0s autopkgtest [22:10:40]: starting date and time: 2024-04-02 22:10:40+0000 0s autopkgtest [22:10:40]: git checkout: 31124158 autopkgtest: take Paride's WIP change regarding wrong src pkg selection 0s autopkgtest [22:10:40]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f2zxaice/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:boost1.83,src:glibc --apt-upgrade shapeit4 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build3 boost1.83/1.83.0-2.1ubuntu3 glibc/2.39-0ubuntu8' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-12.secgroup --name adt-noble-ppc64el-shapeit4-20240402-221040-juju-7f2275-prod-proposed-migration-environment-3-91e402cb-1ed6-44c7-a08a-be0383fc5a5d --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 132s autopkgtest [22:12:52]: testbed dpkg architecture: ppc64el 132s autopkgtest [22:12:52]: testbed apt version: 2.7.14 132s autopkgtest [22:12:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 133s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 134s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [469 kB] 134s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7348 B] 134s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3879 kB] 134s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [61.8 kB] 134s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [655 kB] 134s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 134s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1192 B] 134s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 134s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4028 kB] 135s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 135s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [30.7 kB] 135s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 138s Fetched 9260 kB in 2s (3873 kB/s) 138s Reading package lists... 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Calculating upgrade... 142s The following packages will be upgraded: 142s dash ftp kbd libc-bin libc-dev-bin libc-devtools libc6 libc6-dev libcbor0.10 142s libmbim-glib4 libmbim-proxy libnewt0.52 libpipeline1 libprotobuf-c1 142s libreiserfscore0t64 librtmp1 libsensors-config libsensors5 142s libtext-charwidth-perl libvolume-key1 locales python3-newt 142s python3-pyrsistent tnftp ubuntu-kernel-accessories ubuntu-minimal 142s ubuntu-standard whiptail 142s 28 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Need to get 11.7 MB of archives. 142s After this operation, 66.6 kB disk space will be freed. 142s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el dash ppc64el 0.5.12-6ubuntu5 [108 kB] 142s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-devtools ppc64el 2.39-0ubuntu8 [29.6 kB] 142s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6-dev ppc64el 2.39-0ubuntu8 [2104 kB] 144s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu8 [21.3 kB] 144s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6 ppc64el 2.39-0ubuntu8 [3275 kB] 147s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-bin ppc64el 2.39-0ubuntu8 [751 kB] 148s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el kbd ppc64el 2.6.4-2ubuntu2 [245 kB] 148s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu2 [21.9 kB] 148s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu2 [61.9 kB] 148s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build3 [9536 B] 148s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el locales all 2.39-0ubuntu8 [4234 kB] 151s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el whiptail ppc64el 0.52.24-2ubuntu2 [19.7 kB] 151s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-minimal ppc64el 1.538build1 [10.9 kB] 151s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el tnftp ppc64el 20230507-2build2 [116 kB] 151s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el ftp all 20230507-2build2 [4724 B] 151s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libcbor0.10 ppc64el 0.10.2-1.2ubuntu2 [28.5 kB] 151s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libpipeline1 ppc64el 1.5.7-2 [26.9 kB] 151s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-standard ppc64el 1.538build1 [10.9 kB] 151s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libmbim-proxy ppc64el 1.31.2-0ubuntu3 [6290 B] 151s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libmbim-glib4 ppc64el 1.31.2-0ubuntu3 [254 kB] 151s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libprotobuf-c1 ppc64el 1.4.1-1ubuntu4 [26.0 kB] 151s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libreiserfscore0t64 ppc64el 1:3.6.27-7.1build1 [92.8 kB] 151s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build7 [64.4 kB] 151s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libsensors-config all 1:3.6.0-9build1 [5546 B] 151s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libsensors5 ppc64el 1:3.6.0-9build1 [32.4 kB] 151s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libvolume-key1 ppc64el 0.3.12-7build2 [47.9 kB] 151s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pyrsistent ppc64el 0.20.0-1build2 [60.4 kB] 151s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-kernel-accessories ppc64el 1.538build1 [10.7 kB] 152s Preconfiguring packages ... 152s Fetched 11.7 MB in 10s (1195 kB/s) 152s (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 ... 103426 files and directories currently installed.) 152s Preparing to unpack .../dash_0.5.12-6ubuntu5_ppc64el.deb ... 152s Unpacking dash (0.5.12-6ubuntu5) over (0.5.12-6ubuntu4) ... 152s Setting up dash (0.5.12-6ubuntu5) ... 152s (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 ... 103426 files and directories currently installed.) 152s Preparing to unpack .../libc-devtools_2.39-0ubuntu8_ppc64el.deb ... 152s Unpacking libc-devtools (2.39-0ubuntu8) over (2.39-0ubuntu6) ... 152s Preparing to unpack .../libc6-dev_2.39-0ubuntu8_ppc64el.deb ... 152s Unpacking libc6-dev:ppc64el (2.39-0ubuntu8) over (2.39-0ubuntu6) ... 152s Preparing to unpack .../libc-dev-bin_2.39-0ubuntu8_ppc64el.deb ... 152s Unpacking libc-dev-bin (2.39-0ubuntu8) over (2.39-0ubuntu6) ... 152s Preparing to unpack .../libc6_2.39-0ubuntu8_ppc64el.deb ... 152s Unpacking libc6:ppc64el (2.39-0ubuntu8) over (2.39-0ubuntu6) ... 153s Setting up libc6:ppc64el (2.39-0ubuntu8) ... 153s (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 ... 103426 files and directories currently installed.) 153s Preparing to unpack .../libc-bin_2.39-0ubuntu8_ppc64el.deb ... 153s Unpacking libc-bin (2.39-0ubuntu8) over (2.39-0ubuntu6) ... 153s Setting up libc-bin (2.39-0ubuntu8) ... 153s (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 ... 103426 files and directories currently installed.) 153s Preparing to unpack .../00-kbd_2.6.4-2ubuntu2_ppc64el.deb ... 153s Unpacking kbd (2.6.4-2ubuntu2) over (2.6.4-2ubuntu1) ... 153s Preparing to unpack .../01-python3-newt_0.52.24-2ubuntu2_ppc64el.deb ... 153s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu2) over (0.52.24-2ubuntu1) ... 153s Preparing to unpack .../02-libnewt0.52_0.52.24-2ubuntu2_ppc64el.deb ... 153s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu2) over (0.52.24-2ubuntu1) ... 153s Preparing to unpack .../03-libtext-charwidth-perl_0.04-11build3_ppc64el.deb ... 153s Unpacking libtext-charwidth-perl:ppc64el (0.04-11build3) over (0.04-11build2) ... 153s Preparing to unpack .../04-locales_2.39-0ubuntu8_all.deb ... 153s Unpacking locales (2.39-0ubuntu8) over (2.39-0ubuntu6) ... 154s Preparing to unpack .../05-whiptail_0.52.24-2ubuntu2_ppc64el.deb ... 154s Unpacking whiptail (0.52.24-2ubuntu2) over (0.52.24-2ubuntu1) ... 154s Preparing to unpack .../06-ubuntu-minimal_1.538build1_ppc64el.deb ... 154s Unpacking ubuntu-minimal (1.538build1) over (1.538) ... 154s Preparing to unpack .../07-tnftp_20230507-2build2_ppc64el.deb ... 154s Unpacking tnftp (20230507-2build2) over (20230507-2build1) ... 154s Preparing to unpack .../08-ftp_20230507-2build2_all.deb ... 154s Unpacking ftp (20230507-2build2) over (20230507-2build1) ... 154s Preparing to unpack .../09-libcbor0.10_0.10.2-1.2ubuntu2_ppc64el.deb ... 154s Unpacking libcbor0.10:ppc64el (0.10.2-1.2ubuntu2) over (0.10.2-1.2ubuntu1) ... 154s Preparing to unpack .../10-libpipeline1_1.5.7-2_ppc64el.deb ... 154s Unpacking libpipeline1:ppc64el (1.5.7-2) over (1.5.7-1) ... 154s Preparing to unpack .../11-ubuntu-standard_1.538build1_ppc64el.deb ... 154s Unpacking ubuntu-standard (1.538build1) over (1.538) ... 154s Preparing to unpack .../12-libmbim-proxy_1.31.2-0ubuntu3_ppc64el.deb ... 154s Unpacking libmbim-proxy (1.31.2-0ubuntu3) over (1.31.2-0ubuntu2) ... 154s Preparing to unpack .../13-libmbim-glib4_1.31.2-0ubuntu3_ppc64el.deb ... 154s Unpacking libmbim-glib4:ppc64el (1.31.2-0ubuntu3) over (1.31.2-0ubuntu2) ... 154s Preparing to unpack .../14-libprotobuf-c1_1.4.1-1ubuntu4_ppc64el.deb ... 154s Unpacking libprotobuf-c1:ppc64el (1.4.1-1ubuntu4) over (1.4.1-1ubuntu3) ... 154s Preparing to unpack .../15-libreiserfscore0t64_1%3a3.6.27-7.1build1_ppc64el.deb ... 154s Unpacking libreiserfscore0t64 (1:3.6.27-7.1build1) over (1:3.6.27-7.1) ... 154s Preparing to unpack .../16-librtmp1_2.4+20151223.gitfa8646d.1-2build7_ppc64el.deb ... 154s Unpacking librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build7) over (2.4+20151223.gitfa8646d.1-2build6) ... 154s Preparing to unpack .../17-libsensors-config_1%3a3.6.0-9build1_all.deb ... 154s Unpacking libsensors-config (1:3.6.0-9build1) over (1:3.6.0-9) ... 154s Preparing to unpack .../18-libsensors5_1%3a3.6.0-9build1_ppc64el.deb ... 154s Unpacking libsensors5:ppc64el (1:3.6.0-9build1) over (1:3.6.0-9) ... 154s Preparing to unpack .../19-libvolume-key1_0.3.12-7build2_ppc64el.deb ... 154s Unpacking libvolume-key1:ppc64el (0.3.12-7build2) over (0.3.12-7build1) ... 154s Preparing to unpack .../20-python3-pyrsistent_0.20.0-1build2_ppc64el.deb ... 154s Unpacking python3-pyrsistent:ppc64el (0.20.0-1build2) over (0.20.0-1) ... 154s Preparing to unpack .../21-ubuntu-kernel-accessories_1.538build1_ppc64el.deb ... 154s Unpacking ubuntu-kernel-accessories (1.538build1) over (1.538) ... 154s Setting up libpipeline1:ppc64el (1.5.7-2) ... 154s Setting up libtext-charwidth-perl:ppc64el (0.04-11build3) ... 154s Setting up ubuntu-kernel-accessories (1.538build1) ... 154s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu2) ... 154s Setting up libcbor0.10:ppc64el (0.10.2-1.2ubuntu2) ... 154s Setting up libsensors-config (1:3.6.0-9build1) ... 154s Setting up libreiserfscore0t64 (1:3.6.27-7.1build1) ... 154s Setting up python3-newt:ppc64el (0.52.24-2ubuntu2) ... 154s Setting up locales (2.39-0ubuntu8) ... 155s Generating locales (this might take a while)... 156s en_US.UTF-8... done 156s Generation complete. 156s Setting up libprotobuf-c1:ppc64el (1.4.1-1ubuntu4) ... 156s Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build7) ... 156s Setting up libsensors5:ppc64el (1:3.6.0-9build1) ... 156s Setting up python3-pyrsistent:ppc64el (0.20.0-1build2) ... 156s Setting up whiptail (0.52.24-2ubuntu2) ... 156s Setting up kbd (2.6.4-2ubuntu2) ... 156s Setting up libvolume-key1:ppc64el (0.3.12-7build2) ... 156s Setting up tnftp (20230507-2build2) ... 156s Setting up libc-dev-bin (2.39-0ubuntu8) ... 156s Setting up libmbim-glib4:ppc64el (1.31.2-0ubuntu3) ... 156s Setting up libc-devtools (2.39-0ubuntu8) ... 156s Setting up ubuntu-minimal (1.538build1) ... 156s Setting up libmbim-proxy (1.31.2-0ubuntu3) ... 156s Setting up ubuntu-standard (1.538build1) ... 156s Setting up ftp (20230507-2build2) ... 156s Setting up libc6-dev:ppc64el (2.39-0ubuntu8) ... 156s Processing triggers for initramfs-tools (0.142ubuntu23) ... 156s update-initramfs: Generating /boot/initrd.img-6.8.0-20-generic 156s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 162s Processing triggers for libc-bin (2.39-0ubuntu8) ... 162s Processing triggers for man-db (2.12.0-3build4) ... 163s Processing triggers for debianutils (5.17) ... 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 164s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 165s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 165s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 166s Reading package lists... 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Calculating upgrade... 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s autopkgtest [22:13:27]: rebooting testbed after setup commands that affected boot 335s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 342s autopkgtest [22:16:22]: testbed running kernel: Linux 6.8.0-20-generic #20-Ubuntu SMP Mon Mar 18 11:46:05 UTC 2024 345s autopkgtest [22:16:25]: @@@@@@@@@@@@@@@@@@@@ apt-source shapeit4 354s Get:1 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build2 (dsc) [2266 B] 354s Get:2 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build2 (tar) [59.0 MB] 354s Get:3 http://ftpmaster.internal/ubuntu noble/universe shapeit4 4.2.2+dfsg-1build2 (diff) [5360 B] 354s gpgv: Signature made Fri Mar 22 16:55:44 2024 UTC 354s gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 354s gpgv: issuer "juliank@ubuntu.com" 354s gpgv: Can't check signature: No public key 354s dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1build2.dsc: no acceptable signature found 356s autopkgtest [22:16:36]: testing package shapeit4 version 4.2.2+dfsg-1build2 356s autopkgtest [22:16:36]: build not needed 364s autopkgtest [22:16:44]: test run-sample-analysis: preparing testbed 366s Reading package lists... 366s Building dependency tree... 366s Reading state information... 367s Starting pkgProblemResolver with broken count: 0 367s Starting 2 pkgProblemResolver with broken count: 0 367s Done 367s The following additional packages will be installed: 367s libboost-iostreams1.83.0 libboost-program-options1.83.0 libhts3t64 367s libhtscodecs2 shapeit4 shapeit4-example 367s The following NEW packages will be installed: 367s autopkgtest-satdep libboost-iostreams1.83.0 libboost-program-options1.83.0 367s libhts3t64 libhtscodecs2 shapeit4 shapeit4-example 367s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 367s Need to get 53.7 MB/53.7 MB of archives. 367s After this operation, 59.8 MB of additional disk space will be used. 367s Get:1 /tmp/autopkgtest.KYUL7w/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 367s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2.1ubuntu3 [260 kB] 368s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2.1ubuntu3 [329 kB] 368s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 368s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhts3t64 ppc64el 1.19+ds-1.1build3 [569 kB] 368s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4 ppc64el 4.2.2+dfsg-1build2 [187 kB] 368s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el shapeit4-example all 4.2.2+dfsg-1build2 [52.3 MB] 373s Fetched 53.7 MB in 6s (8934 kB/s) 373s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 374s (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 ... 103425 files and directories currently installed.) 374s Preparing to unpack .../0-libboost-iostreams1.83.0_1.83.0-2.1ubuntu3_ppc64el.deb ... 374s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 374s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 374s Preparing to unpack .../1-libboost-program-options1.83.0_1.83.0-2.1ubuntu3_ppc64el.deb ... 374s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 374s Selecting previously unselected package libhtscodecs2:ppc64el. 374s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_ppc64el.deb ... 374s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 374s Selecting previously unselected package libhts3t64:ppc64el. 374s Preparing to unpack .../3-libhts3t64_1.19+ds-1.1build3_ppc64el.deb ... 374s Unpacking libhts3t64:ppc64el (1.19+ds-1.1build3) ... 374s Selecting previously unselected package shapeit4. 374s Preparing to unpack .../4-shapeit4_4.2.2+dfsg-1build2_ppc64el.deb ... 374s Unpacking shapeit4 (4.2.2+dfsg-1build2) ... 374s Selecting previously unselected package shapeit4-example. 374s Preparing to unpack .../5-shapeit4-example_4.2.2+dfsg-1build2_all.deb ... 374s Unpacking shapeit4-example (4.2.2+dfsg-1build2) ... 374s Selecting previously unselected package autopkgtest-satdep. 374s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 374s Unpacking autopkgtest-satdep (0) ... 374s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 374s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 374s Setting up shapeit4-example (4.2.2+dfsg-1build2) ... 374s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 374s Setting up libhts3t64:ppc64el (1.19+ds-1.1build3) ... 374s Setting up shapeit4 (4.2.2+dfsg-1build2) ... 374s Setting up autopkgtest-satdep (0) ... 374s Processing triggers for man-db (2.12.0-3build4) ... 375s Processing triggers for libc-bin (2.39-0ubuntu8) ... 378s (Reading database ... 103484 files and directories currently installed.) 378s Removing autopkgtest-satdep (0) ... 379s autopkgtest [22:16:59]: test run-sample-analysis: [----------------------- 379s + shapeit4 --input unphased.vcf.gz --map chr20.b37.gmap.gz --region 20:2000000-3000000 --thread 4 --output phased.vcf.gz 379s 379s SHAPEIT 379s * Author : Olivier DELANEAU, University of Lausanne 379s * Contact : olivier.delaneau@gmail.com 379s * Version : 4.2.2 379s * Run date : 02/04/2024 - 22:16:59 379s 379s Files: 379s * Input VCF : [unphased.vcf.gz] 379s * Genetic Map : [chr20.b37.gmap.gz] 379s * Output VCF : [phased.vcf.gz] 379s 379s Parameters: 379s * Seed : 15052011 379s * Threads : 4 threads 379s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 379s * PBWT : Depth of PBWT neighbours to condition on: 4 379s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 379s * HMM : K is variable / min W is 2.50cM / Ne is 15000 379s * HMM : Recombination rates given by genetic map 379s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 379s 379s Initialization: 379s * VCF/BCF scanning ... * VCF/BCF scanning [N=203 / L=8651 / Reg=20:2000000-3000000] (0.08s) 379s * 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 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Burn-in iteration [1/1] 398s * V2H transpose (0.00s) 398s * 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 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(2.35s) 400s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 400s * HAP update (0.01s) 400s * H2V transpose (0.00s) 400s 400s Pruning iteration [1/1] 400s * V2H transpose (0.00s) 400s * 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 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PBWT selection [94%] * PBWT selection [95%] * PBWT selection [96%] * PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.01s) 408s * C2H transpose (0.00s) 410s * 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 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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=212.5+/-16.2 / W=1.00Mb / U=2] (1.81s) 410s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 410s * HAP update (0.01s) 410s * H2V transpose (0.00s) 410s 410s Main iteration [3/5] 410s * V2H transpose (0.00s) 410s * PBWT 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#contraints=0 / #merged = 0] 412s * HAP update (0.01s) 412s * H2V transpose (0.00s) 412s 412s Main iteration [4/5] 412s * V2H transpose (0.00s) 412s * 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 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computations [99%] * HMM computations [100%] * HMM computations [K=209.054+/-17.073 / W=1.00Mb] (1.77s) 414s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 414s * HAP update (0.01s) 414s * H2V transpose (0.00s) 414s 414s Main iteration [5/5] 414s * V2H transpose (0.00s) 414s * 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 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* 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] (0.17s) 416s * Total running time = 36 seconds 416s + 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 416s 416s SHAPEIT 416s * Author : Olivier DELANEAU, University of Lausanne 416s * Contact : olivier.delaneau@gmail.com 416s * Version : 4.2.2 416s * Run date : 02/04/2024 - 22:17:36 416s 416s Files: 416s * Input VCF : [unphased.bcf] 416s * Reference VCF : [reference.bcf] 416s * Scaffold VCF : [scaffold.bcf] 416s * Genetic Map : [chr20.b37.gmap.gz] 416s * Output VCF : [phased.bcf] 416s * Output LOG : [phased.log] 416s 416s Parameters: 416s * Seed : 15052011 416s * Threads : 4 threads 416s * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] 416s * PBWT : Depth of PBWT neighbours to condition on: 4 416s * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM] 416s * HMM : K is variable / min W is 2.50cM / Ne is 15000 416s * HMM : Recombination rates given by genetic map 416s * HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001 416s * HMM : AVX2 optimization inactive / Activating AVX2 substantially improves performance 416s 416s Initialization: 416s * VCF/BCF scanning ... * VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.09s) 416s * VCF/BCF parsing [0%] * VCF/BCF parsing [1%] * VCF/BCF parsing [2%] * VCF/BCF parsing [3%] * VCF/BCF parsing [4%] * VCF/BCF parsing [5%] * 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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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PBWT selection [97%] * PBWT selection [98%] * PBWT selection [99%] * PBWT selection [100%] * PBWT selection (0.04s) 465s * C2H transpose (0.00s) 480s * 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 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[K=425.734+/-116.332 / W=2.25Mb] (14.57s) 509s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 509s * HAP update (0.01s) 509s * H2V transpose (0.00s) 509s * Trimming [pc=42.01%] 509s 509s Burn-in iteration [1/1] 509s * V2H transpose (0.00s) 509s * 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 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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 (0.04s) 509s * C2H transpose (0.00s) 520s * 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%] * 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HMM computations [95%] * HMM computations [96%] * HMM computations [97%] * HMM computations [98%] * HMM computations [99%] * HMM computations [100%] * HMM computations [K=415.299+/-120.387 / W=2.17Mb] (11.23s) 520s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 520s * HAP update (0.01s) 520s * H2V transpose (0.00s) 520s 520s Pruning iteration [1/1] 520s * V2H transpose (0.00s) 520s * 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 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(8.95s) 569s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 569s * HAP update (0.01s) 569s * H2V transpose (0.00s) 569s 569s Main iteration [3/5] 569s * V2H transpose (0.00s) 569s * 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 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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 (0.04s) 588s * C2H transpose (0.00s) 597s * 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=394.717+/-110.922 / W=2.21Mb] (8.91s) 597s * IBD2 constraints [#inds=0 / #contraints=0 / #merged = 0] 597s * HAP update (0.01s) 597s * H2V transpose (0.00s) 597s 597s Finalization: 597s * HAP solving (0.03s) 597s * HAP update (0.01s) 597s * H2V transpose (0.00s) 597s * 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] (0.21s) 597s * Total running time = 180 seconds 597s autopkgtest [22:20:37]: test run-sample-analysis: -----------------------] 598s run-sample-analysis PASS 598s autopkgtest [22:20:38]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 598s autopkgtest [22:20:38]: @@@@@@@@@@@@@@@@@@@@ summary 598s run-sample-analysis PASS 611s Creating nova instance adt-noble-ppc64el-shapeit4-20240402-221040-juju-7f2275-prod-proposed-migration-environment-3-91e402cb-1ed6-44c7-a08a-be0383fc5a5d from image adt/ubuntu-noble-ppc64el-server-20240402.img (UUID 67e198d3-b53a-4c90-85e1-65baa46c2da6)...