0s autopkgtest [02:24:43]: starting date and time: 2024-03-14 02:24:43+0000 0s autopkgtest [02:24:43]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [02:24:43]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7rpyzacz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:boost1.83,src:openmpi,src:pmix --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=boost1.83/1.83.0-2.1ubuntu2 openmpi/4.1.6-5.1ubuntu3 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-6.secgroup --name adt-noble-ppc64el-shapeit4-20240314-022442-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 588s autopkgtest [02:34:31]: testbed dpkg architecture: ppc64el 589s autopkgtest [02:34:32]: testbed apt version: 2.7.12 589s autopkgtest [02:34:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 589s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 590s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2835 kB] 590s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 590s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [448 kB] 590s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [45.5 kB] 590s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [595 kB] 590s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 590s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 590s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 590s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3189 kB] 591s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 591s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [41.2 kB] 591s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 594s Fetched 7290 kB in 2s (2929 kB/s) 594s Reading package lists... 595s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 596s Reading package lists... 603s Reading package lists... 603s Building dependency tree... 603s Reading state information... 603s Calculating upgrade... 604s The following packages will be upgraded: 604s console-setup console-setup-linux keyboard-configuration 604s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 604s Need to get 2202 kB of archives. 604s After this operation, 2048 B of additional disk space will be used. 604s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el console-setup-linux all 1.226ubuntu1 [1880 kB] 604s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el console-setup all 1.226ubuntu1 [110 kB] 604s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el keyboard-configuration all 1.226ubuntu1 [212 kB] 605s Preconfiguring packages ... 605s Fetched 2202 kB in 1s (3163 kB/s) 605s (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 ... 70112 files and directories currently installed.) 605s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 605s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 605s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 605s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 605s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 605s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 605s Setting up keyboard-configuration (1.226ubuntu1) ... 606s Your console font configuration will be updated the next time your system 606s boots. If you want to update it now, run 'setupcon' from a virtual console. 606s update-initramfs: deferring update (trigger activated) 606s Setting up console-setup-linux (1.226ubuntu1) ... 608s Setting up console-setup (1.226ubuntu1) ... 609s update-initramfs: deferring update (trigger activated) 609s Processing triggers for man-db (2.12.0-3) ... 610s Processing triggers for initramfs-tools (0.142ubuntu20) ... 610s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 610s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 616s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 616s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 616s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 616s Reading package lists... 617s Building dependency tree... 617s Reading state information... 617s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 617s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 618s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 618s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 618s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 618s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 623s Reading package lists... 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 623s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 623s Reading package lists... 624s Building dependency tree... 624s Reading state information... 624s Calculating upgrade... 624s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 624s Reading package lists... 624s Building dependency tree... 624s Reading state information... 625s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 625s autopkgtest [02:35:08]: rebooting testbed after setup commands that affected boot 817s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 830s autopkgtest [02:38:33]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 833s autopkgtest [02:38:36]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 839s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (dsc) [2158 B] 839s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (tar) [59.0 MB] 839s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build1 (diff) [5280 B] 839s gpgv: Signature made Tue Dec 19 15:03:10 2023 UTC 839s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 839s gpgv: Can't check signature: No public key 839s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build1.dsc: no acceptable signature found 841s autopkgtest [02:38:44]: testing package shapeit4 version 4.2.2+dfsg-1build1 841s autopkgtest [02:38:44]: build not needed 965s autopkgtest [02:40:48]: test run-sample-analysis: preparing testbed 968s Reading package lists... 968s Building dependency tree... 968s Reading state information... 968s Starting pkgProblemResolver with broken count: 0 968s Starting 2 pkgProblemResolver with broken count: 0 968s Done 969s The following additional packages will be installed: 969s libboost-iostreams1.83.0 libboost-program-options1.83.0 libdeflate0 libhts3 969s libhtscodecs2 shapeit4 shapeit4-example 969s The following NEW packages will be installed: 969s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 969s libdeflate0 libhts3 libhtscodecs2 shapeit4 shapeit4-example 969s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 969s Need to get 53.8 MB/53.8 MB of archives. 969s After this operation, 59.8 MB of additional disk space will be used. 969s Get:1 /tmp/autopkgtest.3rTAJH/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 969s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2.1ubuntu2 [259 kB] 969s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2.1ubuntu2 [328 kB] 969s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 969s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 969s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 969s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build1 [186 kB] 970s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build1 [52.3 MB] 971s Fetched 53.8 MB in 2s (23.4 MB/s) 971s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 972s (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 ... 70112 files and directories currently installed.) 972s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2.1ubuntu2_ppc64el.deb ... 972s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu2) ... 972s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 972s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2.1ubuntu2_ppc64el.deb ... 972s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu2) ... 972s Selecting previously unselected package libdeflate0:ppc64el. 972s Preparing to unpack .../2-libdeflate0_1.19-1_ppc64el.deb ... 972s Unpacking libdeflate0:ppc64el (1.19-1) ... 972s Selecting previously unselected package libhtscodecs2:ppc64el. 972s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 972s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 972s Selecting previously unselected package libhts3:ppc64el. 972s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 972s Unpacking libhts3:ppc64el (1.18+ds-1) ... 972s Selecting previously unselected package shapeit4. 972s Preparing to unpack .../5-shapeit4_4.2.2+dfsg-1build1_ppc64el.deb ... 972s Unpacking shapeit4 (4.2.2+dfsg-1build1) ... 972s Selecting previously unselected package shapeit4-example. 972s Preparing to unpack .../6-shapeit4-example_4.2.2+dfsg-1build1_all.deb ... 972s Unpacking shapeit4-example (4.2.2+dfsg-1build1) ... 972s Selecting previously unselected package autopkgtest-satdep. 972s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 972s Unpacking autopkgtest-satdep (0) ... 972s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 972s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu2) ... 972s Setting up libdeflate0:ppc64el (1.19-1) ... 972s Setting up shapeit4-example (4.2.2+dfsg-1build1) ... 972s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu2) ... 972s Setting up libhts3:ppc64el (1.18+ds-1) ... 972s Setting up shapeit4 (4.2.2+dfsg-1build1) ... 972s Setting up autopkgtest-satdep (0) ... 972s Processing triggers for man-db (2.12.0-3) ... 973s Processing triggers for libc-bin (2.39-0ubuntu2) ... 976s (Reading database ... 70174 files and directories currently installed.) 976s Removing autopkgtest-satdep (0) ... 977s autopkgtest [02:41:00]: test run-sample-analysis: [----------------------- 977s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 977s 977s SHAPEIT 977s * Author : Olivier DELANEAU, University of Lausanne 977s * Contact : olivier.delaneau@gmail.com 977s * Version : 4.2.2 977s * Run date : 14/03/2024 - 02:41:00 977s 977s Files: 977s * Input VCF : [unphased.vcf.gz] 977s * Genetic Map : [chr20.b37.gmap.gz] 977s * Output VCF : [phased.vcf.gz] 977s 977s Parameters: 977s * Seed : 15052011 977s * Threads : 4 threads 977s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 977s * PBWT : Depth of PBWT neighbours to condition on: 4 977s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 977s * HMM : K is variable / min W is 2.50cM / Ne is 15000 977s * HMM : Recombination rates given by genetic map 977s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 977s 977s Initialization: 977s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.13s) 977s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * 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PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.01s) 988s * C2H transpose (0.00s) 992s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM 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[K=210.374+/-15.642 / W=1.00Mb] (2.04s) 1013s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1013s * HAP update (0.01s) 1013s * H2V transpose (0.00s) 1013s 1013s Main iteration [3/5] 1013s * V2H transpose (0.00s) 1013s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection 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HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=207.384+/-15.777 / W=1.00Mb] (2.04s) 1017s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1017s * HAP update (0.01s) 1017s * H2V transpose (0.00s) 1017s 1017s Main iteration [5/5] 1017s * V2H transpose (0.00s) 1017s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * 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HMM computations [44%] * HMM computations [45%] * HMM computations [46%] * HMM computations [47%] * HMM computations [48%] * HMM computations [49%] * HMM computations [50%] * HMM computations [51%] * HMM computations [52%] * HMM computations [53%] * HMM computations [54%] * HMM computations [55%] * HMM computations [56%] * HMM computations [57%] * HMM computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=207.256+/-16.581 / W=1.00Mb] (2.02s) 1019s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1019s * HAP update (0.01s) 1019s * H2V transpose (0.00s) 1019s 1019s Finalization: 1019s * HAP solving (0.02s) 1019s * HAP update (0.01s) 1019s * H2V transpose (0.00s) 1019s * VCF writing [0%] * VCF writing [1%] * VCF writing [2%] * VCF writing [3%] * VCF writing [4%] * VCF writing [5%] * VCF writing [6%] * VCF writing [7%] * VCF writing [8%] * VCF writing [9%] * VCF writing [10%] * VCF writing [11%] * VCF writing [12%] * VCF writing [13%] * VCF writing [14%] * VCF writing [15%] * VCF writing [16%] * VCF writing [17%] * VCF writing [18%] * VCF writing [19%] * VCF writing [20%] * VCF writing [21%] * VCF writing [22%] * VCF writing [23%] * VCF writing [24%] * VCF writing [25%] * VCF writing [26%] * VCF writing [27%] * VCF writing [28%] * VCF writing [29%] * VCF writing [30%] * VCF writing [31%] * VCF writing [32%] * VCF writing [33%] * VCF writing [34%] * VCF writing [35%] * VCF writing [36%] * VCF writing [37%] * VCF writing [38%] * VCF writing [39%] * VCF writing [40%] * VCF writing [41%] * VCF writing [42%] * VCF writing [43%] * VCF writing [44%] * VCF writing [45%] * VCF writing [46%] * VCF writing [47%] * VCF writing [48%] * VCF writing [49%] * VCF writing [50%] * VCF writing [51%] * VCF writing [52%] * VCF writing [53%] * VCF writing [54%] * VCF writing [55%] * VCF writing [56%] * VCF writing [57%] * VCF writing [58%] * VCF writing [59%] * VCF writing [60%] * VCF writing [61%] * VCF writing [62%] * VCF writing [63%] * VCF writing [64%] * VCF writing [65%] * VCF writing [66%] * VCF writing [67%] * VCF writing [68%] * VCF writing [69%] * VCF writing [70%] * VCF writing [71%] * VCF writing [72%] * VCF writing [73%] * VCF writing [74%] * VCF writing [75%] * VCF writing [76%] * VCF writing [77%] * VCF writing [78%] * VCF writing [79%] * VCF writing [80%] * VCF writing [81%] * VCF writing [82%] * VCF writing [83%] * VCF writing [84%] * VCF writing [85%] * VCF writing [86%] * VCF writing [87%] * VCF writing [88%] * VCF writing [89%] * VCF writing [90%] * VCF writing [91%] * VCF writing [92%] * VCF writing [93%] * VCF writing [94%] * VCF writing [95%] * VCF writing [96%] * VCF writing [97%] * VCF writing [98%] * VCF writing [99%] * VCF writing [100%] * VCF writing [Compressed / N=203 / L=8651] (0.22s) 1019s * Total running time = 42 seconds 1019s + shapeit4 --input unphased.bcf --map chr20.b37.gmap.gz --region 20 --reference reference.bcf --scaffold scaffold.bcf --use-PS 0.0001 --thread 4 --log phased.log --output phased.bcf 1019s 1019s SHAPEIT 1019s * Author : Olivier DELANEAU, University of Lausanne 1019s * Contact : olivier.delaneau@gmail.com 1019s * Version : 4.2.2 1019s * Run date : 14/03/2024 - 02:41:42 1019s 1019s Files: 1019s * Input VCF : [unphased.bcf] 1019s * Reference VCF : [reference.bcf] 1019s * Scaffold VCF : [scaffold.bcf] 1019s * Genetic Map : [chr20.b37.gmap.gz] 1019s * Output VCF : [phased.bcf] 1019s * Output LOG : [phased.log] 1019s 1019s Parameters: 1019s * Seed : 15052011 1019s * Threads : 4 threads 1019s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 1019s * PBWT : Depth of PBWT neighbours to condition on: 4 1019s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 1019s * HMM : K is variable / min W is 2.50cM / Ne is 15000 1019s * HMM : Recombination rates given by genetic map 1019s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 1019s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 1019s 1019s Initialization: 1019s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.10s) 1020s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF parsing [4%] * VCF/BCF parsing [5%] * VCF/BCF parsing [6%] * VCF/BCF parsing [7%] * VCF/BCF parsing [8%] * VCF/BCF parsing [9%] * VCF/BCF parsing [10%] * VCF/BCF parsing [11%] * VCF/BCF parsing [12%] * VCF/BCF parsing [13%] * VCF/BCF parsing [14%] * VCF/BCF parsing [15%] * VCF/BCF parsing [16%] * VCF/BCF parsing [17%] * VCF/BCF parsing [18%] * VCF/BCF parsing [19%] * VCF/BCF parsing [20%] * VCF/BCF parsing [21%] * VCF/BCF parsing [22%] * VCF/BCF parsing [23%] * VCF/BCF parsing [24%] * VCF/BCF parsing [25%] * VCF/BCF parsing [26%] * VCF/BCF parsing [27%] * VCF/BCF parsing [28%] * VCF/BCF parsing [29%] * VCF/BCF parsing [30%] * VCF/BCF parsing [31%] * VCF/BCF parsing [32%] * VCF/BCF parsing [33%] * VCF/BCF parsing [34%] * VCF/BCF parsing [35%] * VCF/BCF parsing [36%] * VCF/BCF parsing [37%] * VCF/BCF parsing [38%] * VCF/BCF parsing [39%] * VCF/BCF parsing [40%] * VCF/BCF parsing [41%] * VCF/BCF parsing [42%] * VCF/BCF parsing [43%] * VCF/BCF parsing [44%] * VCF/BCF parsing [45%] * VCF/BCF parsing [46%] * VCF/BCF parsing [47%] * VCF/BCF parsing [48%] * VCF/BCF parsing [49%] * VCF/BCF parsing [50%] * VCF/BCF parsing [51%] * VCF/BCF parsing [52%] * VCF/BCF parsing [53%] * VCF/BCF parsing [54%] * VCF/BCF parsing [55%] * VCF/BCF parsing [56%] * VCF/BCF parsing [57%] * VCF/BCF parsing [58%] * VCF/BCF parsing [59%] * VCF/BCF parsing [60%] * VCF/BCF parsing [61%] * VCF/BCF parsing [62%] * VCF/BCF parsing [63%] * VCF/BCF parsing [64%] * VCF/BCF parsing [65%] * VCF/BCF parsing [66%] * VCF/BCF parsing [67%] * VCF/BCF parsing [68%] * VCF/BCF parsing [69%] * VCF/BCF parsing [70%] * VCF/BCF parsing [71%] * VCF/BCF parsing [72%] * VCF/BCF parsing [73%] * VCF/BCF parsing [74%] * VCF/BCF parsing [75%] * VCF/BCF parsing [76%] * VCF/BCF parsing [77%] * VCF/BCF parsing [78%] * VCF/BCF parsing [79%] * VCF/BCF parsing [80%] * VCF/BCF parsing [81%] * VCF/BCF parsing [82%] * VCF/BCF parsing [83%] * VCF/BCF parsing [84%] * VCF/BCF parsing [85%] * VCF/BCF parsing [86%] * VCF/BCF parsing [87%] * VCF/BCF parsing [88%] * VCF/BCF parsing [89%] * VCF/BCF parsing [90%] * VCF/BCF parsing [91%] * VCF/BCF parsing [92%] * VCF/BCF parsing [93%] * VCF/BCF parsing [94%] * VCF/BCF parsing [95%] * VCF/BCF parsing [96%] * VCF/BCF parsing [97%] * VCF/BCF parsing [98%] * VCF/BCF parsing [99%] * VCF/BCF parsing [100%] * VCF/BCF parsing [Hom=90.0% / Het=10.0% / Pha=2.668% / Sca=0.778% / Mis=0.0%] (0.37s) 1020s * GMAP parsing [n=82962] (0.07s) 1020s * cM interpolation [s=3296 / i=21694] (0.00s) 1020s * Region length [2999624 bp / 6.6 cM] 1020s * HMM parameters [Ne=15000 / Error=0.0001 / #rare=9606] 1020s * PBWT indexing [l=328] (0.00s) 1020s * HAP update (0.04s) 1020s * H2V transpose (0.01s) 1020s * PBWT phase sweep [0%] * PBWT phase sweep [1%] * PBWT phase sweep [2%] * PBWT phase sweep [3%] * PBWT phase sweep [4%] * PBWT phase sweep [5%] * PBWT phase sweep [6%] * PBWT phase sweep [7%] * PBWT phase sweep [8%] * PBWT phase sweep [9%] * PBWT phase sweep [10%] * PBWT phase sweep [11%] * PBWT phase sweep [12%] * PBWT phase sweep [13%] * PBWT phase sweep [14%] * PBWT phase sweep [15%] * PBWT phase sweep [16%] * PBWT phase sweep [17%] * PBWT phase sweep [18%] * PBWT phase sweep [19%] * PBWT phase sweep [20%] * PBWT phase sweep [21%] * PBWT phase sweep [22%] * PBWT phase sweep [23%] * PBWT phase sweep [24%] * PBWT phase sweep [25%] * PBWT phase sweep [26%] * PBWT phase sweep [27%] * PBWT phase sweep [28%] * PBWT phase sweep [29%] * PBWT phase sweep [30%] * PBWT phase sweep [31%] * PBWT phase sweep [32%] * PBWT phase sweep [33%] * PBWT phase sweep [34%] * PBWT phase sweep [35%] * PBWT phase sweep [36%] * PBWT phase sweep [37%] * PBWT phase sweep [38%] * PBWT phase sweep [39%] * PBWT phase sweep [40%] * PBWT phase sweep [41%] * PBWT 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phase sweep [82%] * PBWT phase sweep [83%] * PBWT phase sweep [84%] * PBWT phase sweep [85%] * PBWT phase sweep [86%] * PBWT phase sweep [87%] * PBWT phase sweep [88%] * PBWT phase sweep [89%] * PBWT phase sweep [90%] * PBWT phase sweep [91%] * PBWT phase sweep [92%] * PBWT phase sweep [93%] * PBWT phase sweep [94%] * PBWT phase sweep [95%] * PBWT phase sweep [96%] * PBWT phase sweep [97%] * PBWT phase sweep [98%] * PBWT phase sweep [99%] * PBWT phase sweep [100%] * PBWT phase sweep (0.28s) 1020s * Build genotype graphs [seg=164449] (0.08s) 1020s 1020s Burn-in iteration [1/5] 1020s * V2H transpose (0.00s) 1020s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] 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selection [60%] * PBWT selection [61%] * PBWT selection [62%] * PBWT selection [63%] * PBWT selection [64%] * PBWT selection [65%] * PBWT selection [66%] * PBWT selection [67%] * PBWT selection [68%] * PBWT selection [69%] * PBWT selection [70%] * PBWT selection [71%] * PBWT selection [72%] * PBWT selection [73%] * PBWT selection [74%] * PBWT selection [75%] * PBWT selection [76%] * PBWT selection [77%] * PBWT selection [78%] * PBWT selection [79%] * PBWT selection [80%] * PBWT selection [81%] * PBWT selection [82%] * PBWT selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.06s) 1020s * C2H transpose (0.00s) 1041s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations [38%] * HMM computations [39%] * HMM 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computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=572.615+/-106.722 / W=2.21Mb] (20.39s) 1041s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1041s * HAP update (0.01s) 1041s * H2V transpose (0.00s) 1041s 1041s Burn-in iteration [2/5] 1041s * V2H transpose (0.00s) 1041s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * PBWT selection [38%] * PBWT selection [39%] * PBWT selection [40%] * PBWT selection [41%] * PBWT selection [42%] * PBWT selection [43%] * PBWT selection [44%] * PBWT selection [45%] * PBWT selection [46%] * PBWT selection [47%] * PBWT selection [48%] * PBWT selection [49%] * PBWT selection [50%] * PBWT selection [51%] * PBWT selection [52%] * PBWT 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[96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 1041s * C2H transpose (0.00s) 1057s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] 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PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.05s) 1057s * C2H transpose (0.00s) 1073s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations 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transpose (0.00s) 1073s 1073s Burn-in iteration [4/5] 1073s * V2H transpose (0.00s) 1073s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * PBWT selection [38%] * PBWT selection [39%] 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selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 1073s * C2H transpose (0.00s) 1089s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM 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computations [K=430.532+/-116.773 / W=2.28Mb] (15.82s) 1089s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1089s * HAP update (0.01s) 1089s * H2V transpose (0.00s) 1089s 1089s Burn-in iteration [5/5] 1089s * V2H transpose (0.00s) 1089s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * 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HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=441.034+/-115.742 / W=2.32Mb] (16.99s) 1122s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1122s * HAP update (0.02s) 1122s * H2V transpose (0.00s) 1122s * Trimming [pc=42.03%] 1122s 1122s Burn-in iteration [1/1] 1122s * V2H transpose (0.00s) 1122s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT 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computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=421.502+/-122.735 / W=2.18Mb] (13.31s) 1135s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1135s * HAP update (0.01s) 1135s * H2V transpose (0.00s) 1135s 1135s Pruning iteration [1/1] 1135s * V2H transpose (0.00s) 1135s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT 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PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 1135s * C2H transpose (0.00s) 1149s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM 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computations [K=395.698+/-115.057 / W=2.19Mb] (11.26s) 1171s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1171s * HAP update (0.01s) 1171s * H2V transpose (0.00s) 1171s * Trimming [pc=78.16%] 1171s 1171s Main iteration [1/5] 1171s * V2H transpose (0.00s) 1171s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] 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selection [75%] * PBWT selection [76%] * PBWT selection [77%] * PBWT selection [78%] * PBWT selection [79%] * PBWT selection [80%] * PBWT selection [81%] * PBWT selection [82%] * PBWT selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.05s) 1171s * C2H transpose (0.00s) 1182s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM 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computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=404.522+/-114.012 / W=2.24Mb] (10.45s) 1182s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1182s * HAP update (0.01s) 1182s * H2V transpose (0.00s) 1182s 1182s Main iteration [2/5] 1182s * V2H transpose (0.00s) 1182s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT 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PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.05s) 1202s * C2H transpose (0.00s) 1212s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * 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HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=398.535+/-111.578 / W=2.25Mb] (10.25s) 1212s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1212s * HAP update (0.01s) 1212s * H2V transpose (0.00s) 1212s 1212s Main iteration [5/5] 1212s * V2H transpose (0.00s) 1213s * PBWT selection [0%] * PBWT selection [1%] * PBWT selection [2%] * PBWT selection [3%] * PBWT selection [4%] * PBWT selection [5%] * PBWT selection [6%] * PBWT selection [7%] * PBWT selection [8%] * PBWT selection [9%] * PBWT selection [10%] * PBWT selection [11%] * PBWT selection [12%] * PBWT selection [13%] * PBWT selection [14%] * PBWT selection [15%] * PBWT selection [16%] * PBWT selection [17%] * PBWT selection [18%] * PBWT selection [19%] * PBWT selection [20%] * PBWT selection [21%] * PBWT selection [22%] * PBWT selection [23%] * PBWT selection [24%] * PBWT selection [25%] * PBWT selection [26%] * PBWT selection [27%] * PBWT selection [28%] * PBWT selection [29%] * PBWT selection [30%] * PBWT selection [31%] * PBWT selection [32%] * PBWT selection [33%] * PBWT selection [34%] * PBWT selection [35%] * PBWT selection [36%] * PBWT selection [37%] * PBWT selection [38%] * PBWT selection [39%] * PBWT selection [40%] * PBWT selection [41%] * PBWT selection [42%] * PBWT selection [43%] * PBWT selection [44%] * PBWT selection [45%] * PBWT selection [46%] * PBWT selection [47%] * PBWT selection [48%] * PBWT selection [49%] * PBWT selection [50%] * PBWT selection [51%] * PBWT selection [52%] * PBWT selection [53%] * PBWT selection [54%] * PBWT selection [55%] * PBWT selection [56%] * PBWT selection [57%] * PBWT selection [58%] * PBWT selection [59%] * PBWT selection [60%] * PBWT selection [61%] * PBWT selection [62%] * PBWT selection [63%] * PBWT selection [64%] * PBWT selection [65%] * PBWT selection [66%] * PBWT selection [67%] * PBWT selection [68%] * PBWT selection [69%] * PBWT selection [70%] * PBWT selection [71%] * PBWT selection [72%] * PBWT selection [73%] * PBWT selection [74%] * PBWT selection [75%] * PBWT selection [76%] * PBWT selection [77%] * PBWT selection [78%] * PBWT selection [79%] * PBWT selection [80%] * PBWT selection [81%] * PBWT selection [82%] * PBWT selection [83%] * PBWT selection [84%] * PBWT selection [85%] * PBWT selection [86%] * PBWT selection [87%] * PBWT selection [88%] * PBWT selection [89%] * PBWT selection [90%] * PBWT selection [91%] * PBWT selection [92%] * PBWT selection [93%] * PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.05s) 1214s * C2H transpose (0.00s) 1223s * HMM computations [0%] * HMM computations [1%] * HMM computations [2%] * HMM computations [3%] * HMM computations [4%] * HMM computations [5%] * HMM computations [6%] * HMM computations [7%] * HMM computations [8%] * HMM computations [9%] * HMM computations [10%] * HMM computations [11%] * HMM computations [12%] * HMM computations [13%] * HMM computations [14%] * HMM computations [15%] * HMM computations [16%] * HMM computations [17%] * HMM computations [18%] * HMM computations [19%] * HMM computations [20%] * HMM computations [21%] * HMM computations [22%] * HMM computations [23%] * HMM computations [24%] * HMM computations [25%] * HMM computations [26%] * HMM computations [27%] * HMM computations [28%] * HMM computations [29%] * HMM computations [30%] * HMM computations [31%] * HMM computations [32%] * HMM computations [33%] * HMM computations [34%] * HMM computations [35%] * HMM computations [36%] * HMM computations [37%] * HMM computations [38%] * HMM computations [39%] * HMM computations [40%] * HMM computations [41%] * HMM computations [42%] * HMM computations [43%] * HMM computations [44%] * HMM computations [45%] * HMM computations [46%] * HMM computations [47%] * HMM computations [48%] * HMM computations [49%] * HMM computations [50%] * HMM computations [51%] * HMM computations [52%] * HMM computations [53%] * HMM computations [54%] * HMM computations [55%] * HMM computations [56%] * HMM computations [57%] * HMM computations [58%] * HMM computations [59%] * HMM computations [60%] * HMM computations [61%] * HMM computations [62%] * HMM computations [63%] * HMM computations [64%] * HMM computations [65%] * HMM computations [66%] * HMM computations [67%] * HMM computations [68%] * HMM computations [69%] * HMM computations [70%] * HMM computations [71%] * HMM computations [72%] * HMM computations [73%] * HMM computations [74%] * HMM computations [75%] * HMM computations [76%] * HMM computations [77%] * HMM computations [78%] * HMM computations [79%] * HMM computations [80%] * HMM computations [81%] * HMM computations [82%] * HMM computations [83%] * HMM computations [84%] * HMM computations [85%] * HMM computations [86%] * HMM computations [87%] * HMM computations [88%] * HMM computations [89%] * HMM computations [90%] * HMM computations [91%] * HMM computations [92%] * HMM computations [93%] * HMM computations [94%] * HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=410.676+/-107.236 / W=2.35Mb] (10.38s) 1223s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 1223s * HAP update (0.01s) 1223s * H2V transpose (0.00s) 1223s 1223s Finalization: 1223s * HAP solving (0.04s) 1223s * HAP update (0.01s) 1223s * H2V transpose (0.00s) 1223s * VCF writing [0%] * VCF writing [1%] * VCF writing [2%] * VCF writing [3%] * VCF writing [4%] * VCF writing [5%] * VCF writing [6%] * VCF writing [7%] * VCF writing [8%] * VCF writing [9%] * VCF writing [10%] * VCF writing [11%] * VCF writing [12%] * VCF writing [13%] * VCF writing [14%] * VCF writing [15%] * VCF writing [16%] * VCF writing [17%] * VCF writing [18%] * VCF writing [19%] * VCF writing [20%] * VCF writing [21%] * VCF writing [22%] * VCF writing [23%] * VCF writing [24%] * VCF writing [25%] * VCF writing [26%] * VCF writing [27%] * VCF writing [28%] * VCF writing [29%] * VCF writing [30%] * VCF writing [31%] * VCF writing [32%] * VCF writing [33%] * VCF writing [34%] * VCF writing [35%] * VCF writing [36%] * VCF writing [37%] * VCF writing [38%] * VCF writing [39%] * VCF writing [40%] * VCF writing [41%] * VCF writing [42%] * VCF writing [43%] * VCF writing [44%] * VCF writing [45%] * VCF writing [46%] * VCF writing [47%] * VCF writing [48%] * VCF writing [49%] * VCF writing [50%] * VCF writing [51%] * VCF writing [52%] * VCF writing [53%] * VCF writing [54%] * VCF writing [55%] * VCF writing [56%] * VCF writing [57%] * VCF writing [58%] * VCF writing [59%] * VCF writing [60%] * VCF writing [61%] * VCF writing [62%] * VCF writing [63%] * VCF writing [64%] * VCF writing [65%] * VCF writing [66%] * VCF writing [67%] * VCF writing [68%] * VCF writing [69%] * VCF writing [70%] * VCF writing [71%] * VCF writing [72%] * VCF writing [73%] * VCF writing [74%] * VCF writing [75%] * VCF writing [76%] * VCF writing [77%] * VCF writing [78%] * VCF writing [79%] * VCF writing [80%] * VCF writing [81%] * VCF writing [82%] * VCF writing [83%] * VCF writing [84%] * VCF writing [85%] * VCF writing [86%] * VCF writing [87%] * VCF writing [88%] * VCF writing [89%] * VCF writing [90%] * VCF writing [91%] * VCF writing [92%] * VCF writing [93%] * VCF writing [94%] * VCF writing [95%] * VCF writing [96%] * VCF writing [97%] * VCF writing [98%] * VCF writing [99%] * VCF writing [100%] * BCF writing [Compressed / N=203 / L=24990] (0.33s) 1223s * Total running time = 203 seconds 1223s autopkgtest [02:45:06]: test run-sample-analysis: -----------------------] 1224s autopkgtest [02:45:07]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 1224s run-sample-analysis PASS 1224s autopkgtest [02:45:07]: @@@@@@@@@@@@@@@@@@@@ summary 1224s run-sample-analysis PASS 1245s Creating nova instance adt-noble-ppc64el-shapeit4-20240314-022442-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240313.img (UUID 1799f203-2779-4c2a-9ae5-df9474cae1d2)...