA) 159s 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Auto: Amino acids 159s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Nucleotides 159s m Model of substitution? HKY (Hasegawa et al. 1985) 159s t Transition/transversion parameter? Estimate from data set 159s f Nucleotide frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Tree reconstruction 159s k Tree search procedure? Quartet puzzling 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s n Number of puzzling steps? 1000 159s o Display as outgroup? HBB_HUMAN (1) 159s z Compute clocklike branch lengths? No 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s OUTPUT OPTIONS 159s 9 List puzzling trees/splits (NEXUS)? No 159s u List unresolved quartets? No 159s j List puzzling step trees? No 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Amino acids 159s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: 159s 159s 159s GENERAL OPTIONS 159s b Type of analysis? Likelihood mapping 159s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 159s g Group sequences in clusters? No 159s n Number of quartets? 35 (all possible) 159s e Parameter estimates? Approximate (faster) 159s x Parameter estimation uses? Neighbor-joining tree 159s SUBSTITUTION PROCESS 159s d Type of sequence input data? Amino acids 159s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 159s f Amino acid frequencies? Estimate from data set 159s RATE HETEROGENEITY 159s w Model of rate heterogeneity? Uniform rate 159s 159s Quit [q], confirm [y], or change [menu] settings: PPP1: 0 (./puzzle1.c:8696) 159s 159s Writing parameters to file tests/lm-pure-prot.prot.puzzle 159s Writing parameters to file tests/lm-pure-prot.prot.puzzle 159s Writing pairwise distances to file tests/lm-pure-prot.prot.dist 159s Writing parameters to file tests/lm-pure-prot.prot.puzzle 159s Writing parameters to file tests/lm-pure-prot.prot.puzzle 159s Performing likelihood mapping analysis 159s 159s All results written to disk: 159s Puzzle report file: tests/lm-pure-prot.prot.puzzle 159s Likelihood distances: tests/lm-pure-prot.prot.dist 159s Likelihood mapping diagram (EPS): tests/lm-pure-prot.prot.eps 159s Likelihood mapping diagram (SVG): tests/lm-pure-prot.prot.svg 159s 159s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 159s PPP1: 1 (./puzzle1.c:8702) 159s Passed 159s 159s autopkgtest [23:33:17]: test run-unit-test: -----------------------] 160s run-unit-test PASS 160s autopkgtest [23:33:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 160s autopkgtest [23:33:18]: @@@@@@@@@@@@@@@@@@@@ summary 160s run-unit-test PASS 176s nova [W] Skipping flock for amd64 176s Creating nova instance adt-plucky-amd64-tree-puzzle-20250315-233037-juju-7f2275-prod-proposed-migration-environment-15-13f3a586-6d53-46c5-8651-13105428a129 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 176s nova [W] Timed out waiting for 8c03d58e-5380-4400-8b2e-959e88d090dd to get deleted.