0s autopkgtest [01:53:50]: starting date and time: 2024-04-19 01:53:50+0000
  0s autopkgtest [01:53:50]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline
  0s autopkgtest [01:53:50]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6858adof/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade qtltools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=gsl/2.7.1+dfsg-6ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-5.secgroup --name adt-noble-s390x-qtltools-20240419-013339-juju-7f2275-prod-proposed-migration-environment-3-62b2451f-66ba-4b17-a8dd-9766ade558a1 --image adt/ubuntu-noble-s390x-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/
210s autopkgtest [01:57:20]: testbed dpkg architecture: s390x
210s autopkgtest [01:57:20]: testbed apt version: 2.7.14build2
210s autopkgtest [01:57:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup
211s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
211s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B]
212s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB]
212s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [338 kB]
212s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [53.4 kB]
212s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [93.9 kB]
212s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B]
212s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [976 B]
212s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B]
212s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [427 kB]
212s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B]
212s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B]
213s Fetched 1055 kB in 1s (1122 kB/s)
213s Reading package lists...
215s sh: 4: dhclient: not found
215s Reading package lists...
215s Building dependency tree...
215s Reading state information...
216s Calculating upgrade...
216s The following packages will be upgraded:
216s   apport apport-core-dump-handler base-passwd bind9-dnsutils bind9-host
216s   bind9-libs cpio cryptsetup-bin dbus dbus-bin dbus-daemon
216s   dbus-session-bus-common dbus-system-bus-common dbus-user-session e2fsprogs
216s   e2fsprogs-l10n ethtool fuse3 grep gzip iptables iputils-ping
216s   iputils-tracepath kmod libargon2-1 libcap2 libcap2-bin libcom-err2
216s   libcrypt-dev libcrypt1 libcryptsetup12 libdb5.3t64 libdbus-1-3 libext2fs2t64
216s   libflashrom1 libfuse3-3 libgmp10 libicu74 libidn2-0 libinih1 libip4tc2
216s   libip6tc2 libjbig0 libjson-c5 libkeyutils1 libkmod2 liblmdb0 liblz4-1
216s   liblzo2-2 libmaxminddb0 libmd0 libmnl0 libmpfr6 libncurses6 libncursesw6
216s   libnetfilter-conntrack3 libnetplan1 libnfnetlink0 libnftables1 libnftnl11
216s   libnghttp2-14 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 libnspr4
216s   libnuma1 libonig5 libp11-kit0 libpam-cap libpam-modules libpam-modules-bin
216s   libpam-runtime libpam0g libpcre2-8-0 libpopt0 libsepol2 libsgutils2-1.46-2
216s   libss2 libtasn1-6 libtinfo6 libuchardet0 libunistring5 libutempter0 libx11-6
216s   libx11-data libxau6 libxdmcp6 libxtables12 libxxhash0 libzstd1 login
216s   logrotate logsave make man-db mawk ncurses-base ncurses-bin ncurses-term
216s   netcat-openbsd netplan-generator netplan.io nftables numactl passwd patch
216s   python-apt-common python3-apport python3-apt python3-netifaces
216s   python3-netplan python3-problem-report python3-systemd rpcsvc-proto rsync
216s   rsyslog screen sed sg3-utils sg3-utils-udev sudo sysvinit-utils tar time
216s   usbutils xauth zstd
216s 127 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
216s Need to get 32.2 MB of archives.
216s After this operation, 264 kB of additional disk space will be used.
216s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-4build1 [173 kB]
216s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x gzip s390x 1.12-1ubuntu3 [107 kB]
216s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-4ubuntu3 [202 kB]
216s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu2 [198 kB]
216s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x sed s390x 4.9-2build1 [198 kB]
216s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.35+dfsg-3build1 [269 kB]
216s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3build1 [51.5 kB]
216s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB]
216s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-term all 6.4+20240113-1ubuntu2 [275 kB]
216s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-6ubuntu3 [34.8 kB]
216s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4build1 [119 kB]
216s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt1 s390x 1:4.4.36-4build1 [88.9 kB]
216s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libpam0g s390x 1.5.3-5ubuntu5 [69.8 kB]
216s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu5 [57.2 kB]
216s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules s390x 1.5.3-5ubuntu5 [289 kB]
216s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu4 [5998 B]
216s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu4 [22.6 kB]
216s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu4 [234 kB]
217s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu4 [614 kB]
217s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x liblz4-1 s390x 1.9.4-1build1 [79.4 kB]
217s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libpopt0 s390x 1.19+dfsg-1build1 [31.7 kB]
217s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2build1 [24.1 kB]
217s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2build1 [341 kB]
217s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x rsync s390x 3.2.7-1ubuntu1 [446 kB]
217s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x python-apt-common all 2.7.7ubuntu1 [20.1 kB]
217s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x python3-apt s390x 2.7.7ubuntu1 [171 kB]
217s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB]
217s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x python3-apport all 2.28.1-0ubuntu1 [92.1 kB]
217s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB]
217s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x apport all 2.28.1-0ubuntu1 [83.5 kB]
217s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libcap2 s390x 1:2.66-5ubuntu2 [31.8 kB]
217s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libgmp10 s390x 2:6.3.0+dfsg-2ubuntu6 [337 kB]
217s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libmd0 s390x 1.1.0-2build1 [24.6 kB]
217s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB]
217s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu2 [245 kB]
217s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2build1 [315 kB]
217s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libncurses6 s390x 6.4+20240113-1ubuntu2 [124 kB]
217s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu2 [161 kB]
217s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu2 [117 kB]
217s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu3 [857 kB]
217s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2build1 [550 kB]
217s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.7-2build1 [67.3 kB]
217s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-4ubuntu2 [320 kB]
217s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libtasn1-6 s390x 4.19.0-3build1 [48.5 kB]
217s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu4 [22.9 kB]
217s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu4 [17.2 kB]
217s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20240123-1build1 [133 kB]
217s Get:48 http://ftpmaster.internal/ubuntu noble/main s390x dbus-system-bus-common all 1.14.10-4ubuntu4 [81.6 kB]
217s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x dbus-session-bus-common all 1.14.10-4ubuntu4 [80.4 kB]
217s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x dbus-user-session s390x 1.14.10-4ubuntu4 [9960 B]
217s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x dbus-daemon s390x 1.14.10-4ubuntu4 [118 kB]
217s Get:52 http://ftpmaster.internal/ubuntu noble/main s390x dbus-bin s390x 1.14.10-4ubuntu4 [41.4 kB]
217s Get:53 http://ftpmaster.internal/ubuntu noble/main s390x dbus s390x 1.14.10-4ubuntu4 [24.3 kB]
217s Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libdbus-1-3 s390x 1.14.10-4ubuntu4 [214 kB]
217s Get:55 http://ftpmaster.internal/ubuntu noble/main s390x libpam-cap s390x 1:2.66-5ubuntu2 [12.3 kB]
217s Get:56 http://ftpmaster.internal/ubuntu noble/main s390x libcap2-bin s390x 1:2.66-5ubuntu2 [34.3 kB]
217s Get:57 http://ftpmaster.internal/ubuntu noble/main s390x iputils-ping s390x 3:20240117-1build1 [46.2 kB]
217s Get:58 http://ftpmaster.internal/ubuntu noble/main s390x kmod s390x 31+20240202-2ubuntu6 [107 kB]
217s Get:59 http://ftpmaster.internal/ubuntu noble/main s390x libkmod2 s390x 31+20240202-2ubuntu6 [56.4 kB]
217s Get:60 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4build1 [54.1 kB]
217s Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libjson-c5 s390x 0.17-1build1 [37.2 kB]
217s Get:62 http://ftpmaster.internal/ubuntu noble/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu4 [264 kB]
217s Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-7 [764 kB]
217s Get:64 http://ftpmaster.internal/ubuntu noble/main s390x libicu74 s390x 74.2-1ubuntu3 [10.9 MB]
218s Get:65 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B]
218s Get:66 http://ftpmaster.internal/ubuntu noble/main s390x libmnl0 s390x 1.0.5-2build1 [12.7 kB]
218s Get:67 http://ftpmaster.internal/ubuntu noble/main s390x netplan-generator s390x 1.0-2ubuntu1 [59.2 kB]
218s Get:68 http://ftpmaster.internal/ubuntu noble/main s390x python3-netplan s390x 1.0-2ubuntu1 [23.0 kB]
218s Get:69 http://ftpmaster.internal/ubuntu noble/main s390x python3-netifaces s390x 0.11.0-2build3 [18.2 kB]
218s Get:70 http://ftpmaster.internal/ubuntu noble/main s390x netplan.io s390x 1.0-2ubuntu1 [65.8 kB]
218s Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libnetplan1 s390x 1.0-2ubuntu1 [126 kB]
218s Get:72 http://ftpmaster.internal/ubuntu noble/main s390x iptables s390x 1.8.10-3ubuntu2 [392 kB]
218s Get:73 http://ftpmaster.internal/ubuntu noble/main s390x libip4tc2 s390x 1.8.10-3ubuntu2 [24.2 kB]
218s Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libip6tc2 s390x 1.8.10-3ubuntu2 [24.3 kB]
218s Get:75 http://ftpmaster.internal/ubuntu noble/main s390x libnfnetlink0 s390x 1.0.2-2build1 [14.8 kB]
218s Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libnetfilter-conntrack3 s390x 1.0.9-6build1 [47.2 kB]
218s Get:77 http://ftpmaster.internal/ubuntu noble/main s390x libnftnl11 s390x 1.2.6-2build1 [66.5 kB]
218s Get:78 http://ftpmaster.internal/ubuntu noble/main s390x libxtables12 s390x 1.8.10-3ubuntu2 [37.6 kB]
218s Get:79 http://ftpmaster.internal/ubuntu noble/main s390x logrotate s390x 3.21.0-2build1 [53.2 kB]
218s Get:80 http://ftpmaster.internal/ubuntu noble/main s390x netcat-openbsd s390x 1.226-1ubuntu2 [44.0 kB]
218s Get:81 http://ftpmaster.internal/ubuntu noble/main s390x rsyslog s390x 8.2312.0-3ubuntu9 [536 kB]
218s Get:82 http://ftpmaster.internal/ubuntu noble/main s390x sudo s390x 1.9.15p5-3ubuntu5 [969 kB]
218s Get:83 http://ftpmaster.internal/ubuntu noble/main s390x liblmdb0 s390x 0.9.31-1build1 [53.0 kB]
218s Get:84 http://ftpmaster.internal/ubuntu noble/main s390x libmaxminddb0 s390x 1.9.1-1build1 [24.7 kB]
218s Get:85 http://ftpmaster.internal/ubuntu noble/main s390x libnghttp2-14 s390x 1.59.0-1build4 [77.9 kB]
218s Get:86 http://ftpmaster.internal/ubuntu noble/main s390x bind9-dnsutils s390x 1:9.18.24-0ubuntu5 [162 kB]
218s Get:87 http://ftpmaster.internal/ubuntu noble/main s390x bind9-host s390x 1:9.18.24-0ubuntu5 [50.5 kB]
218s Get:88 http://ftpmaster.internal/ubuntu noble/main s390x bind9-libs s390x 1:9.18.24-0ubuntu5 [1243 kB]
218s Get:89 http://ftpmaster.internal/ubuntu noble/main s390x cpio s390x 2.15+dfsg-1ubuntu2 [88.3 kB]
218s Get:90 http://ftpmaster.internal/ubuntu noble/main s390x fuse3 s390x 3.14.0-5build1 [26.1 kB]
218s Get:91 http://ftpmaster.internal/ubuntu noble/main s390x libfuse3-3 s390x 3.14.0-5build1 [82.7 kB]
218s Get:92 http://ftpmaster.internal/ubuntu noble/main s390x iputils-tracepath s390x 3:20240117-1build1 [13.5 kB]
218s Get:93 http://ftpmaster.internal/ubuntu noble/main s390x nftables s390x 1.0.9-1build1 [70.4 kB]
218s Get:94 http://ftpmaster.internal/ubuntu noble/main s390x libnftables1 s390x 1.0.9-1build1 [380 kB]
218s Get:95 http://ftpmaster.internal/ubuntu noble/main s390x libnuma1 s390x 2.0.18-1build1 [25.1 kB]
218s Get:96 http://ftpmaster.internal/ubuntu noble/main s390x libuchardet0 s390x 0.0.8-1build1 [76.7 kB]
218s Get:97 http://ftpmaster.internal/ubuntu noble/main s390x libx11-data all 2:1.8.7-1build1 [115 kB]
218s Get:98 http://ftpmaster.internal/ubuntu noble/main s390x libx11-6 s390x 2:1.8.7-1build1 [676 kB]
218s Get:99 http://ftpmaster.internal/ubuntu noble/main s390x libxau6 s390x 1:1.0.9-1build6 [7336 B]
218s Get:100 http://ftpmaster.internal/ubuntu noble/main s390x libxdmcp6 s390x 1:1.1.3-0ubuntu6 [10.8 kB]
218s Get:101 http://ftpmaster.internal/ubuntu noble/main s390x man-db s390x 2.12.0-4build2 [1253 kB]
218s Get:102 http://ftpmaster.internal/ubuntu noble/main s390x time s390x 1.9-0.2build1 [45.6 kB]
219s Get:103 http://ftpmaster.internal/ubuntu noble/main s390x usbutils s390x 1:017-3build1 [85.3 kB]
219s Get:104 http://ftpmaster.internal/ubuntu noble/main s390x xauth s390x 1:1.1.2-1build1 [26.0 kB]
219s Get:105 http://ftpmaster.internal/ubuntu noble/main s390x cryptsetup-bin s390x 2:2.7.0-1ubuntu4 [211 kB]
219s Get:106 http://ftpmaster.internal/ubuntu noble/main s390x ethtool s390x 1:6.7-1build1 [229 kB]
219s Get:107 http://ftpmaster.internal/ubuntu noble/main s390x libflashrom1 s390x 1.3.0-2.1ubuntu2 [143 kB]
219s Get:108 http://ftpmaster.internal/ubuntu noble/main s390x libinih1 s390x 55-1ubuntu2 [7440 B]
219s Get:109 http://ftpmaster.internal/ubuntu noble/main s390x liblzo2-2 s390x 2.10-2build4 [64.2 kB]
219s Get:110 http://ftpmaster.internal/ubuntu noble/main s390x libmpfr6 s390x 4.2.1-1build1 [322 kB]
219s Get:111 http://ftpmaster.internal/ubuntu noble/main s390x libnl-genl-3-200 s390x 3.7.0-0.3build1 [12.6 kB]
219s Get:112 http://ftpmaster.internal/ubuntu noble/main s390x libnl-route-3-200 s390x 3.7.0-0.3build1 [191 kB]
219s Get:113 http://ftpmaster.internal/ubuntu noble/main s390x libnl-3-200 s390x 3.7.0-0.3build1 [59.7 kB]
219s Get:114 http://ftpmaster.internal/ubuntu noble/main s390x libnspr4 s390x 2:4.35-1.1build1 [125 kB]
219s Get:115 http://ftpmaster.internal/ubuntu noble/main s390x libonig5 s390x 6.9.9-1build1 [186 kB]
219s Get:116 http://ftpmaster.internal/ubuntu noble/main s390x libsgutils2-1.46-2 s390x 1.46-3ubuntu4 [96.1 kB]
219s Get:117 http://ftpmaster.internal/ubuntu noble/main s390x libutempter0 s390x 1.2.1-3build1 [9590 B]
219s Get:118 http://ftpmaster.internal/ubuntu noble/main s390x make s390x 4.3-4.1build2 [196 kB]
219s Get:119 http://ftpmaster.internal/ubuntu noble/main s390x numactl s390x 2.0.18-1build1 [40.0 kB]
219s Get:120 http://ftpmaster.internal/ubuntu noble/main s390x patch s390x 2.7.6-7build3 [113 kB]
219s Get:121 http://ftpmaster.internal/ubuntu noble/main s390x python3-systemd s390x 235-1build4 [42.5 kB]
219s Get:122 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu7 [66.4 kB]
219s Get:123 http://ftpmaster.internal/ubuntu noble/main s390x screen s390x 4.9.1-1build1 [681 kB]
219s Get:124 http://ftpmaster.internal/ubuntu noble/main s390x sg3-utils s390x 1.46-3ubuntu4 [847 kB]
219s Get:125 http://ftpmaster.internal/ubuntu noble/main s390x sg3-utils-udev all 1.46-3ubuntu4 [5922 B]
219s Get:126 http://ftpmaster.internal/ubuntu noble/main s390x zstd s390x 1.5.5+dfsg2-2build1 [710 kB]
219s Get:127 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB]
220s Preconfiguring packages ...
220s Fetched 32.2 MB in 3s (9331 kB/s)
220s (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 ... 53991 files and directories currently installed.)
220s Preparing to unpack .../grep_3.11-4build1_s390x.deb ...
220s Unpacking grep (3.11-4build1) over (3.11-4) ...
220s Setting up grep (3.11-4build1) ...
220s (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 ... 53991 files and directories currently installed.)
220s Preparing to unpack .../gzip_1.12-1ubuntu3_s390x.deb ...
220s Unpacking gzip (1.12-1ubuntu3) over (1.12-1ubuntu2) ...
220s Setting up gzip (1.12-1ubuntu3) ...
220s (Reading database ... 
(Reading database ... 5%
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221s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu5_s390x.deb ...
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221s Setting up libpam-modules-bin (1.5.3-5ubuntu5) ...
222s pam_namespace.service is a disabled or a static unit not running, not starting it.
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222s Leaving 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2 to /lib/s390x-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64'
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222s Unpacking libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ...
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223s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu5_all.deb ...
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226s info: The user `syslog' is already a member of `adm'.
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229s Setting up python-apt-common (2.7.7ubuntu1) ...
229s Setting up libcrypt-dev:s390x (1:4.4.36-4build1) ...
229s Setting up libnfnetlink0:s390x (1.0.2-2build1) ...
229s Setting up dbus-session-bus-common (1.14.10-4ubuntu4) ...
229s Setting up libuchardet0:s390x (0.0.8-1build1) ...
229s Setting up libnl-3-200:s390x (3.7.0-0.3build1) ...
229s Setting up python3-netplan (1.0-2ubuntu1) ...
229s Setting up libx11-6:s390x (2:1.8.7-1build1) ...
229s Setting up mawk (1.3.4.20240123-1build1) ...
229s Setting up netplan-generator (1.0-2ubuntu1) ...
229s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
229s Setting up dbus-system-bus-common (1.14.10-4ubuntu4) ...
229s Setting up libpam-cap:s390x (1:2.66-5ubuntu2) ...
229s Setting up iputils-ping (3:20240117-1build1) ...
229s Setting up libjson-c5:s390x (0.17-1build1) ...
229s Setting up zstd (1.5.5+dfsg2-2build1) ...
229s Setting up dbus-bin (1.14.10-4ubuntu4) ...
229s Setting up libonig5:s390x (6.9.9-1build1) ...
229s Setting up iputils-tracepath (3:20240117-1build1) ...
229s Setting up python3-systemd (235-1build4) ...
229s Setting up libkmod2:s390x (31+20240202-2ubuntu6) ...
229s Setting up libpopt0:s390x (1.19+dfsg-1build1) ...
229s Setting up ethtool (1:6.7-1build1) ...
229s Setting up sg3-utils (1.46-3ubuntu4) ...
229s Setting up ncurses-term (6.4+20240113-1ubuntu2) ...
229s Setting up logrotate (3.21.0-2build1) ...
230s logrotate.service is a disabled or a static unit not running, not starting it.
230s Setting up numactl (2.0.18-1build1) ...
230s Setting up bind9-libs:s390x (1:9.18.24-0ubuntu5) ...
230s Setting up python3-apt (2.7.7ubuntu1) ...
230s Setting up screen (4.9.1-1build1) ...
230s Setting up libnftnl11:s390x (1.2.6-2build1) ...
230s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ...
230s update-initramfs: deferring update (trigger activated)
231s e2scrub_all.service is a disabled or a static unit not running, not starting it.
231s Setting up dbus-daemon (1.14.10-4ubuntu4) ...
231s Setting up kmod (31+20240202-2ubuntu6) ...
231s Setting up sg3-utils-udev (1.46-3ubuntu4) ...
231s update-initramfs: deferring update (trigger activated)
231s Setting up python3-apport (2.28.1-0ubuntu1) ...
231s Setting up netplan.io (1.0-2ubuntu1) ...
231s Setting up libnl-route-3-200:s390x (3.7.0-0.3build1) ...
231s Setting up fuse3 (3.14.0-5build1) ...
231s update-initramfs: deferring update (trigger activated)
231s Setting up dbus-user-session (1.14.10-4ubuntu4) ...
231s Setting up dbus (1.14.10-4ubuntu4) ...
231s A reboot is required to replace the running dbus-daemon.
231s Please reboot the system when convenient.
232s Setting up xauth (1:1.1.2-1build1) ...
232s Setting up libnetfilter-conntrack3:s390x (1.0.9-6build1) ...
232s Setting up libnl-genl-3-200:s390x (3.7.0-0.3build1) ...
232s Setting up libcryptsetup12:s390x (2:2.7.0-1ubuntu4) ...
232s Setting up bind9-host (1:9.18.24-0ubuntu5) ...
232s Setting up rsync (3.2.7-1ubuntu1) ...
232s rsync.service is a disabled or a static unit not running, not starting it.
232s Setting up cryptsetup-bin (2:2.7.0-1ubuntu4) ...
232s Setting up libnftables1:s390x (1.0.9-1build1) ...
232s Setting up nftables (1.0.9-1build1) ...
233s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu4) ...
233s Setting up iptables (1.8.10-3ubuntu2) ...
233s Setting up bind9-dnsutils (1:9.18.24-0ubuntu5) ...
233s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ...
234s Setting up apport (2.28.1-0ubuntu1) ...
234s Installing new version of config file /etc/apport/crashdb.conf ...
234s apport-autoreport.service is a disabled or a static unit not running, not starting it.
235s Processing triggers for debianutils (5.17build1) ...
235s Processing triggers for install-info (7.1-3build2) ...
235s Processing triggers for initramfs-tools (0.142ubuntu24) ...
235s update-initramfs: Generating /boot/initrd.img-6.8.0-22-generic
235s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
239s Using config file '/etc/zipl.conf'
239s Building bootmap in '/boot'
239s Adding IPL section 'ubuntu' (default)
239s Preparing boot device for LD-IPL: vda (0000).
239s Done.
239s Processing triggers for libc-bin (2.39-0ubuntu8) ...
239s Reading package lists...
239s Building dependency tree...
239s Reading state information...
240s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
240s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
240s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
240s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
240s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
241s Reading package lists...
241s Reading package lists...
241s Building dependency tree...
241s Reading state information...
241s Calculating upgrade...
242s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
242s Reading package lists...
242s Building dependency tree...
242s Reading state information...
242s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
242s autopkgtest [01:57:52]: rebooting testbed after setup commands that affected boot
275s autopkgtest [01:58:25]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP Thu Apr  4 21:54:17 UTC 2024
278s autopkgtest [01:58:28]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools
284s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (dsc) [2293 B]
284s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (tar) [141 kB]
284s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (diff) [13.6 MB]
284s gpgv: Signature made Mon Apr  1 07:33:53 2024 UTC
284s gpgv:                using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984
284s gpgv: Can't check signature: No public key
284s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build3.dsc: no acceptable signature found
285s autopkgtest [01:58:35]: testing package qtltools version 1.3.1+dfsg-4build3
291s autopkgtest [01:58:41]: build not needed
302s autopkgtest [01:58:52]: test run-sample-analysis: preparing testbed
303s Reading package lists...
303s Building dependency tree...
303s Reading state information...
303s Starting pkgProblemResolver with broken count: 0
303s Starting 2 pkgProblemResolver with broken count: 0
303s Done
304s The following additional packages will be installed:
304s   fontconfig libblas3 libboost-iostreams1.83.0 libboost-program-options1.83.0
304s   libcairo2 libdatrie1 libgfortran5 libgomp1 libgraphite2-3 libgsl27
304s   libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 liblapack3
304s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
304s   libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6
304s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 qtltools
304s   qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils zip
304s Suggested packages:
304s   gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6
304s   elpa-ess r-doc-info | r-doc-pdf r-base-html
304s Recommended packages:
304s   r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl
304s   libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
304s The following NEW packages will be installed:
304s   autopkgtest-satdep fontconfig libblas3 libboost-iostreams1.83.0
304s   libboost-program-options1.83.0 libcairo2 libdatrie1 libgfortran5 libgomp1
304s   libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2
304s   libice6 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
304s   libpaper-utils libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data
304s   libthai0 libtk8.6 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1
304s   libxt6t64 qtltools qtltools-example r-base-core r-mathlib unzip x11-common
304s   xdg-utils zip
304s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded.
304s Need to get 54.9 MB/54.9 MB of archives.
304s After this operation, 99.0 MB of additional disk space will be used.
304s Get:1 /tmp/autopkgtest.1BW2GD/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B]
304s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig s390x 2.15.0-1.1ubuntu2 [191 kB]
304s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3build1 [245 kB]
304s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libboost-iostreams1.83.0 s390x 1.83.0-2.1ubuntu3 [259 kB]
304s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2.1ubuntu3 [325 kB]
304s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1build1 [206 kB]
304s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB]
304s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B]
304s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB]
304s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-3build1 [589 kB]
304s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB]
304s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240412-0ubuntu1 [600 kB]
305s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240412-0ubuntu1 [151 kB]
305s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2build1 [80.0 kB]
305s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu2 [150 kB]
305s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu2 [1084 kB]
305s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2build2 [515 kB]
305s Get:18 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB]
305s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3t64 s390x 1.19+ds-1.1build3 [474 kB]
305s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB]
305s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libice6 s390x 2:1.0.10-1build3 [44.8 kB]
305s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB]
305s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2build1 [158 kB]
305s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB]
305s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libpango-1.0-0 s390x 1.52.1+ds-1build1 [243 kB]
305s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libpangoft2-1.0-0 s390x 1.52.1+ds-1build1 [44.0 kB]
305s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libpangocairo-1.0-0 s390x 1.52.1+ds-1build1 [28.8 kB]
305s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libpaper1 s390x 1.1.29build1 [13.4 kB]
305s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29build1 [8442 B]
305s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build3 [17.7 kB]
305s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libtcl8.6 s390x 8.6.14+dfsg-1build1 [1038 kB]
306s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB]
306s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B]
306s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libtk8.6 s390x 8.6.14-1build1 [833 kB]
306s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB]
306s Get:36 http://ftpmaster.internal/ubuntu noble/universe s390x r-mathlib s390x 4.3.3-2build2 [2383 kB]
306s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x zip s390x 3.0-13build1 [189 kB]
306s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x unzip s390x 6.0-28ubuntu4 [180 kB]
306s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
306s Get:40 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-core s390x 4.3.3-2build2 [27.1 MB]
307s Get:41 http://ftpmaster.internal/ubuntu noble/universe s390x qtltools s390x 1.3.1+dfsg-4build3 [706 kB]
307s Get:42 http://ftpmaster.internal/ubuntu noble/universe s390x qtltools-example all 1.3.1+dfsg-4build3 [13.6 MB]
308s Preconfiguring packages ...
308s Fetched 54.9 MB in 4s (13.5 MB/s)
308s Selecting previously unselected package fontconfig.
308s (Reading database ... 
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(Reading database ... 53983 files and directories currently installed.)
308s Preparing to unpack .../00-fontconfig_2.15.0-1.1ubuntu2_s390x.deb ...
308s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
308s Selecting previously unselected package libblas3:s390x.
308s Preparing to unpack .../01-libblas3_3.12.0-3build1_s390x.deb ...
308s Unpacking libblas3:s390x (3.12.0-3build1) ...
308s Selecting previously unselected package libboost-iostreams1.83.0:s390x.
308s Preparing to unpack .../02-libboost-iostreams1.83.0_1.83.0-2.1ubuntu3_s390x.deb ...
308s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-2.1ubuntu3) ...
308s Selecting previously unselected package libboost-program-options1.83.0:s390x.
308s Preparing to unpack .../03-libboost-program-options1.83.0_1.83.0-2.1ubuntu3_s390x.deb ...
308s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2.1ubuntu3) ...
308s Selecting previously unselected package libpixman-1-0:s390x.
308s Preparing to unpack .../04-libpixman-1-0_0.42.2-1build1_s390x.deb ...
308s Unpacking libpixman-1-0:s390x (0.42.2-1build1) ...
308s Selecting previously unselected package libxcb-render0:s390x.
308s Preparing to unpack .../05-libxcb-render0_1.15-1_s390x.deb ...
308s Unpacking libxcb-render0:s390x (1.15-1) ...
308s Selecting previously unselected package libxcb-shm0:s390x.
308s Preparing to unpack .../06-libxcb-shm0_1.15-1_s390x.deb ...
308s Unpacking libxcb-shm0:s390x (1.15-1) ...
308s Selecting previously unselected package libxrender1:s390x.
308s Preparing to unpack .../07-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ...
308s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ...
308s Selecting previously unselected package libcairo2:s390x.
308s Preparing to unpack .../08-libcairo2_1.18.0-3build1_s390x.deb ...
308s Unpacking libcairo2:s390x (1.18.0-3build1) ...
308s Selecting previously unselected package libdatrie1:s390x.
308s Preparing to unpack .../09-libdatrie1_0.2.13-3build1_s390x.deb ...
308s Unpacking libdatrie1:s390x (0.2.13-3build1) ...
308s Selecting previously unselected package libgfortran5:s390x.
308s Preparing to unpack .../10-libgfortran5_14-20240412-0ubuntu1_s390x.deb ...
308s Unpacking libgfortran5:s390x (14-20240412-0ubuntu1) ...
308s Selecting previously unselected package libgomp1:s390x.
308s Preparing to unpack .../11-libgomp1_14-20240412-0ubuntu1_s390x.deb ...
308s Unpacking libgomp1:s390x (14-20240412-0ubuntu1) ...
308s Selecting previously unselected package libgraphite2-3:s390x.
308s Preparing to unpack .../12-libgraphite2-3_1.3.14-2build1_s390x.deb ...
308s Unpacking libgraphite2-3:s390x (1.3.14-2build1) ...
308s Selecting previously unselected package libgslcblas0:s390x.
308s Preparing to unpack .../13-libgslcblas0_2.7.1+dfsg-6ubuntu2_s390x.deb ...
308s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ...
308s Selecting previously unselected package libgsl27:s390x.
308s Preparing to unpack .../14-libgsl27_2.7.1+dfsg-6ubuntu2_s390x.deb ...
308s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ...
308s Selecting previously unselected package libharfbuzz0b:s390x.
308s Preparing to unpack .../15-libharfbuzz0b_8.3.0-2build2_s390x.deb ...
308s Unpacking libharfbuzz0b:s390x (8.3.0-2build2) ...
308s Selecting previously unselected package libhtscodecs2:s390x.
308s Preparing to unpack .../16-libhtscodecs2_1.6.0-1_s390x.deb ...
308s Unpacking libhtscodecs2:s390x (1.6.0-1) ...
308s Selecting previously unselected package libhts3t64:s390x.
308s Preparing to unpack .../17-libhts3t64_1.19+ds-1.1build3_s390x.deb ...
308s Unpacking libhts3t64:s390x (1.19+ds-1.1build3) ...
308s Selecting previously unselected package x11-common.
308s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ...
308s Unpacking x11-common (1:7.7+23ubuntu3) ...
308s Selecting previously unselected package libice6:s390x.
308s Preparing to unpack .../19-libice6_2%3a1.0.10-1build3_s390x.deb ...
308s Unpacking libice6:s390x (2:1.0.10-1build3) ...
308s Selecting previously unselected package liblapack3:s390x.
308s Preparing to unpack .../20-liblapack3_3.12.0-3build1_s390x.deb ...
308s Unpacking liblapack3:s390x (3.12.0-3build1) ...
309s Selecting previously unselected package libthai-data.
309s Preparing to unpack .../21-libthai-data_0.1.29-2build1_all.deb ...
309s Unpacking libthai-data (0.1.29-2build1) ...
309s Selecting previously unselected package libthai0:s390x.
309s Preparing to unpack .../22-libthai0_0.1.29-2build1_s390x.deb ...
309s Unpacking libthai0:s390x (0.1.29-2build1) ...
309s Selecting previously unselected package libpango-1.0-0:s390x.
309s Preparing to unpack .../23-libpango-1.0-0_1.52.1+ds-1build1_s390x.deb ...
309s Unpacking libpango-1.0-0:s390x (1.52.1+ds-1build1) ...
309s Selecting previously unselected package libpangoft2-1.0-0:s390x.
309s Preparing to unpack .../24-libpangoft2-1.0-0_1.52.1+ds-1build1_s390x.deb ...
309s Unpacking libpangoft2-1.0-0:s390x (1.52.1+ds-1build1) ...
309s Selecting previously unselected package libpangocairo-1.0-0:s390x.
309s Preparing to unpack .../25-libpangocairo-1.0-0_1.52.1+ds-1build1_s390x.deb ...
309s Unpacking libpangocairo-1.0-0:s390x (1.52.1+ds-1build1) ...
309s Selecting previously unselected package libpaper1:s390x.
309s Preparing to unpack .../26-libpaper1_1.1.29build1_s390x.deb ...
309s Unpacking libpaper1:s390x (1.1.29build1) ...
309s Selecting previously unselected package libpaper-utils.
309s Preparing to unpack .../27-libpaper-utils_1.1.29build1_s390x.deb ...
309s Unpacking libpaper-utils (1.1.29build1) ...
309s Selecting previously unselected package libsm6:s390x.
309s Preparing to unpack .../28-libsm6_2%3a1.2.3-1build3_s390x.deb ...
309s Unpacking libsm6:s390x (2:1.2.3-1build3) ...
309s Selecting previously unselected package libtcl8.6:s390x.
309s Preparing to unpack .../29-libtcl8.6_8.6.14+dfsg-1build1_s390x.deb ...
309s Unpacking libtcl8.6:s390x (8.6.14+dfsg-1build1) ...
309s Selecting previously unselected package libxft2:s390x.
309s Preparing to unpack .../30-libxft2_2.3.6-1build1_s390x.deb ...
309s Unpacking libxft2:s390x (2.3.6-1build1) ...
309s Selecting previously unselected package libxss1:s390x.
309s Preparing to unpack .../31-libxss1_1%3a1.2.3-1build3_s390x.deb ...
309s Unpacking libxss1:s390x (1:1.2.3-1build3) ...
309s Selecting previously unselected package libtk8.6:s390x.
309s Preparing to unpack .../32-libtk8.6_8.6.14-1build1_s390x.deb ...
309s Unpacking libtk8.6:s390x (8.6.14-1build1) ...
309s Selecting previously unselected package libxt6t64:s390x.
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309s Unpacking autopkgtest-satdep (0) ...
309s Setting up libhtscodecs2:s390x (1.6.0-1) ...
309s Setting up libgraphite2-3:s390x (1.3.14-2build1) ...
309s Setting up qtltools-example (1.3.1+dfsg-4build3) ...
309s Setting up libboost-program-options1.83.0:s390x (1.83.0-2.1ubuntu3) ...
309s Setting up libpixman-1-0:s390x (0.42.2-1build1) ...
309s Setting up libpaper1:s390x (1.1.29build1) ...
310s 
310s Creating config file /etc/papersize with new version
310s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
312s Regenerating fonts cache... done.
312s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ...
312s Setting up libdatrie1:s390x (0.2.13-3build1) ...
312s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ...
312s Setting up libxcb-render0:s390x (1.15-1) ...
312s Setting up unzip (6.0-28ubuntu4) ...
312s Setting up x11-common (1:7.7+23ubuntu3) ...
312s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ...
312s Setting up libxcb-shm0:s390x (1.15-1) ...
312s Setting up libpaper-utils (1.1.29build1) ...
312s Setting up libgomp1:s390x (14-20240412-0ubuntu1) ...
312s Setting up libcairo2:s390x (1.18.0-3build1) ...
312s Setting up zip (3.0-13build1) ...
312s Setting up libblas3:s390x (3.12.0-3build1) ...
312s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode
312s Setting up libboost-iostreams1.83.0:s390x (1.83.0-2.1ubuntu3) ...
312s Setting up libtcl8.6:s390x (8.6.14+dfsg-1build1) ...
312s Setting up libgfortran5:s390x (14-20240412-0ubuntu1) ...
312s Setting up r-mathlib (4.3.3-2build2) ...
312s Setting up libhts3t64:s390x (1.19+ds-1.1build3) ...
312s Setting up libharfbuzz0b:s390x (8.3.0-2build2) ...
312s Setting up libthai-data (0.1.29-2build1) ...
312s Setting up libxss1:s390x (1:1.2.3-1build3) ...
312s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
312s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
312s Setting up libice6:s390x (2:1.0.10-1build3) ...
312s Setting up liblapack3:s390x (3.12.0-3build1) ...
312s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode
312s Setting up libxft2:s390x (2.3.6-1build1) ...
312s Setting up libtk8.6:s390x (8.6.14-1build1) ...
312s Setting up libthai0:s390x (0.1.29-2build1) ...
312s Setting up libsm6:s390x (2:1.2.3-1build3) ...
312s Setting up libpango-1.0-0:s390x (1.52.1+ds-1build1) ...
312s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ...
312s Setting up libpangoft2-1.0-0:s390x (1.52.1+ds-1build1) ...
312s Setting up libpangocairo-1.0-0:s390x (1.52.1+ds-1build1) ...
312s Setting up r-base-core (4.3.3-2build2) ...
312s 
312s Creating config file /etc/R/Renviron with new version
312s Setting up qtltools (1.3.1+dfsg-4build3) ...
312s Setting up autopkgtest-satdep (0) ...
312s Processing triggers for man-db (2.12.0-4build2) ...
313s Processing triggers for install-info (7.1-3build2) ...
313s Processing triggers for libc-bin (2.39-0ubuntu8) ...
316s (Reading database ... 55907 files and directories currently installed.)
316s Removing autopkgtest-satdep (0) ...
317s autopkgtest [01:59:07]: test run-sample-analysis: [-----------------------
317s ./genes.50percent.chr22.bed.gz
317s ./genes.50percent.chr22.bed.gz.tbi
317s ./genes.covariates.pc50.txt.gz
317s ./genes.simulated.chr22.bed.gz
317s ./genes.simulated.chr22.bed.gz.tbi
317s ./genotypes.chr22.vcf.gz
318s ./genotypes.chr22.vcf.gz.tbi
318s 
318s QTLtools
318s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
318s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
318s   * Webpage : https://qtltools.github.io/qtltools/
318s   * Version : 1.3.1
318s   * Date    : 19/04/2024 - 01:59:08
318s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
318s 
318s CONDUCT PCA ON DATA
318s 
318s Initialize random number generator
318s   * Built-in seed is 15112011
318s   * First Integer = 30553
318s   * First Double = 0.0126695
318s 
318s Reading sample list from [genes.50percent.chr22.bed.gz]
318s   * #samples = 358
318s 
318s Merging sample sets from all input files
318s   * #files = 1
318s   * #samples in all files = 358
318s 
318s Reading phenotype data in [genes.50percent.chr22.bed.gz]
318s   * 358 samples included
318s   * 608 phenotypes included
318s 
318s Calculating PCA with a matrix 358 x 608
318s   * Calculated mean and sd
318s   * 0 sd==0 columns removed
318s   * Variables centered
318s   * Variables scaled to unit variance
318s   * Running SVD
319s   * SVD complete
319s   * Calculated sd and var for PCs
319s   * Calculated cumulative var for PCs
319s   * Done!
319s 
319s Running time: 1 seconds
319s 
319s QTLtools
319s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
319s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
319s   * Webpage : https://qtltools.github.io/qtltools/
319s   * Version : 1.3.1
319s   * Date    : 19/04/2024 - 01:59:09
319s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
319s 
319s MAPPING QTL IN CIS
319s   * TASK: Report all nominal associations with p <= 0.01
319s   * Linear model: Phe ~ Var + Cov
319s   * Cis-window size is 1000000 bp
319s   * Region = [chr22:17000000-18000000]
319s 
319s Initialize random number generator
319s   * Built-in seed is 15112011
319s   * First Integer = 30553
319s   * First Double = 0.0126695
319s 
319s Reading sample list from [genes.50percent.chr22.bed.gz]
319s   * #samples = 358
319s 
319s Read sample list from [genotypes.chr22.vcf.gz]
319s   * #samples = 358
319s 
319s Reading sample list from [genes.covariates.pc50.txt.gz]
319s   * #samples = 358
319s 
319s Merging sample sets from all input files
319s   * #files = 3
319s   * #samples in all files = 358
319s 
319s Reading phenotype data in [genes.50percent.chr22.bed.gz]
319s   * target region [chr22:17000000-18000000]
319s   * 8 phenotypes included
319s   * 3 phenotypes are on the negative strand
319s 
319s Reading genotype data in [genotypes.chr22.vcf.gz]
319s   * File format detected: VCF
319s   * target region [chr22:16000000-19000000]
320s   * 6404 variants included
320s 
320s Reading covariates in [genes.covariates.pc50.txt.gz]
320s   * 53 covariates included
320s 
320s Residualize phenotypes for covariates
320s   * #covariates = 53
320s 
320s Processing phenotype [ENSG00000237438.2] [1/8]
320s   * #variants in cis = 5095
320s   * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518]
320s 
320s Processing phenotype [ENSG00000273203.1] [2/8]
320s   * #variants in cis = 5170
320s   * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406]
320s 
320s Processing phenotype [ENSG00000273442.1] [3/8]
320s   * #variants in cis = 5188
320s   * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340]
320s 
320s Processing phenotype [ENSG00000177663.9] [4/8]
320s   * #variants in cis = 5193
320s   * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096]
320s 
320s Processing phenotype [ENSG00000183307.3] [5/8]
320s   * #variants in cis = 5230
320s   * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078]
320s 
320s Processing phenotype [ENSG00000069998.8] [6/8]
320s   * #variants in cis = 5291
320s   * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147]
320s 
320s Processing phenotype [ENSG00000093072.11] [7/8]
320s   * #variants in cis = 5293
320s   * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404]
320s 
320s Processing phenotype [ENSG00000099954.14] [8/8]
320s   * #variants in cis = 5435
320s   * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067]
320s 
320s Running time: 0 seconds
320s 
320s QTLtools
320s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
320s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
320s   * Webpage : https://qtltools.github.io/qtltools/
320s   * Version : 1.3.1
320s   * Date    : 19/04/2024 - 01:59:10
320s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
320s 
320s MAPPING QTL IN CIS
320s   * TASK: Perform 1000 permutations
320s   * Linear model: Phe ~ Var + Cov
320s   * Cis-window size is 1000000 bp
320s   * Region = [chr22:17000000-18000000]
320s 
320s Initialize random number generator
320s   * Built-in seed is 15112011
320s   * First Integer = 30553
320s   * First Double = 0.0126695
320s 
320s Reading sample list from [genes.50percent.chr22.bed.gz]
320s   * #samples = 358
320s 
320s Read sample list from [genotypes.chr22.vcf.gz]
320s   * #samples = 358
320s 
320s Reading sample list from [genes.covariates.pc50.txt.gz]
320s   * #samples = 358
320s 
320s Merging sample sets from all input files
320s   * #files = 3
320s   * #samples in all files = 358
320s 
320s Reading phenotype data in [genes.50percent.chr22.bed.gz]
320s   * target region [chr22:17000000-18000000]
320s   * 8 phenotypes included
320s   * 3 phenotypes are on the negative strand
320s 
320s Reading genotype data in [genotypes.chr22.vcf.gz]
320s   * File format detected: VCF
320s   * target region [chr22:16000000-19000000]
320s   * 6404 variants included
320s 
320s Reading covariates in [genes.covariates.pc50.txt.gz]
320s   * 53 covariates included
320s 
320s Residualize phenotypes for covariates
320s   * #covariates = 53
320s 
320s Processing phenotype [ENSG00000237438.2] [1/8]
320s   * #variants in cis = 5095
321s   * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518]
321s   * Beta parameters: [s1=1.00995, s2=621.053]
321s   * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20]
321s 
321s Processing phenotype [ENSG00000273203.1] [2/8]
321s   * #variants in cis = 5170
322s   * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406]
322s   * Beta parameters: [s1=1.11817, s2=641.379]
322s   * Adjusted p-values: [emp=0.00799201, beta=0.00751892]
322s 
322s Processing phenotype [ENSG00000273442.1] [3/8]
322s   * #variants in cis = 5188
323s   * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340]
323s   * Beta parameters: [s1=1.08364, s2=467.63]
323s   * Adjusted p-values: [emp=0.297702, beta=0.293948]
323s 
323s Processing phenotype [ENSG00000177663.9] [4/8]
323s   * #variants in cis = 5193
324s   * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096]
324s   * Beta parameters: [s1=0.989061, s2=704.553]
324s   * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10]
324s 
324s Processing phenotype [ENSG00000183307.3] [5/8]
324s   * #variants in cis = 5230
326s   * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078]
326s   * Beta parameters: [s1=1.01322, s2=559.49]
326s   * Adjusted p-values: [emp=0.000999001, beta=0.00050707]
326s 
326s Processing phenotype [ENSG00000069998.8] [6/8]
326s   * #variants in cis = 5291
327s   * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147]
327s   * Beta parameters: [s1=1.02312, s2=563.339]
327s   * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10]
327s 
327s Processing phenotype [ENSG00000093072.11] [7/8]
327s   * #variants in cis = 5293
328s   * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404]
328s   * Beta parameters: [s1=0.957514, s2=559.397]
328s   * Adjusted p-values: [emp=0.574426, beta=0.562826]
328s 
328s Processing phenotype [ENSG00000099954.14] [8/8]
328s   * #variants in cis = 5435
329s   * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067]
329s   * Beta parameters: [s1=0.938041, s2=226.852]
329s   * Adjusted p-values: [emp=0.842158, beta=0.84836]
329s 
329s Running time: 9 seconds
329s 
329s QTLtools
329s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
329s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
329s   * Webpage : https://qtltools.github.io/qtltools/
329s   * Version : 1.3.1
329s   * Date    : 19/04/2024 - 01:59:19
329s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
329s 
329s MAPPING QTL IN TRANS
329s   * TASK: Perform a full nominal pass, do not adjust p-values
329s   * Cis-window size is 5000000 bp
329s   * #bins = 1000
329s   * threshold = 1e-05
329s 
329s Initialize random number generator
329s   * Built-in seed is 15112011
329s   * First Integer = 30553
329s   * First Double = 0.0126695
329s 
329s Read sample list from [genotypes.chr22.vcf.gz]
329s   * #samples = 358
329s 
329s Checking sample list in [genes.simulated.chr22.bed.gz]
329s   * #samples = 358
329s 
329s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0
329s   * 358 samples included
329s   * 608 phenotypes included
329s   * 275 phenotypes is on the negative strand
329s 
329s Calculate correlation threshold
329s   * thres = 1e-05
329s   * corr = 0.2311
329s 
329s Sweep through genotype data in [genotypes.chr22.vcf.gz]
330s   * #variants=1950	#multi_allelic=0	#not_processed=0	#hits=101/1000000	speed=3.92MT/s
330s   * #variants=4001	#multi_allelic=0	#not_processed=0	#hits=153/2000000	speed=3.89MT/s
330s   * #variants=6187	#multi_allelic=0	#not_processed=0	#hits=244/3000000	speed=3.86MT/s
330s   * #variants=8537	#multi_allelic=0	#not_processed=0	#hits=285/4000000	speed=3.79MT/s
331s   * #variants=11025	#multi_allelic=0	#not_processed=0	#hits=312/5000000	speed=3.75MT/s
331s   * #variants=13621	#multi_allelic=0	#not_processed=0	#hits=320/6000000	speed=3.72MT/s
331s   * #variants=16217	#multi_allelic=0	#not_processed=0	#hits=342/7000000	speed=3.72MT/s
332s   * #variants=18755	#multi_allelic=0	#not_processed=0	#hits=401/8000000	speed=3.73MT/s
332s   * #variants=21237	#multi_allelic=0	#not_processed=0	#hits=402/9000000	speed=3.76MT/s
332s   * #variants=23680	#multi_allelic=0	#not_processed=0	#hits=455/10000000	speed=3.76MT/s
332s   * #variants=26171	#multi_allelic=0	#not_processed=0	#hits=463/11000000	speed=3.76MT/s
333s   * #variants=28609	#multi_allelic=0	#not_processed=0	#hits=469/12000000	speed=3.77MT/s
333s   * #variants=30861	#multi_allelic=0	#not_processed=0	#hits=973/13000000	speed=3.82MT/s
333s   * #variants=32932	#multi_allelic=0	#not_processed=0	#hits=979/14000000	speed=3.91MT/s
333s   * #variants=34974	#multi_allelic=0	#not_processed=0	#hits=1085/15000000	speed=3.91MT/s
334s   * #variants=37021	#multi_allelic=0	#not_processed=0	#hits=1086/16000000	speed=3.92MT/s
334s   * #variants=39122	#multi_allelic=0	#not_processed=0	#hits=1089/17000000	speed=3.88MT/s
334s   * #variants=41334	#multi_allelic=0	#not_processed=0	#hits=1089/18000000	speed=3.80MT/s
334s   * #variants=43627	#multi_allelic=0	#not_processed=0	#hits=1096/19000000	speed=3.83MT/s
335s   * #variants=45897	#multi_allelic=0	#not_processed=0	#hits=1153/20000000	speed=3.83MT/s
335s   * #variants=48114	#multi_allelic=0	#not_processed=0	#hits=1243/21000000	speed=3.80MT/s
335s   * #variants=50410	#multi_allelic=0	#not_processed=0	#hits=1249/22000000	speed=3.82MT/s
335s   * #variants=52820	#multi_allelic=0	#not_processed=0	#hits=1259/23000000	speed=3.76MT/s
336s   * #variants=55279	#multi_allelic=0	#not_processed=0	#hits=1498/24000000	speed=3.76MT/s
336s   * #variants=57789	#multi_allelic=0	#not_processed=0	#hits=1724/25000000	speed=3.73MT/s
336s   * #variants=60201	#multi_allelic=0	#not_processed=0	#hits=2168/26000000	speed=3.75MT/s
337s   * #variants=62476	#multi_allelic=0	#not_processed=0	#hits=2452/27000000	speed=3.82MT/s
337s   * #variants=64608	#multi_allelic=0	#not_processed=0	#hits=2544/28000000	speed=3.88MT/s
337s   * #variants=66709	#multi_allelic=0	#not_processed=0	#hits=2684/29000000	speed=3.89MT/s
337s   * #variants=68871	#multi_allelic=0	#not_processed=0	#hits=2688/30000000	speed=3.88MT/s
338s   * #variants=71070	#multi_allelic=0	#not_processed=0	#hits=2720/31000000	speed=3.86MT/s
338s   * #variants=73151	#multi_allelic=0	#not_processed=0	#hits=2891/32000000	speed=3.89MT/s
338s   * #variants=75122	#multi_allelic=0	#not_processed=0	#hits=3110/33000000	speed=3.92MT/s
338s   * #variants=77058	#multi_allelic=0	#not_processed=0	#hits=3209/34000000	speed=3.95MT/s
339s   * #variants=78989	#multi_allelic=0	#not_processed=0	#hits=3218/35000000	speed=3.97MT/s
339s   * #variants=80903	#multi_allelic=0	#not_processed=0	#hits=3250/36000000	speed=3.97MT/s
339s   * #variants=82811	#multi_allelic=0	#not_processed=0	#hits=3463/37000000	speed=3.95MT/s
339s   * #variants=84694	#multi_allelic=0	#not_processed=0	#hits=4035/38000000	speed=3.94MT/s
339s   * #variants=85485	#multi_allelic=0	#not_processed=0	#hits=4036/38425275	speed=4.01MT/s
339s 
339s Running time: 10 seconds
339s 
339s QTLtools
339s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
339s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
339s   * Webpage : https://qtltools.github.io/qtltools/
339s   * Version : 1.3.1
339s   * Date    : 19/04/2024 - 01:59:29
339s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
339s 
339s MAPPING QTL IN TRANS
339s   * TASK: Permute randomly chosen phenotypes 1000 times and test
339s   * Cis-window size is 5000000 bp
339s   * #bins = 1000
339s   * threshold = 1e-05
339s 
339s Initialize random number generator
339s   * Built-in seed is 15112011
340s   * First Integer = 30553
340s   * First Double = 0.0126695
340s 
340s Read sample list from [genotypes.chr22.vcf.gz]
340s   * #samples = 358
340s 
340s Checking sample list in [genes.simulated.chr22.bed.gz]
340s   * #samples = 358
340s 
340s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0
340s   * 358 samples included
340s   * 608 phenotypes included
340s   * 275 phenotypes is on the negative strand
340s 
340s Normal transform phenotypes
340s 
340s Calculate correlation threshold
340s   * thres = 1e-05
340s   * corr = 0.2311
340s 
340s Sweep through genotype data in [genotypes.chr22.vcf.gz]
340s   * #variants=1177	#multi_allelic=0	#not_processed=0	#hits=28/1000000	speed=4.13MT/s
340s   * #variants=2383	#multi_allelic=0	#not_processed=0	#hits=38/2000000	speed=4.03MT/s
340s   * #variants=3633	#multi_allelic=0	#not_processed=0	#hits=53/3000000	speed=3.97MT/s
341s   * #variants=4928	#multi_allelic=0	#not_processed=0	#hits=53/4000000	speed=3.95MT/s
341s   * #variants=6269	#multi_allelic=0	#not_processed=0	#hits=71/5000000	speed=3.92MT/s
341s   * #variants=7675	#multi_allelic=0	#not_processed=0	#hits=72/6000000	speed=3.88MT/s
341s   * #variants=9151	#multi_allelic=0	#not_processed=0	#hits=88/7000000	speed=3.85MT/s
342s   * #variants=10663	#multi_allelic=0	#not_processed=0	#hits=96/8000000	speed=3.80MT/s
342s   * #variants=12202	#multi_allelic=0	#not_processed=0	#hits=96/9000000	speed=3.79MT/s
342s   * #variants=13804	#multi_allelic=0	#not_processed=0	#hits=96/10000000	speed=3.75MT/s
342s   * #variants=15381	#multi_allelic=0	#not_processed=0	#hits=120/11000000	speed=3.75MT/s
343s   * #variants=16946	#multi_allelic=0	#not_processed=0	#hits=123/12000000	speed=3.77MT/s
343s   * #variants=18483	#multi_allelic=0	#not_processed=0	#hits=129/13000000	speed=3.69MT/s
343s   * #variants=19995	#multi_allelic=0	#not_processed=0	#hits=131/14000000	speed=3.79MT/s
343s   * #variants=21489	#multi_allelic=0	#not_processed=0	#hits=132/15000000	speed=3.82MT/s
344s   * #variants=22947	#multi_allelic=0	#not_processed=0	#hits=151/16000000	speed=3.82MT/s
344s   * #variants=24445	#multi_allelic=0	#not_processed=0	#hits=168/17000000	speed=3.83MT/s
344s   * #variants=25965	#multi_allelic=0	#not_processed=0	#hits=175/18000000	speed=3.80MT/s
345s   * #variants=27472	#multi_allelic=0	#not_processed=0	#hits=179/19000000	speed=3.82MT/s
345s   * #variants=28933	#multi_allelic=0	#not_processed=0	#hits=181/20000000	speed=3.83MT/s
345s   * #variants=30325	#multi_allelic=0	#not_processed=0	#hits=181/21000000	speed=3.23MT/s
345s   * #variants=31617	#multi_allelic=0	#not_processed=0	#hits=182/22000000	speed=3.86MT/s
346s   * #variants=32875	#multi_allelic=0	#not_processed=0	#hits=190/23000000	speed=4.00MT/s
346s   * #variants=34127	#multi_allelic=0	#not_processed=0	#hits=192/24000000	speed=4.00MT/s
346s   * #variants=35392	#multi_allelic=0	#not_processed=0	#hits=206/25000000	speed=3.98MT/s
346s   * #variants=36652	#multi_allelic=0	#not_processed=0	#hits=206/26000000	speed=4.00MT/s
347s   * #variants=37940	#multi_allelic=0	#not_processed=0	#hits=213/27000000	speed=3.94MT/s
347s   * #variants=39255	#multi_allelic=0	#not_processed=0	#hits=238/28000000	speed=3.95MT/s
347s   * #variants=40602	#multi_allelic=0	#not_processed=0	#hits=239/29000000	speed=4.00MT/s
347s   * #variants=41998	#multi_allelic=0	#not_processed=0	#hits=245/30000000	speed=3.97MT/s
348s   * #variants=43398	#multi_allelic=0	#not_processed=0	#hits=245/31000000	speed=4.02MT/s
348s   * #variants=44803	#multi_allelic=0	#not_processed=0	#hits=260/32000000	speed=4.05MT/s
348s   * #variants=46187	#multi_allelic=0	#not_processed=0	#hits=261/33000000	speed=4.05MT/s
348s   * #variants=47545	#multi_allelic=0	#not_processed=0	#hits=268/34000000	speed=4.05MT/s
349s   * #variants=48904	#multi_allelic=0	#not_processed=0	#hits=280/35000000	speed=4.08MT/s
349s   * #variants=50309	#multi_allelic=0	#not_processed=0	#hits=306/36000000	speed=3.97MT/s
349s   * #variants=51731	#multi_allelic=0	#not_processed=0	#hits=314/37000000	speed=3.97MT/s
349s   * #variants=53171	#multi_allelic=0	#not_processed=0	#hits=320/38000000	speed=4.02MT/s
350s   * #variants=54621	#multi_allelic=0	#not_processed=0	#hits=323/39000000	speed=3.98MT/s
350s   * #variants=56099	#multi_allelic=0	#not_processed=0	#hits=323/40000000	speed=4.00MT/s
350s   * #variants=57584	#multi_allelic=0	#not_processed=0	#hits=340/41000000	speed=3.97MT/s
350s   * #variants=59032	#multi_allelic=0	#not_processed=0	#hits=344/42000000	speed=4.02MT/s
351s   * #variants=60437	#multi_allelic=0	#not_processed=0	#hits=345/43000000	speed=4.05MT/s
351s   * #variants=61810	#multi_allelic=0	#not_processed=0	#hits=357/44000000	speed=4.03MT/s
351s   * #variants=63129	#multi_allelic=0	#not_processed=0	#hits=384/45000000	speed=4.08MT/s
351s   * #variants=64409	#multi_allelic=0	#not_processed=0	#hits=391/46000000	speed=4.08MT/s
352s   * #variants=65679	#multi_allelic=0	#not_processed=0	#hits=430/47000000	speed=4.08MT/s
352s   * #variants=66953	#multi_allelic=0	#not_processed=0	#hits=436/48000000	speed=4.12MT/s
352s   * #variants=68247	#multi_allelic=0	#not_processed=0	#hits=446/49000000	speed=4.12MT/s
352s   * #variants=69595	#multi_allelic=0	#not_processed=0	#hits=460/50000000	speed=3.95MT/s
353s   * #variants=70918	#multi_allelic=0	#not_processed=0	#hits=481/51000000	speed=4.10MT/s
353s   * #variants=72211	#multi_allelic=0	#not_processed=0	#hits=492/52000000	speed=4.12MT/s
353s   * #variants=73449	#multi_allelic=0	#not_processed=0	#hits=492/53000000	speed=4.15MT/s
353s   * #variants=74662	#multi_allelic=0	#not_processed=0	#hits=500/54000000	speed=4.15MT/s
354s   * #variants=75863	#multi_allelic=0	#not_processed=0	#hits=506/55000000	speed=4.08MT/s
354s   * #variants=77058	#multi_allelic=0	#not_processed=0	#hits=513/56000000	speed=3.98MT/s
354s   * #variants=78253	#multi_allelic=0	#not_processed=0	#hits=515/57000000	speed=4.07MT/s
354s   * #variants=79446	#multi_allelic=0	#not_processed=0	#hits=530/58000000	speed=4.07MT/s
355s   * #variants=80634	#multi_allelic=0	#not_processed=0	#hits=581/59000000	speed=4.08MT/s
355s   * #variants=81817	#multi_allelic=0	#not_processed=0	#hits=594/60000000	speed=4.08MT/s
355s   * #variants=82993	#multi_allelic=0	#not_processed=0	#hits=598/61000000	speed=4.05MT/s
355s   * #variants=84160	#multi_allelic=0	#not_processed=0	#hits=599/62000000	speed=4.10MT/s
356s   * #variants=85304	#multi_allelic=0	#not_processed=0	#hits=609/63000000	speed=4.07MT/s
356s   * #variants=85485	#multi_allelic=0	#not_processed=0	#hits=609/63157827	speed=4.15MT/s
356s 
356s Running time: 16 seconds
356s autopkgtest [01:59:46]: test run-sample-analysis: -----------------------]
357s run-sample-analysis  PASS
357s autopkgtest [01:59:47]: test run-sample-analysis:  - - - - - - - - - - results - - - - - - - - - -
357s autopkgtest [01:59:47]: @@@@@@@@@@@@@@@@@@@@ summary
357s run-sample-analysis  PASS
389s Creating nova instance adt-noble-s390x-qtltools-20240419-013339-juju-7f2275-prod-proposed-migration-environment-3-62b2451f-66ba-4b17-a8dd-9766ade558a1 from image adt/ubuntu-noble-s390x-server-20240417.img (UUID 3d9b7fbd-ef84-45b7-835e-e8d6cdd55008)...