0s autopkgtest [01:49:05]: starting date and time: 2024-04-19 01:49:05+0000
  0s autopkgtest [01:49:05]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline
  0s autopkgtest [01:49:05]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m8ajlynr/out --timeout-copy=6000 --setup-commands 'dhclient || true; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.173 lxd-armhf-10.145.243.173:autopkgtest/ubuntu/noble/armhf
 43s autopkgtest [01:49:48]: testbed dpkg architecture: armhf
 45s autopkgtest [01:49:50]: testbed apt version: 2.7.14build2
 45s autopkgtest [01:49:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 72s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 81s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B]
 82s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [53.4 kB]
 82s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [338 kB]
 82s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB]
 82s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [80.5 kB]
 82s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B]
 82s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [976 B]
 82s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B]
 82s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [389 kB]
 83s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B]
 83s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B]
 97s Fetched 1004 kB in 25s (40.1 kB/s)
 98s Reading package lists...
122s sh: 1: dhclient: not found
124s tee: /proc/self/fd/2: Permission denied
192s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
192s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
192s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
192s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
212s Reading package lists...
212s Reading package lists...
212s Building dependency tree...
212s Reading state information...
212s Calculating upgrade...
213s The following packages will be upgraded:
213s   apport apport-core-dump-handler apport-symptoms base-passwd bcache-tools
213s   bind9-dnsutils bind9-host bind9-libs bzip2 cloud-init cpio cryptsetup-bin
213s   dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common
213s   dbus-user-session diffutils dmidecode dracut-install e2fsprogs
213s   e2fsprogs-l10n eatmydata ethtool findutils ftp gcc-13-base gcc-14-base
213s   gettext-base grep gzip hdparm hostname htop iptables iputils-ping
213s   iputils-tracepath kmod libacl1 libargon2-1 libassuan0 libatasmart4 libattr1
213s   libbytesize-common libbytesize1 libbz2-1.0 libcap2 libcap2-bin libcom-err2
213s   libcrypt1 libcryptsetup12 libdb5.3t64 libdbus-1-3 libdrm-common libdrm2
213s   libeatmydata1 libedit2 libestr0 libevdev2 libext2fs2t64 libfastjson4 libffi8
213s   libfido2-1 libflashrom1 libfribidi0 libgcc-s1 libgcrypt20 libgmp10
213s   libgpg-error-l10n libgpg-error0 libicu74 libidn2-0 libinih1 libip4tc2
213s   libip6tc2 libjson-c5 libkeyutils1 libkmod2 liblmdb0 liblz4-1 liblzo2-2
213s   libmaxminddb0 libmd0 libmnl0 libmpfr6 libncurses6 libncursesw6
213s   libnetfilter-conntrack3 libnetplan1 libnfnetlink0 libnftables1 libnftnl11
213s   libnghttp2-14 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 libnspr4
213s   libnss3 libnuma1 libonig5 libp11-kit0 libpam-cap libpam-modules
213s   libpam-modules-bin libpam-runtime libpam0g libpci3 libpcre2-8-0 libpopt0
213s   libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libsepol2
213s   libsgutils2-1.46-2 libsigsegv2 libss2 libstdc++6 libtasn1-6 libtinfo6
213s   libuchardet0 libunistring5 libutempter0 libx11-6 libx11-data libxau6
213s   libxdmcp6 libxext6 libxkbcommon0 libxmlb2 libxtables12 libxxhash0
213s   libyaml-0-2 libzstd1 login logrotate logsave make man-db mawk nano
213s   ncurses-base ncurses-bin ncurses-term netcat-openbsd netplan-generator
213s   netplan.io nftables numactl openssh-client openssh-server
213s   openssh-sftp-server passwd patch pci.ids pciutils python-apt-common python3
213s   python3-apport python3-apt python3-cffi-backend python3-gdbm python3-minimal
213s   python3-netifaces python3-netplan python3-problem-report python3-systemd
213s   python3.12 python3.12-minimal rsync rsyslog screen sed sg3-utils
213s   sg3-utils-udev sudo sysstat sysvinit-utils tar tcpdump time tnftp tzdata ufw
213s   usb.ids usbutils xauth xdg-user-dirs xkb-data zstd
213s 190 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
213s Need to get 43.9 MB of archives.
213s After this operation, 585 kB disk space will be freed.
213s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1build1 [167 kB]
214s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf findutils armhf 4.9.0-5build1 [293 kB]
214s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-4build1 [157 kB]
214s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf gzip armhf 1.12-1ubuntu3 [95.8 kB]
214s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf hostname armhf 3.23+nmu2ubuntu2 [10.4 kB]
214s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf login armhf 1:4.13+dfsg1-4ubuntu3 [200 kB]
214s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-bin armhf 6.4+20240113-1ubuntu2 [178 kB]
214s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf sed armhf 4.9-2build1 [190 kB]
214s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf tar armhf 1.35+dfsg-3build1 [236 kB]
214s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.3build1 [50.9 kB]
214s Get:11 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB]
214s Get:12 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-term all 6.4+20240113-1ubuntu2 [275 kB]
214s Get:13 http://ftpmaster.internal/ubuntu noble/main armhf sysvinit-utils armhf 3.08-6ubuntu3 [33.8 kB]
214s Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt1 armhf 1:4.4.36-4build1 [92.6 kB]
214s Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libpam0g armhf 1.5.3-5ubuntu5 [62.1 kB]
214s Get:16 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu5 [47.0 kB]
214s Get:17 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules armhf 1.5.3-5ubuntu5 [260 kB]
214s Get:18 http://ftpmaster.internal/ubuntu noble/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu4 [5998 B]
214s Get:19 http://ftpmaster.internal/ubuntu noble/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu4 [22.0 kB]
214s Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu4 [202 kB]
214s Get:21 http://ftpmaster.internal/ubuntu noble/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu4 [571 kB]
214s Get:22 http://ftpmaster.internal/ubuntu noble/main armhf tzdata all 2024a-2ubuntu1 [273 kB]
214s Get:23 http://ftpmaster.internal/ubuntu noble/main armhf python3.12 armhf 3.12.3-1 [651 kB]
214s Get:24 http://ftpmaster.internal/ubuntu noble/main armhf bzip2 armhf 1.0.8-5.1 [33.5 kB]
214s Get:25 http://ftpmaster.internal/ubuntu noble/main armhf libbz2-1.0 armhf 1.0.8-5.1 [31.1 kB]
214s Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-7 [662 kB]
214s Get:27 http://ftpmaster.internal/ubuntu noble/main armhf gcc-14-base armhf 14-20240412-0ubuntu1 [47.6 kB]
214s Get:28 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-s1 armhf 14-20240412-0ubuntu1 [41.5 kB]
214s Get:29 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++6 armhf 14-20240412-0ubuntu1 [714 kB]
214s Get:30 http://ftpmaster.internal/ubuntu noble/main armhf libffi8 armhf 3.4.6-1build1 [21.2 kB]
214s Get:31 http://ftpmaster.internal/ubuntu noble/main armhf libncurses6 armhf 6.4+20240113-1ubuntu2 [88.1 kB]
214s Get:32 http://ftpmaster.internal/ubuntu noble/main armhf libncursesw6 armhf 6.4+20240113-1ubuntu2 [119 kB]
214s Get:33 http://ftpmaster.internal/ubuntu noble/main armhf libtinfo6 armhf 6.4+20240113-1ubuntu2 [90.8 kB]
214s Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.12-stdlib armhf 3.12.3-1 [1925 kB]
214s Get:35 http://ftpmaster.internal/ubuntu noble/main armhf python3.12-minimal armhf 3.12.3-1 [2023 kB]
214s Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libpython3.12-minimal armhf 3.12.3-1 [817 kB]
214s Get:37 http://ftpmaster.internal/ubuntu noble/main armhf python3-minimal armhf 3.12.3-0ubuntu1 [27.2 kB]
214s Get:38 http://ftpmaster.internal/ubuntu noble/main armhf python3 armhf 3.12.3-0ubuntu1 [24.1 kB]
214s Get:39 http://ftpmaster.internal/ubuntu noble/main armhf libpython3-stdlib armhf 3.12.3-0ubuntu1 [9896 B]
214s Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libacl1 armhf 2.3.2-1build1 [15.1 kB]
214s Get:41 http://ftpmaster.internal/ubuntu noble/main armhf liblz4-1 armhf 1.9.4-1build1 [58.0 kB]
214s Get:42 http://ftpmaster.internal/ubuntu noble/main armhf libpopt0 armhf 1.19+dfsg-1build1 [25.0 kB]
214s Get:43 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2build1 [31.5 kB]
214s Get:44 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2build1 [265 kB]
215s Get:45 http://ftpmaster.internal/ubuntu noble/main armhf rsync armhf 3.2.7-1ubuntu1 [413 kB]
215s Get:46 http://ftpmaster.internal/ubuntu noble/main armhf python-apt-common all 2.7.7ubuntu1 [20.1 kB]
215s Get:47 http://ftpmaster.internal/ubuntu noble/main armhf python3-apt armhf 2.7.7ubuntu1 [162 kB]
215s Get:48 http://ftpmaster.internal/ubuntu noble/main armhf python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB]
215s Get:49 http://ftpmaster.internal/ubuntu noble/main armhf python3-apport all 2.28.1-0ubuntu1 [92.1 kB]
215s Get:50 http://ftpmaster.internal/ubuntu noble/main armhf apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB]
215s Get:51 http://ftpmaster.internal/ubuntu noble/main armhf apport all 2.28.1-0ubuntu1 [83.5 kB]
215s Get:52 http://ftpmaster.internal/ubuntu noble/main armhf passwd armhf 1:4.13+dfsg1-4ubuntu3 [817 kB]
215s Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libedit2 armhf 3.1-20230828-1build1 [78.7 kB]
215s Get:54 http://ftpmaster.internal/ubuntu noble/main armhf libfido2-1 armhf 1.14.0-1build3 [75.8 kB]
215s Get:55 http://ftpmaster.internal/ubuntu noble/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu13 [35.5 kB]
215s Get:56 http://ftpmaster.internal/ubuntu noble/main armhf openssh-server armhf 1:9.6p1-3ubuntu13 [504 kB]
215s Get:57 http://ftpmaster.internal/ubuntu noble/main armhf openssh-client armhf 1:9.6p1-3ubuntu13 [890 kB]
215s Get:58 http://ftpmaster.internal/ubuntu noble/main armhf libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB]
215s Get:59 http://ftpmaster.internal/ubuntu noble/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu4 [21.9 kB]
215s Get:60 http://ftpmaster.internal/ubuntu noble/main armhf libattr1 armhf 1:2.5.2-1build1 [10.2 kB]
215s Get:61 http://ftpmaster.internal/ubuntu noble/main armhf libcap2 armhf 1:2.66-5ubuntu2 [25.8 kB]
215s Get:62 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error-l10n all 1.47-3build2 [8064 B]
215s Get:63 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error0 armhf 1.47-3build2 [61.6 kB]
215s Get:64 http://ftpmaster.internal/ubuntu noble/main armhf libgcrypt20 armhf 1.10.3-2build1 [454 kB]
215s Get:65 http://ftpmaster.internal/ubuntu noble/main armhf libgmp10 armhf 2:6.3.0+dfsg-2ubuntu6 [207 kB]
215s Get:66 http://ftpmaster.internal/ubuntu noble/main armhf libmd0 armhf 1.1.0-2build1 [23.0 kB]
215s Get:67 http://ftpmaster.internal/ubuntu noble/main armhf libpcre2-8-0 armhf 10.42-4ubuntu2 [198 kB]
215s Get:68 http://ftpmaster.internal/ubuntu noble/main armhf libsepol2 armhf 3.5-2build1 [263 kB]
215s Get:69 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2build1 [513 kB]
215s Get:70 http://ftpmaster.internal/ubuntu noble/main armhf libidn2-0 armhf 2.3.7-2build1 [96.2 kB]
215s Get:71 http://ftpmaster.internal/ubuntu noble/main armhf libp11-kit0 armhf 0.25.3-4ubuntu2 [258 kB]
215s Get:72 http://ftpmaster.internal/ubuntu noble/main armhf libtasn1-6 armhf 4.19.0-3build1 [37.2 kB]
215s Get:73 http://ftpmaster.internal/ubuntu noble/main armhf libassuan0 armhf 2.5.6-1build1 [31.3 kB]
215s Get:74 http://ftpmaster.internal/ubuntu noble/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu4 [14.7 kB]
215s Get:75 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20240123-1build1 [115 kB]
215s Get:76 http://ftpmaster.internal/ubuntu noble/main armhf dbus-system-bus-common all 1.14.10-4ubuntu4 [81.6 kB]
215s Get:77 http://ftpmaster.internal/ubuntu noble/main armhf dbus-session-bus-common all 1.14.10-4ubuntu4 [80.4 kB]
215s Get:78 http://ftpmaster.internal/ubuntu noble/main armhf dbus-user-session armhf 1.14.10-4ubuntu4 [9960 B]
215s Get:79 http://ftpmaster.internal/ubuntu noble/main armhf dbus-daemon armhf 1.14.10-4ubuntu4 [109 kB]
215s Get:80 http://ftpmaster.internal/ubuntu noble/main armhf dbus-bin armhf 1.14.10-4ubuntu4 [37.1 kB]
215s Get:81 http://ftpmaster.internal/ubuntu noble/main armhf dbus armhf 1.14.10-4ubuntu4 [28.1 kB]
215s Get:82 http://ftpmaster.internal/ubuntu noble/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu4 [190 kB]
215s Get:83 http://ftpmaster.internal/ubuntu noble/main armhf libpam-cap armhf 1:2.66-5ubuntu2 [11.6 kB]
215s Get:84 http://ftpmaster.internal/ubuntu noble/main armhf libcap2-bin armhf 1:2.66-5ubuntu2 [32.3 kB]
215s Get:85 http://ftpmaster.internal/ubuntu noble/main armhf iputils-ping armhf 3:20240117-1build1 [43.1 kB]
215s Get:86 http://ftpmaster.internal/ubuntu noble/main armhf kmod armhf 31+20240202-2ubuntu6 [91.8 kB]
215s Get:87 http://ftpmaster.internal/ubuntu noble/main armhf libkmod2 armhf 31+20240202-2ubuntu6 [45.0 kB]
215s Get:88 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4build1 [22.6 kB]
215s Get:89 http://ftpmaster.internal/ubuntu noble/main armhf libjson-c5 armhf 0.17-1build1 [31.3 kB]
215s Get:90 http://ftpmaster.internal/ubuntu noble/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu4 [238 kB]
215s Get:91 http://ftpmaster.internal/ubuntu noble/main armhf libestr0 armhf 0.1.11-1build1 [6770 B]
215s Get:92 http://ftpmaster.internal/ubuntu noble/main armhf libfastjson4 armhf 1.2304.0-1build1 [20.1 kB]
215s Get:93 http://ftpmaster.internal/ubuntu noble/main armhf libfribidi0 armhf 1.0.13-3build1 [23.9 kB]
215s Get:94 http://ftpmaster.internal/ubuntu noble/main armhf libicu74 armhf 74.2-1ubuntu3 [10.5 MB]
215s Get:95 http://ftpmaster.internal/ubuntu noble/main armhf libkeyutils1 armhf 1.6.3-3build1 [8236 B]
215s Get:96 http://ftpmaster.internal/ubuntu noble/main armhf libmnl0 armhf 1.0.5-2build1 [10.5 kB]
215s Get:97 http://ftpmaster.internal/ubuntu noble/main armhf netplan-generator armhf 1.0-2ubuntu1 [58.8 kB]
215s Get:98 http://ftpmaster.internal/ubuntu noble/main armhf python3-cffi-backend armhf 1.16.0-2build1 [68.0 kB]
215s Get:99 http://ftpmaster.internal/ubuntu noble/main armhf python3-netplan armhf 1.0-2ubuntu1 [22.5 kB]
215s Get:100 http://ftpmaster.internal/ubuntu noble/main armhf python3-netifaces armhf 0.11.0-2build3 [17.2 kB]
215s Get:101 http://ftpmaster.internal/ubuntu noble/main armhf netplan.io armhf 1.0-2ubuntu1 [64.7 kB]
216s Get:102 http://ftpmaster.internal/ubuntu noble/main armhf libyaml-0-2 armhf 0.2.5-1build1 [45.2 kB]
216s Get:103 http://ftpmaster.internal/ubuntu noble/main armhf libnetplan1 armhf 1.0-2ubuntu1 [115 kB]
216s Get:104 http://ftpmaster.internal/ubuntu noble/main armhf iptables armhf 1.8.10-3ubuntu2 [338 kB]
216s Get:105 http://ftpmaster.internal/ubuntu noble/main armhf libip4tc2 armhf 1.8.10-3ubuntu2 [21.3 kB]
216s Get:106 http://ftpmaster.internal/ubuntu noble/main armhf libip6tc2 armhf 1.8.10-3ubuntu2 [21.7 kB]
216s Get:107 http://ftpmaster.internal/ubuntu noble/main armhf libnfnetlink0 armhf 1.0.2-2build1 [12.9 kB]
216s Get:108 http://ftpmaster.internal/ubuntu noble/main armhf libnetfilter-conntrack3 armhf 1.0.9-6build1 [37.5 kB]
216s Get:109 http://ftpmaster.internal/ubuntu noble/main armhf libnftnl11 armhf 1.2.6-2build1 [52.5 kB]
216s Get:110 http://ftpmaster.internal/ubuntu noble/main armhf libxtables12 armhf 1.8.10-3ubuntu2 [32.4 kB]
216s Get:111 http://ftpmaster.internal/ubuntu noble/main armhf logrotate armhf 3.21.0-2build1 [50.3 kB]
216s Get:112 http://ftpmaster.internal/ubuntu noble/main armhf netcat-openbsd armhf 1.226-1ubuntu2 [42.8 kB]
216s Get:113 http://ftpmaster.internal/ubuntu noble/main armhf rsyslog armhf 8.2312.0-3ubuntu9 [460 kB]
216s Get:114 http://ftpmaster.internal/ubuntu noble/main armhf sudo armhf 1.9.15p5-3ubuntu5 [936 kB]
216s Get:115 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1build1 [17.3 kB]
216s Get:116 http://ftpmaster.internal/ubuntu noble/main armhf xkb-data all 2.41-2ubuntu1 [395 kB]
216s Get:117 http://ftpmaster.internal/ubuntu noble/main armhf liblmdb0 armhf 0.9.31-1build1 [39.9 kB]
216s Get:118 http://ftpmaster.internal/ubuntu noble/main armhf libmaxminddb0 armhf 1.9.1-1build1 [23.2 kB]
216s Get:119 http://ftpmaster.internal/ubuntu noble/main armhf libnghttp2-14 armhf 1.59.0-1build4 [68.2 kB]
216s Get:120 http://ftpmaster.internal/ubuntu noble/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu5 [149 kB]
216s Get:121 http://ftpmaster.internal/ubuntu noble/main armhf bind9-host armhf 1:9.18.24-0ubuntu5 [47.4 kB]
216s Get:122 http://ftpmaster.internal/ubuntu noble/main armhf bind9-libs armhf 1:9.18.24-0ubuntu5 [1148 kB]
216s Get:123 http://ftpmaster.internal/ubuntu noble/main armhf cpio armhf 2.15+dfsg-1ubuntu2 [81.8 kB]
216s Get:124 http://ftpmaster.internal/ubuntu noble/main armhf dmidecode armhf 3.5-3build1 [58.6 kB]
216s Get:125 http://ftpmaster.internal/ubuntu noble/main armhf tnftp armhf 20230507-2build3 [98.7 kB]
216s Get:126 http://ftpmaster.internal/ubuntu noble/main armhf ftp all 20230507-2build3 [4728 B]
216s Get:127 http://ftpmaster.internal/ubuntu noble/main armhf gettext-base armhf 0.21-14ubuntu2 [38.1 kB]
216s Get:128 http://ftpmaster.internal/ubuntu noble/main armhf hdparm armhf 9.65+ds-1build1 [96.7 kB]
216s Get:129 http://ftpmaster.internal/ubuntu noble/main armhf iputils-tracepath armhf 3:20240117-1build1 [12.8 kB]
216s Get:130 http://ftpmaster.internal/ubuntu noble/main armhf libdrm-common all 2.4.120-2build1 [8096 B]
216s Get:131 http://ftpmaster.internal/ubuntu noble/main armhf libdrm2 armhf 2.4.120-2build1 [36.6 kB]
216s Get:132 http://ftpmaster.internal/ubuntu noble/main armhf nftables armhf 1.0.9-1build1 [69.5 kB]
216s Get:133 http://ftpmaster.internal/ubuntu noble/main armhf libnftables1 armhf 1.0.9-1build1 [309 kB]
217s Get:134 http://ftpmaster.internal/ubuntu noble/main armhf libnuma1 armhf 2.0.18-1build1 [19.8 kB]
217s Get:135 http://ftpmaster.internal/ubuntu noble/main armhf pci.ids all 0.0~2024.03.31-1 [275 kB]
217s Get:136 http://ftpmaster.internal/ubuntu noble/main armhf pciutils armhf 1:3.10.0-2build1 [64.4 kB]
217s Get:137 http://ftpmaster.internal/ubuntu noble/main armhf libpci3 armhf 1:3.10.0-2build1 [29.5 kB]
217s Get:138 http://ftpmaster.internal/ubuntu noble/main armhf libuchardet0 armhf 0.0.8-1build1 [73.9 kB]
217s Get:139 http://ftpmaster.internal/ubuntu noble/main armhf libx11-data all 2:1.8.7-1build1 [115 kB]
217s Get:140 http://ftpmaster.internal/ubuntu noble/main armhf libx11-6 armhf 2:1.8.7-1build1 [583 kB]
217s Get:141 http://ftpmaster.internal/ubuntu noble/main armhf libxau6 armhf 1:1.0.9-1build6 [6312 B]
217s Get:142 http://ftpmaster.internal/ubuntu noble/main armhf libxdmcp6 armhf 1:1.1.3-0ubuntu6 [8738 B]
217s Get:143 http://ftpmaster.internal/ubuntu noble/main armhf libxext6 armhf 2:1.3.4-1build2 [25.3 kB]
217s Get:144 http://ftpmaster.internal/ubuntu noble/main armhf man-db armhf 2.12.0-4build2 [1202 kB]
217s Get:145 http://ftpmaster.internal/ubuntu noble/main armhf nano armhf 7.2-2build1 [269 kB]
217s Get:146 http://ftpmaster.internal/ubuntu noble/main armhf python3-gdbm armhf 3.12.3-0ubuntu1 [15.2 kB]
217s Get:147 http://ftpmaster.internal/ubuntu noble/main armhf tcpdump armhf 4.99.4-3ubuntu4 [425 kB]
217s Get:148 http://ftpmaster.internal/ubuntu noble/main armhf time armhf 1.9-0.2build1 [45.8 kB]
217s Get:149 http://ftpmaster.internal/ubuntu noble/main armhf ufw all 0.36.2-6 [169 kB]
217s Get:150 http://ftpmaster.internal/ubuntu noble/main armhf usb.ids all 2024.03.18-1 [223 kB]
217s Get:151 http://ftpmaster.internal/ubuntu noble/main armhf usbutils armhf 1:017-3build1 [75.6 kB]
217s Get:152 http://ftpmaster.internal/ubuntu noble/main armhf xauth armhf 1:1.1.2-1build1 [22.7 kB]
217s Get:153 http://ftpmaster.internal/ubuntu noble/main armhf apport-symptoms all 0.25 [13.1 kB]
217s Get:154 http://ftpmaster.internal/ubuntu noble/main armhf bcache-tools armhf 1.0.8-5build1 [20.2 kB]
217s Get:155 http://ftpmaster.internal/ubuntu noble/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu4 [214 kB]
217s Get:156 http://ftpmaster.internal/ubuntu noble/main armhf dracut-install armhf 060+5-1ubuntu3 [34.1 kB]
217s Get:157 http://ftpmaster.internal/ubuntu noble/main armhf libeatmydata1 armhf 131-1ubuntu1 [7188 B]
217s Get:158 http://ftpmaster.internal/ubuntu noble/main armhf eatmydata all 131-1ubuntu1 [5584 B]
217s Get:159 http://ftpmaster.internal/ubuntu noble/main armhf ethtool armhf 1:6.7-1build1 [218 kB]
217s Get:160 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-base armhf 13.2.0-23ubuntu4 [48.9 kB]
217s Get:161 http://ftpmaster.internal/ubuntu noble/main armhf libnl-genl-3-200 armhf 3.7.0-0.3build1 [10.3 kB]
217s Get:162 http://ftpmaster.internal/ubuntu noble/main armhf libnl-route-3-200 armhf 3.7.0-0.3build1 [162 kB]
217s Get:163 http://ftpmaster.internal/ubuntu noble/main armhf libnl-3-200 armhf 3.7.0-0.3build1 [49.0 kB]
217s Get:164 http://ftpmaster.internal/ubuntu noble/main armhf htop armhf 3.3.0-4build1 [139 kB]
217s Get:165 http://ftpmaster.internal/ubuntu noble/main armhf libatasmart4 armhf 0.19-5build3 [24.0 kB]
217s Get:166 http://ftpmaster.internal/ubuntu noble/main armhf libmpfr6 armhf 4.2.1-1build1 [229 kB]
217s Get:167 http://ftpmaster.internal/ubuntu noble/main armhf libbytesize1 armhf 2.10-1ubuntu2 [11.7 kB]
217s Get:168 http://ftpmaster.internal/ubuntu noble/main armhf libbytesize-common all 2.10-1ubuntu2 [3396 B]
217s Get:169 http://ftpmaster.internal/ubuntu noble/main armhf libflashrom1 armhf 1.3.0-2.1ubuntu2 [138 kB]
217s Get:170 http://ftpmaster.internal/ubuntu noble/main armhf libinih1 armhf 55-1ubuntu2 [6506 B]
217s Get:171 http://ftpmaster.internal/ubuntu noble/main armhf liblzo2-2 armhf 2.10-2build4 [46.1 kB]
217s Get:172 http://ftpmaster.internal/ubuntu noble/main armhf libnspr4 armhf 2:4.35-1.1build1 [93.0 kB]
217s Get:173 http://ftpmaster.internal/ubuntu noble/main armhf libnss3 armhf 2:3.98-1build1 [1288 kB]
217s Get:174 http://ftpmaster.internal/ubuntu noble/main armhf libonig5 armhf 6.9.9-1build1 [148 kB]
217s Get:175 http://ftpmaster.internal/ubuntu noble/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu4 [82.7 kB]
217s Get:176 http://ftpmaster.internal/ubuntu noble/main armhf libsigsegv2 armhf 2.14-1ubuntu2 [14.2 kB]
217s Get:177 http://ftpmaster.internal/ubuntu noble/main armhf libutempter0 armhf 1.2.1-3build1 [8862 B]
217s Get:178 http://ftpmaster.internal/ubuntu noble/main armhf libxkbcommon0 armhf 1.6.0-1build1 [108 kB]
217s Get:179 http://ftpmaster.internal/ubuntu noble/main armhf libxmlb2 armhf 0.3.18-1 [56.9 kB]
217s Get:180 http://ftpmaster.internal/ubuntu noble/main armhf make armhf 4.3-4.1build2 [162 kB]
217s Get:181 http://ftpmaster.internal/ubuntu noble/main armhf numactl armhf 2.0.18-1build1 [38.2 kB]
217s Get:182 http://ftpmaster.internal/ubuntu noble/main armhf patch armhf 2.7.6-7build3 [110 kB]
217s Get:183 http://ftpmaster.internal/ubuntu noble/main armhf python3-systemd armhf 235-1build4 [39.7 kB]
217s Get:184 http://ftpmaster.internal/ubuntu noble/main armhf screen armhf 4.9.1-1build1 [638 kB]
217s Get:185 http://ftpmaster.internal/ubuntu noble/main armhf sg3-utils armhf 1.46-3ubuntu4 [816 kB]
217s Get:186 http://ftpmaster.internal/ubuntu noble/main armhf sg3-utils-udev all 1.46-3ubuntu4 [5922 B]
217s Get:187 http://ftpmaster.internal/ubuntu noble/main armhf sysstat armhf 12.6.1-2 [479 kB]
217s Get:188 http://ftpmaster.internal/ubuntu noble/main armhf zstd armhf 1.5.5+dfsg2-2build1 [683 kB]
217s Get:189 http://ftpmaster.internal/ubuntu noble/main armhf cloud-init all 24.1.3-0ubuntu3 [598 kB]
217s Get:190 http://ftpmaster.internal/ubuntu noble/main armhf libevdev2 armhf 1.13.1+dfsg-1build1 [29.8 kB]
219s Preconfiguring packages ...
220s Fetched 43.9 MB in 4s (10.6 MB/s)
220s (Reading database ... 
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220s Preparing to unpack .../diffutils_1%3a3.10-1build1_armhf.deb ...
220s Unpacking diffutils (1:3.10-1build1) over (1:3.10-1) ...
220s Setting up diffutils (1:3.10-1build1) ...
220s (Reading database ... 
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220s Preparing to unpack .../findutils_4.9.0-5build1_armhf.deb ...
220s Unpacking findutils (4.9.0-5build1) over (4.9.0-5) ...
220s Setting up findutils (4.9.0-5build1) ...
220s (Reading database ... 
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220s Preparing to unpack .../grep_3.11-4build1_armhf.deb ...
220s Unpacking grep (3.11-4build1) over (3.11-4) ...
220s Setting up grep (3.11-4build1) ...
220s (Reading database ... 
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220s Preparing to unpack .../gzip_1.12-1ubuntu3_armhf.deb ...
220s Unpacking gzip (1.12-1ubuntu3) over (1.12-1ubuntu2) ...
220s Setting up gzip (1.12-1ubuntu3) ...
220s (Reading database ... 
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220s Preparing to unpack .../hostname_3.23+nmu2ubuntu2_armhf.deb ...
220s Unpacking hostname (3.23+nmu2ubuntu2) over (3.23+nmu2ubuntu1) ...
220s Setting up hostname (3.23+nmu2ubuntu2) ...
220s (Reading database ... 
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220s Preparing to unpack .../login_1%3a4.13+dfsg1-4ubuntu3_armhf.deb ...
220s Unpacking login (1:4.13+dfsg1-4ubuntu3) over (1:4.13+dfsg1-4ubuntu1) ...
221s Setting up login (1:4.13+dfsg1-4ubuntu3) ...
221s (Reading database ... 
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221s Preparing to unpack .../ncurses-bin_6.4+20240113-1ubuntu2_armhf.deb ...
221s Unpacking ncurses-bin (6.4+20240113-1ubuntu2) over (6.4+20240113-1ubuntu1) ...
221s Setting up ncurses-bin (6.4+20240113-1ubuntu2) ...
221s (Reading database ... 
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221s Preparing to unpack .../sed_4.9-2build1_armhf.deb ...
221s Unpacking sed (4.9-2build1) over (4.9-2) ...
221s Setting up sed (4.9-2build1) ...
221s (Reading database ... 
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221s Preparing to unpack .../tar_1.35+dfsg-3build1_armhf.deb ...
221s Unpacking tar (1.35+dfsg-3build1) over (1.35+dfsg-3) ...
221s Setting up tar (1.35+dfsg-3build1) ...
221s (Reading database ... 
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221s Preparing to unpack .../base-passwd_3.6.3build1_armhf.deb ...
221s Unpacking base-passwd (3.6.3build1) over (3.6.3) ...
221s Setting up base-passwd (3.6.3build1) ...
221s (Reading database ... 
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221s Preparing to unpack .../ncurses-base_6.4+20240113-1ubuntu2_all.deb ...
221s Unpacking ncurses-base (6.4+20240113-1ubuntu2) over (6.4+20240113-1ubuntu1) ...
221s Setting up ncurses-base (6.4+20240113-1ubuntu2) ...
222s (Reading database ... 
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222s Preparing to unpack .../ncurses-term_6.4+20240113-1ubuntu2_all.deb ...
222s Unpacking ncurses-term (6.4+20240113-1ubuntu2) over (6.4+20240113-1ubuntu1) ...
222s Preparing to unpack .../sysvinit-utils_3.08-6ubuntu3_armhf.deb ...
222s Unpacking sysvinit-utils (3.08-6ubuntu3) over (3.08-6ubuntu2) ...
223s Setting up sysvinit-utils (3.08-6ubuntu3) ...
223s (Reading database ... 
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223s Preparing to unpack .../libcrypt1_1%3a4.4.36-4build1_armhf.deb ...
223s Unpacking libcrypt1:armhf (1:4.4.36-4build1) over (1:4.4.36-4) ...
223s Setting up libcrypt1:armhf (1:4.4.36-4build1) ...
223s (Reading database ... 
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223s Preparing to unpack .../libpam0g_1.5.3-5ubuntu5_armhf.deb ...
223s Unpacking libpam0g:armhf (1.5.3-5ubuntu5) over (1.5.3-5ubuntu4) ...
223s Setting up libpam0g:armhf (1.5.3-5ubuntu5) ...
223s (Reading database ... 
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223s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu5_armhf.deb ...
223s Unpacking libpam-modules-bin (1.5.3-5ubuntu5) over (1.5.3-5ubuntu4) ...
223s Setting up libpam-modules-bin (1.5.3-5ubuntu5) ...
224s pam_namespace.service is a disabled or a static unit not running, not starting it.
224s (Reading database ... 
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224s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu5_armhf.deb ...
224s Unpacking libpam-modules:armhf (1.5.3-5ubuntu5) over (1.5.3-5ubuntu4) ...
224s Setting up libpam-modules:armhf (1.5.3-5ubuntu5) ...
224s (Reading database ... 
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224s Preparing to unpack .../e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu4_all.deb ...
224s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ...
224s Preparing to unpack .../logsave_1.47.0-2.4~exp1ubuntu4_armhf.deb ...
224s Unpacking logsave (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ...
224s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu4_armhf.deb ...
224s Leaving 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64'
224s Leaving 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64'
224s Leaving 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64'
224s Leaving 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64'
224s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ...
224s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu4) ...
224s (Reading database ... 
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224s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu4_armhf.deb ...
224s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2.4~exp1ubuntu3) ...
224s Preparing to unpack .../tzdata_2024a-2ubuntu1_all.deb ...
224s Unpacking tzdata (2024a-2ubuntu1) over (2024a-1ubuntu1) ...
225s Preparing to unpack .../python3.12_3.12.3-1_armhf.deb ...
225s Unpacking python3.12 (3.12.3-1) over (3.12.2-5ubuntu3) ...
225s Preparing to unpack .../bzip2_1.0.8-5.1_armhf.deb ...
225s Unpacking bzip2 (1.0.8-5.1) over (1.0.8-5ubuntu1) ...
225s Preparing to unpack .../libbz2-1.0_1.0.8-5.1_armhf.deb ...
225s Unpacking libbz2-1.0:armhf (1.0.8-5.1) over (1.0.8-5ubuntu1) ...
225s Setting up libbz2-1.0:armhf (1.0.8-5.1) ...
225s (Reading database ... 
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(Reading database ... 58470 files and directories currently installed.)
225s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_armhf.deb ...
225s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-7) over (5.3.28+dfsg2-6build1) ...
225s Preparing to unpack .../gcc-14-base_14-20240412-0ubuntu1_armhf.deb ...
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232s Preparing to unpack .../libsepol2_3.5-2build1_armhf.deb ...
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303s Unpacking patch (2.7.6-7build3) over (2.7.6-7build2) ...
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303s Unpacking python3-systemd (235-1build4) over (235-1build3) ...
303s Preparing to unpack .../110-screen_4.9.1-1build1_armhf.deb ...
303s Unpacking screen (4.9.1-1build1) over (4.9.1-1) ...
303s Preparing to unpack .../111-sg3-utils_1.46-3ubuntu4_armhf.deb ...
303s Unpacking sg3-utils (1.46-3ubuntu4) over (1.46-3ubuntu3) ...
303s Preparing to unpack .../112-sg3-utils-udev_1.46-3ubuntu4_all.deb ...
303s Unpacking sg3-utils-udev (1.46-3ubuntu4) over (1.46-3ubuntu3) ...
303s Preparing to unpack .../113-sysstat_12.6.1-2_armhf.deb ...
303s Unpacking sysstat (12.6.1-2) over (12.6.1-1ubuntu1) ...
303s Preparing to unpack .../114-zstd_1.5.5+dfsg2-2build1_armhf.deb ...
303s Unpacking zstd (1.5.5+dfsg2-2build1) over (1.5.5+dfsg2-2) ...
303s Preparing to unpack .../115-cloud-init_24.1.3-0ubuntu3_all.deb ...
304s Unpacking cloud-init (24.1.3-0ubuntu3) over (24.1.3-0ubuntu2) ...
304s Preparing to unpack .../116-libevdev2_1.13.1+dfsg-1build1_armhf.deb ...
304s Unpacking libevdev2:armhf (1.13.1+dfsg-1build1) over (1.13.1+dfsg-1) ...
304s Setting up libip4tc2:armhf (1.8.10-3ubuntu2) ...
304s Setting up cpio (2.15+dfsg-1ubuntu2) ...
304s Setting up liblmdb0:armhf (0.9.31-1build1) ...
304s Setting up bcache-tools (1.0.8-5build1) ...
304s Setting up tcpdump (4.99.4-3ubuntu4) ...
304s apparmor_parser: Unable to replace "tcpdump".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
304s 
304s Setting up libxau6:armhf (1:1.0.9-1build6) ...
304s Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu6) ...
304s Setting up time (1.9-0.2build1) ...
304s Setting up libkeyutils1:armhf (1.6.3-3build1) ...
304s Setting up pci.ids (0.0~2024.03.31-1) ...
304s Setting up xdg-user-dirs (0.18-1build1) ...
304s Setting up libyaml-0-2:armhf (0.2.5-1build1) ...
304s Setting up libip6tc2:armhf (1.8.10-3ubuntu2) ...
304s Setting up libestr0:armhf (0.1.11-1build1) ...
304s Setting up libfastjson4:armhf (1.2304.0-1build1) ...
304s Setting up libinih1:armhf (55-1ubuntu2) ...
304s Setting up libmaxminddb0:armhf (1.9.1-1build1) ...
304s Setting up libargon2-1:armhf (0~20190702+dfsg-4build1) ...
304s Setting up libxmlb2:armhf (0.3.18-1) ...
304s Setting up libedit2:armhf (3.1-20230828-1build1) ...
304s Setting up rsyslog (8.2312.0-3ubuntu9) ...
306s info: The user `syslog' is already a member of `adm'.
307s apparmor_parser: Unable to replace "rsyslogd".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
311s Setting up netcat-openbsd (1.226-1ubuntu2) ...
311s Setting up libnghttp2-14:armhf (1.59.0-1build4) ...
311s Setting up libsgutils2-1.46-2:armhf (1.46-3ubuntu4) ...
311s Setting up gettext-base (0.21-14ubuntu2) ...
311s Setting up xkb-data (2.41-2ubuntu1) ...
311s Setting up liblzo2-2:armhf (2.10-2build4) ...
311s Setting up hdparm (9.65+ds-1build1) ...
311s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu4) ...
311s Setting up libnetplan1:armhf (1.0-2ubuntu1) ...
311s Setting up bzip2 (1.0.8-5.1) ...
311s Setting up man-db (2.12.0-4build2) ...
312s Updating database of manual pages ...
314s apparmor_parser: Unable to replace "/usr/bin/man".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
314s 
315s man-db.service is a disabled or a static unit not running, not starting it.
316s Setting up apport-symptoms (0.25) ...
316s Setting up usbutils (1:017-3build1) ...
316s Setting up tzdata (2024a-2ubuntu1) ...
316s 
316s Current default time zone: 'Etc/UTC'
316s Local time is now:      Fri Apr 19 01:54:21 UTC 2024.
316s Universal Time is now:  Fri Apr 19 01:54:21 UTC 2024.
316s Run 'dpkg-reconfigure tzdata' if you wish to change it.
316s 
316s Setting up libcap2-bin (1:2.66-5ubuntu2) ...
316s Setting up gcc-13-base:armhf (13.2.0-23ubuntu4) ...
316s Setting up libatasmart4:armhf (0.19-5build3) ...
316s Setting up libx11-data (2:1.8.7-1build1) ...
316s Setting up make (4.3-4.1build2) ...
316s Setting up libmpfr6:armhf (4.2.1-1build1) ...
316s Setting up libnspr4:armhf (2:4.35-1.1build1) ...
316s Setting up libncurses6:armhf (6.4+20240113-1ubuntu2) ...
316s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu4) ...
316s Setting up libsigsegv2:armhf (2.14-1ubuntu2) ...
316s Setting up libfribidi0:armhf (1.0.13-3build1) ...
316s Setting up libbytesize-common (2.10-1ubuntu2) ...
316s Setting up libmnl0:armhf (1.0.5-2build1) ...
316s Setting up patch (2.7.6-7build3) ...
316s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu4) ...
316s Setting up usb.ids (2024.03.18-1) ...
316s Setting up sudo (1.9.15p5-3ubuntu5) ...
316s Setting up libncursesw6:armhf (6.4+20240113-1ubuntu2) ...
316s Setting up libxtables12:armhf (1.8.10-3ubuntu2) ...
316s Setting up logsave (1.47.0-2.4~exp1ubuntu4) ...
316s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-7) ...
316s Setting up libutempter0:armhf (1.2.1-3build1) ...
316s Setting up libicu74:armhf (74.2-1ubuntu3) ...
316s Setting up nano (7.2-2build1) ...
316s Setting up libpci3:armhf (1:3.10.0-2build1) ...
316s Setting up libnuma1:armhf (2.0.18-1build1) ...
316s Setting up python-apt-common (2.7.7ubuntu1) ...
316s Setting up libnfnetlink0:armhf (1.0.2-2build1) ...
316s Setting up dbus-session-bus-common (1.14.10-4ubuntu4) ...
316s Setting up libuchardet0:armhf (0.0.8-1build1) ...
316s Setting up libeatmydata1:armhf (131-1ubuntu1) ...
316s Setting up libnl-3-200:armhf (3.7.0-0.3build1) ...
316s Setting up libx11-6:armhf (2:1.8.7-1build1) ...
316s Setting up mawk (1.3.4.20240123-1build1) ...
316s Setting up libbytesize1:armhf (2.10-1ubuntu2) ...
316s Setting up tnftp (20230507-2build3) ...
316s Setting up netplan-generator (1.0-2ubuntu1) ...
316s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
316s Setting up dmidecode (3.5-3build1) ...
316s Setting up dbus-system-bus-common (1.14.10-4ubuntu4) ...
316s Setting up libfido2-1:armhf (1.14.0-1build3) ...
316s Setting up libgpg-error-l10n (1.47-3build2) ...
316s Setting up libdrm-common (2.4.120-2build1) ...
316s Setting up libpam-cap:armhf (1:2.66-5ubuntu2) ...
317s Setting up iputils-ping (3:20240117-1build1) ...
317s Setting up libjson-c5:armhf (0.17-1build1) ...
317s Setting up libevdev2:armhf (1.13.1+dfsg-1build1) ...
317s Setting up sysstat (12.6.1-2) ...
320s Setting up zstd (1.5.5+dfsg2-2build1) ...
320s Setting up dbus-bin (1.14.10-4ubuntu4) ...
320s Setting up libonig5:armhf (6.9.9-1build1) ...
320s Setting up iputils-tracepath (3:20240117-1build1) ...
320s Setting up libkmod2:armhf (31+20240202-2ubuntu6) ...
320s Setting up libpopt0:armhf (1.19+dfsg-1build1) ...
320s Setting up ethtool (1:6.7-1build1) ...
320s Setting up sg3-utils (1.46-3ubuntu4) ...
320s Setting up ncurses-term (6.4+20240113-1ubuntu2) ...
320s Setting up libxkbcommon0:armhf (1.6.0-1build1) ...
320s Setting up logrotate (3.21.0-2build1) ...
320s logrotate.service is a disabled or a static unit not running, not starting it.
320s Setting up eatmydata (131-1ubuntu1) ...
320s Setting up libpython3.12-stdlib:armhf (3.12.3-1) ...
320s Setting up numactl (2.0.18-1build1) ...
320s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu5) ...
320s Setting up openssh-client (1:9.6p1-3ubuntu13) ...
321s Setting up python3.12 (3.12.3-1) ...
322s Setting up libxext6:armhf (2:1.3.4-1build2) ...
322s Setting up screen (4.9.1-1build1) ...
322s Setting up libnftnl11:armhf (1.2.6-2build1) ...
322s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ...
322s update-initramfs: deferring update (trigger activated)
323s e2scrub_all.service is a disabled or a static unit not running, not starting it.
323s Setting up libnss3:armhf (2:3.98-1build1) ...
323s Setting up dbus-daemon (1.14.10-4ubuntu4) ...
323s Setting up kmod (31+20240202-2ubuntu6) ...
325s Setting up sg3-utils-udev (1.46-3ubuntu4) ...
325s update-initramfs: deferring update (trigger activated)
325s Setting up libnl-route-3-200:armhf (3.7.0-0.3build1) ...
325s Setting up dbus-user-session (1.14.10-4ubuntu4) ...
325s Setting up libflashrom1:armhf (1.3.0-2.1ubuntu2) ...
325s Setting up dbus (1.14.10-4ubuntu4) ...
325s A reboot is required to replace the running dbus-daemon.
325s Please reboot the system when convenient.
328s Setting up ftp (20230507-2build3) ...
328s Setting up pciutils (1:3.10.0-2build1) ...
328s Setting up libdrm2:armhf (2.4.120-2build1) ...
328s Setting up dracut-install (060+5-1ubuntu3) ...
328s Setting up xauth (1:1.1.2-1build1) ...
328s Setting up libnetfilter-conntrack3:armhf (1.0.9-6build1) ...
328s Setting up libnl-genl-3-200:armhf (3.7.0-0.3build1) ...
328s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu4) ...
328s Setting up bind9-host (1:9.18.24-0ubuntu5) ...
328s Setting up rsync (3.2.7-1ubuntu1) ...
335s rsync.service is a disabled or a static unit not running, not starting it.
335s Setting up libpython3-stdlib:armhf (3.12.3-0ubuntu1) ...
335s Setting up cryptsetup-bin (2:2.7.0-1ubuntu4) ...
335s Setting up openssh-sftp-server (1:9.6p1-3ubuntu13) ...
335s Setting up libnftables1:armhf (1.0.9-1build1) ...
335s Setting up nftables (1.0.9-1build1) ...
336s Setting up openssh-server (1:9.6p1-3ubuntu13) ...
339s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu4) ...
339s Setting up iptables (1.8.10-3ubuntu2) ...
339s Setting up htop (3.3.0-4build1) ...
339s Setting up python3 (3.12.3-0ubuntu1) ...
339s Setting up python3-netifaces:armhf (0.11.0-2build3) ...
339s Setting up bind9-dnsutils (1:9.18.24-0ubuntu5) ...
339s Setting up python3-systemd (235-1build4) ...
339s Setting up python3-cffi-backend:armhf (1.16.0-2build1) ...
339s Setting up python3-gdbm:armhf (3.12.3-0ubuntu1) ...
339s Setting up python3-problem-report (2.28.1-0ubuntu1) ...
340s Setting up python3-apt (2.7.7ubuntu1) ...
340s Setting up ufw (0.36.2-6) ...
342s Setting up python3-apport (2.28.1-0ubuntu1) ...
343s Setting up python3-netplan (1.0-2ubuntu1) ...
343s Setting up netplan.io (1.0-2ubuntu1) ...
343s Setting up cloud-init (24.1.3-0ubuntu3) ...
345s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ...
346s Setting up apport (2.28.1-0ubuntu1) ...
346s Installing new version of config file /etc/apport/crashdb.conf ...
346s apport-autoreport.service is a disabled or a static unit not running, not starting it.
346s Processing triggers for debianutils (5.17build1) ...
347s Processing triggers for install-info (7.1-3build2) ...
347s Processing triggers for initramfs-tools (0.142ubuntu24) ...
347s Processing triggers for libc-bin (2.39-0ubuntu8) ...
347s Processing triggers for systemd (255.4-1ubuntu7) ...
348s Reading package lists...
348s Building dependency tree...
348s Reading state information...
349s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
351s autopkgtest [01:54:56]: rebooting testbed after setup commands that affected boot
423s autopkgtest [01:56:08]: testbed running kernel: Linux 5.15.0-102-generic #112-Ubuntu SMP Tue Mar 5 16:49:56 UTC 2024
457s autopkgtest [01:56:42]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools
489s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (dsc) [2293 B]
489s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (tar) [141 kB]
489s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build3 (diff) [13.6 MB]
491s gpgv: Signature made Mon Apr  1 07:33:53 2024 UTC
491s gpgv:                using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984
491s gpgv: Can't check signature: No public key
491s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build3.dsc: no acceptable signature found
492s autopkgtest [01:57:17]: testing package qtltools version 1.3.1+dfsg-4build3
505s autopkgtest [01:57:30]: build not needed
517s autopkgtest [01:57:42]: test run-sample-analysis: preparing testbed
530s Reading package lists...
530s Building dependency tree...
530s Reading state information...
531s Starting pkgProblemResolver with broken count: 0
531s Starting 2 pkgProblemResolver with broken count: 0
531s Done
531s The following additional packages will be installed:
531s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
531s   libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1
531s   libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3
531s   libgsl27 libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6
531s   libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
531s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
531s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
531s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
531s   qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils
532s   zip
532s Suggested packages:
532s   gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6
532s   elpa-ess r-doc-info | r-doc-pdf r-base-html
532s Recommended packages:
532s   r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl
532s   libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
532s The following NEW packages will be installed:
532s   autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core
532s   fonts-dejavu-mono libblas3 libboost-iostreams1.83.0
532s   libboost-program-options1.83.0 libcairo2 libdatrie1 libdeflate0
532s   libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libgsl27
532s   libgslcblas0 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libjbig0
532s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
532s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
532s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
532s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
532s   qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils
532s   zip
532s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded.
532s Need to get 54.7 MB/54.7 MB of archives.
532s After this operation, 91.3 MB of additional disk space will be used.
532s Get:1 /tmp/autopkgtest.2tkRNE/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B]
533s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libfreetype6 armhf 2.13.2+dfsg-1build3 [331 kB]
533s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-mono all 2.37-8 [502 kB]
533s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-core all 2.37-8 [835 kB]
533s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB]
533s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB]
533s Get:7 http://ftpmaster.internal/ubuntu noble/main armhf fontconfig armhf 2.15.0-1.1ubuntu2 [189 kB]
533s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.12.0-3build1 [123 kB]
533s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libboost-iostreams1.83.0 armhf 1.83.0-2.1ubuntu3 [257 kB]
533s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libboost-program-options1.83.0 armhf 1.83.0-2.1ubuntu3 [344 kB]
533s Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libpixman-1-0 armhf 0.42.2-1build1 [193 kB]
533s Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-render0 armhf 1.15-1 [15.2 kB]
533s Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-shm0 armhf 1.15-1 [5852 B]
533s Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB]
533s Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libcairo2 armhf 1.18.0-3build1 [482 kB]
533s Get:16 http://ftpmaster.internal/ubuntu noble/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB]
533s Get:17 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1build1 [41.5 kB]
533s Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libgfortran5 armhf 14-20240412-0ubuntu1 [316 kB]
533s Get:19 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 14-20240412-0ubuntu1 [125 kB]
533s Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libgraphite2-3 armhf 1.3.14-2build1 [64.6 kB]
533s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libgslcblas0 armhf 2.7.1+dfsg-6ubuntu2 [77.8 kB]
534s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libgsl27 armhf 2.7.1+dfsg-6ubuntu2 [827 kB]
534s Get:23 http://ftpmaster.internal/ubuntu noble/main armhf libharfbuzz0b armhf 8.3.0-2build2 [446 kB]
534s Get:24 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB]
534s Get:25 http://ftpmaster.internal/ubuntu noble/universe armhf libhts3t64 armhf 1.19+ds-1.1build3 [389 kB]
534s Get:26 http://ftpmaster.internal/ubuntu noble/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB]
534s Get:27 http://ftpmaster.internal/ubuntu noble/main armhf libice6 armhf 2:1.0.10-1build3 [35.4 kB]
534s Get:28 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB]
534s Get:29 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B]
534s Get:30 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB]
534s Get:31 http://ftpmaster.internal/ubuntu noble/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB]
534s Get:32 http://ftpmaster.internal/ubuntu noble/main armhf libthai-data all 0.1.29-2build1 [158 kB]
534s Get:33 http://ftpmaster.internal/ubuntu noble/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB]
534s Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libpango-1.0-0 armhf 1.52.1+ds-1build1 [207 kB]
534s Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libpangoft2-1.0-0 armhf 1.52.1+ds-1build1 [36.5 kB]
534s Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libpangocairo-1.0-0 armhf 1.52.1+ds-1build1 [25.0 kB]
534s Get:37 http://ftpmaster.internal/ubuntu noble/main armhf libpaper1 armhf 1.1.29build1 [12.6 kB]
534s Get:38 http://ftpmaster.internal/ubuntu noble/main armhf libpaper-utils armhf 1.1.29build1 [8184 B]
534s Get:39 http://ftpmaster.internal/ubuntu noble/main armhf libsharpyuv0 armhf 1.3.2-0.4build3 [13.6 kB]
534s Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libsm6 armhf 2:1.2.3-1build3 [14.1 kB]
534s Get:41 http://ftpmaster.internal/ubuntu noble/main armhf libtcl8.6 armhf 8.6.14+dfsg-1build1 [903 kB]
534s Get:42 http://ftpmaster.internal/ubuntu noble/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB]
534s Get:43 http://ftpmaster.internal/ubuntu noble/main armhf libwebp7 armhf 1.3.2-0.4build3 [183 kB]
534s Get:44 http://ftpmaster.internal/ubuntu noble/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu2 [178 kB]
534s Get:45 http://ftpmaster.internal/ubuntu noble/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB]
534s Get:46 http://ftpmaster.internal/ubuntu noble/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B]
534s Get:47 http://ftpmaster.internal/ubuntu noble/main armhf libtk8.6 armhf 8.6.14-1build1 [681 kB]
534s Get:48 http://ftpmaster.internal/ubuntu noble/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB]
534s Get:49 http://ftpmaster.internal/ubuntu noble/universe armhf r-mathlib armhf 4.3.3-2build2 [2363 kB]
534s Get:50 http://ftpmaster.internal/ubuntu noble/main armhf zip armhf 3.0-13build1 [163 kB]
534s Get:51 http://ftpmaster.internal/ubuntu noble/main armhf unzip armhf 6.0-28ubuntu4 [163 kB]
534s Get:52 http://ftpmaster.internal/ubuntu noble/main armhf xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
534s Get:53 http://ftpmaster.internal/ubuntu noble/universe armhf r-base-core armhf 4.3.3-2build2 [26.6 MB]
535s Get:54 http://ftpmaster.internal/ubuntu noble/universe armhf qtltools armhf 1.3.1+dfsg-4build3 [926 kB]
535s Get:55 http://ftpmaster.internal/ubuntu noble/universe armhf qtltools-example all 1.3.1+dfsg-4build3 [13.6 MB]
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556s 
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556s Setting up qtltools (1.3.1+dfsg-4build3) ...
556s Setting up autopkgtest-satdep (0) ...
556s Processing triggers for man-db (2.12.0-4build2) ...
557s Processing triggers for install-info (7.1-3build2) ...
557s Processing triggers for libc-bin (2.39-0ubuntu8) ...
576s (Reading database ... 60566 files and directories currently installed.)
576s Removing autopkgtest-satdep (0) ...
583s autopkgtest [01:58:48]: test run-sample-analysis: [-----------------------
586s ./genes.50percent.chr22.bed.gz
586s ./genes.50percent.chr22.bed.gz.tbi
586s ./genes.covariates.pc50.txt.gz
586s ./genes.simulated.chr22.bed.gz
586s ./genes.simulated.chr22.bed.gz.tbi
586s ./genotypes.chr22.vcf.gz
586s ./genotypes.chr22.vcf.gz.tbi
586s 
586s QTLtools
586s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
586s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
586s   * Webpage : https://qtltools.github.io/qtltools/
586s   * Version : 1.3.1
586s   * Date    : 19/04/2024 - 01:58:51
586s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
587s 
587s CONDUCT PCA ON DATA
587s 
587s Initialize random number generator
587s   * Built-in seed is 15112011
587s   * First Integer = 30553
587s   * First Double = 0.0126695
587s 
587s Reading sample list from [genes.50percent.chr22.bed.gz]
587s   * #samples = 358
587s 
587s Merging sample sets from all input files
587s   * #files = 1
587s   * #samples in all files = 358
587s 
587s Reading phenotype data in [genes.50percent.chr22.bed.gz]
587s   * 358 samples included
587s   * 608 phenotypes included
587s 
587s Calculating PCA with a matrix 358 x 608
587s   * Calculated mean and sd
587s   * 0 sd==0 columns removed
587s   * Variables centered
587s   * Variables scaled to unit variance
587s   * Running SVD
588s   * SVD complete
588s   * Calculated sd and var for PCs
588s   * Calculated cumulative var for PCs
588s   * Done!
588s 
588s Running time: 1 seconds
588s 
588s QTLtools
588s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
588s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
588s   * Webpage : https://qtltools.github.io/qtltools/
588s   * Version : 1.3.1
588s   * Date    : 19/04/2024 - 01:58:53
588s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
588s 
588s MAPPING QTL IN CIS
588s   * TASK: Report all nominal associations with p <= 0.01
588s   * Linear model: Phe ~ Var + Cov
588s   * Cis-window size is 1000000 bp
588s   * Region = [chr22:17000000-18000000]
588s 
588s Initialize random number generator
588s   * Built-in seed is 15112011
588s   * First Integer = 30553
588s   * First Double = 0.0126695
588s 
588s Reading sample list from [genes.50percent.chr22.bed.gz]
588s   * #samples = 358
588s 
588s Read sample list from [genotypes.chr22.vcf.gz]
588s   * #samples = 358
588s 
588s Reading sample list from [genes.covariates.pc50.txt.gz]
588s   * #samples = 358
588s 
588s Merging sample sets from all input files
588s   * #files = 3
588s   * #samples in all files = 358
588s 
588s Reading phenotype data in [genes.50percent.chr22.bed.gz]
588s   * target region [chr22:17000000-18000000]
588s   * 8 phenotypes included
588s   * 3 phenotypes are on the negative strand
588s 
588s Reading genotype data in [genotypes.chr22.vcf.gz]
588s   * File format detected: VCF
588s   * target region [chr22:16000000-19000000]
589s   * 6404 variants included
589s 
589s Reading covariates in [genes.covariates.pc50.txt.gz]
589s   * 53 covariates included
589s 
589s Residualize phenotypes for covariates
589s   * #covariates = 53
589s 
589s Processing phenotype [ENSG00000237438.2] [1/8]
589s   * #variants in cis = 5095
589s   * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518]
589s 
589s Processing phenotype [ENSG00000273203.1] [2/8]
589s   * #variants in cis = 5170
589s   * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406]
589s 
589s Processing phenotype [ENSG00000273442.1] [3/8]
589s   * #variants in cis = 5188
589s   * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340]
589s 
589s Processing phenotype [ENSG00000177663.9] [4/8]
589s   * #variants in cis = 5193
589s   * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096]
589s 
589s Processing phenotype [ENSG00000183307.3] [5/8]
589s   * #variants in cis = 5230
589s   * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078]
589s 
589s Processing phenotype [ENSG00000069998.8] [6/8]
589s   * #variants in cis = 5291
589s   * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147]
589s 
589s Processing phenotype [ENSG00000093072.11] [7/8]
589s   * #variants in cis = 5293
589s   * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404]
589s 
589s Processing phenotype [ENSG00000099954.14] [8/8]
589s   * #variants in cis = 5435
589s   * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067]
589s 
589s Running time: 0 seconds
589s 
589s QTLtools
589s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
589s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
589s   * Webpage : https://qtltools.github.io/qtltools/
589s   * Version : 1.3.1
589s   * Date    : 19/04/2024 - 01:58:54
589s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
589s 
589s MAPPING QTL IN CIS
589s   * TASK: Perform 1000 permutations
589s   * Linear model: Phe ~ Var + Cov
589s   * Cis-window size is 1000000 bp
589s   * Region = [chr22:17000000-18000000]
589s 
589s Initialize random number generator
589s   * Built-in seed is 15112011
589s   * First Integer = 30553
589s   * First Double = 0.0126695
589s 
589s Reading sample list from [genes.50percent.chr22.bed.gz]
589s   * #samples = 358
589s 
589s Read sample list from [genotypes.chr22.vcf.gz]
589s   * #samples = 358
589s 
589s Reading sample list from [genes.covariates.pc50.txt.gz]
589s   * #samples = 358
589s 
589s Merging sample sets from all input files
589s   * #files = 3
589s   * #samples in all files = 358
589s 
589s Reading phenotype data in [genes.50percent.chr22.bed.gz]
589s   * target region [chr22:17000000-18000000]
589s   * 8 phenotypes included
589s   * 3 phenotypes are on the negative strand
589s 
589s Reading genotype data in [genotypes.chr22.vcf.gz]
589s   * File format detected: VCF
589s   * target region [chr22:16000000-19000000]
589s   * 6404 variants included
589s 
589s Reading covariates in [genes.covariates.pc50.txt.gz]
589s   * 53 covariates included
589s 
589s Residualize phenotypes for covariates
589s   * #covariates = 53
589s 
589s Processing phenotype [ENSG00000237438.2] [1/8]
589s   * #variants in cis = 5095
591s   * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518]
591s   * Beta parameters: [s1=1.00995, s2=621.053]
591s   * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20]
591s 
591s Processing phenotype [ENSG00000273203.1] [2/8]
591s   * #variants in cis = 5170
593s   * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406]
593s   * Beta parameters: [s1=1.11817, s2=641.379]
593s   * Adjusted p-values: [emp=0.00799201, beta=0.00751892]
593s 
593s Processing phenotype [ENSG00000273442.1] [3/8]
593s   * #variants in cis = 5188
595s   * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340]
595s   * Beta parameters: [s1=1.08364, s2=467.63]
595s   * Adjusted p-values: [emp=0.297702, beta=0.293948]
595s 
595s Processing phenotype [ENSG00000177663.9] [4/8]
595s   * #variants in cis = 5193
600s   * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096]
601s   * Beta parameters: [s1=0.989061, s2=704.553]
601s   * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10]
601s 
601s Processing phenotype [ENSG00000183307.3] [5/8]
601s   * #variants in cis = 5230
603s   * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078]
603s   * Beta parameters: [s1=1.01322, s2=559.49]
603s   * Adjusted p-values: [emp=0.000999001, beta=0.00050707]
603s 
603s Processing phenotype [ENSG00000069998.8] [6/8]
603s   * #variants in cis = 5291
605s   * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147]
605s   * Beta parameters: [s1=1.02312, s2=563.339]
605s   * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10]
605s 
605s Processing phenotype [ENSG00000093072.11] [7/8]
605s   * #variants in cis = 5293
607s   * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404]
607s   * Beta parameters: [s1=0.957514, s2=559.397]
607s   * Adjusted p-values: [emp=0.574426, beta=0.562826]
607s 
607s Processing phenotype [ENSG00000099954.14] [8/8]
607s   * #variants in cis = 5435
609s   * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067]
609s   * Beta parameters: [s1=0.938041, s2=226.852]
609s   * Adjusted p-values: [emp=0.842158, beta=0.84836]
609s 
609s Running time: 20 seconds
611s 
611s QTLtools
611s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
611s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
611s   * Webpage : https://qtltools.github.io/qtltools/
611s   * Version : 1.3.1
611s   * Date    : 19/04/2024 - 01:59:16
611s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
611s 
611s MAPPING QTL IN TRANS
611s   * TASK: Perform a full nominal pass, do not adjust p-values
611s   * Cis-window size is 5000000 bp
611s   * #bins = 1000
611s   * threshold = 1e-05
611s 
611s Initialize random number generator
611s   * Built-in seed is 15112011
611s   * First Integer = 30553
611s   * First Double = 0.0126695
611s 
611s Read sample list from [genotypes.chr22.vcf.gz]
612s   * #samples = 358
612s 
612s Checking sample list in [genes.simulated.chr22.bed.gz]
612s   * #samples = 358
612s 
612s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0
612s   * 358 samples included
612s   * 608 phenotypes included
612s   * 275 phenotypes is on the negative strand
612s 
612s Calculate correlation threshold
612s   * thres = 1e-05
612s   * corr = 0.2311
612s 
612s Sweep through genotype data in [genotypes.chr22.vcf.gz]
613s   * #variants=1950	#multi_allelic=0	#not_processed=0	#hits=101/1000000	speed=1.37MT/s
613s   * #variants=4001	#multi_allelic=0	#not_processed=0	#hits=153/2000000	speed=2.48MT/s
614s   * #variants=6187	#multi_allelic=0	#not_processed=0	#hits=244/3000000	speed=2.46MT/s
614s   * #variants=8537	#multi_allelic=0	#not_processed=0	#hits=285/4000000	speed=2.43MT/s
615s   * #variants=11025	#multi_allelic=0	#not_processed=0	#hits=312/5000000	speed=2.42MT/s
615s   * #variants=13621	#multi_allelic=0	#not_processed=0	#hits=320/6000000	speed=2.41MT/s
616s   * #variants=16217	#multi_allelic=0	#not_processed=0	#hits=342/7000000	speed=0.90MT/s
617s   * #variants=18755	#multi_allelic=0	#not_processed=0	#hits=401/8000000	speed=1.16MT/s
618s   * #variants=21237	#multi_allelic=0	#not_processed=0	#hits=402/9000000	speed=2.42MT/s
618s   * #variants=23680	#multi_allelic=0	#not_processed=0	#hits=455/10000000	speed=2.42MT/s
618s   * #variants=26171	#multi_allelic=0	#not_processed=0	#hits=463/11000000	speed=2.42MT/s
619s   * #variants=28609	#multi_allelic=0	#not_processed=0	#hits=469/12000000	speed=2.43MT/s
619s   * #variants=30861	#multi_allelic=0	#not_processed=0	#hits=973/13000000	speed=2.42MT/s
620s   * #variants=32932	#multi_allelic=0	#not_processed=0	#hits=979/14000000	speed=2.48MT/s
620s   * #variants=34974	#multi_allelic=0	#not_processed=0	#hits=1085/15000000	speed=2.48MT/s
620s   * #variants=37021	#multi_allelic=0	#not_processed=0	#hits=1086/16000000	speed=2.49MT/s
622s   * #variants=39122	#multi_allelic=0	#not_processed=0	#hits=1089/17000000	speed=0.51MT/s
623s   * #variants=41334	#multi_allelic=0	#not_processed=0	#hits=1089/18000000	speed=2.47MT/s
626s   * #variants=43627	#multi_allelic=0	#not_processed=0	#hits=1096/19000000	speed=0.31MT/s
627s   * #variants=45897	#multi_allelic=0	#not_processed=0	#hits=1153/20000000	speed=0.88MT/s
629s   * #variants=48114	#multi_allelic=0	#not_processed=0	#hits=1243/21000000	speed=0.94MT/s
629s   * #variants=50410	#multi_allelic=0	#not_processed=0	#hits=1249/22000000	speed=2.44MT/s
629s   * #variants=52820	#multi_allelic=0	#not_processed=0	#hits=1259/23000000	speed=2.43MT/s
630s   * #variants=55279	#multi_allelic=0	#not_processed=0	#hits=1498/24000000	speed=2.42MT/s
630s   * #variants=57789	#multi_allelic=0	#not_processed=0	#hits=1724/25000000	speed=2.41MT/s
631s   * #variants=60201	#multi_allelic=0	#not_processed=0	#hits=2168/26000000	speed=1.60MT/s
631s   * #variants=62476	#multi_allelic=0	#not_processed=0	#hits=2452/27000000	speed=2.43MT/s
632s   * #variants=64608	#multi_allelic=0	#not_processed=0	#hits=2544/28000000	speed=2.46MT/s
632s   * #variants=66709	#multi_allelic=0	#not_processed=0	#hits=2684/29000000	speed=2.47MT/s
632s   * #variants=68871	#multi_allelic=0	#not_processed=0	#hits=2688/30000000	speed=2.46MT/s
633s   * #variants=71070	#multi_allelic=0	#not_processed=0	#hits=2720/31000000	speed=2.46MT/s
633s   * #variants=73151	#multi_allelic=0	#not_processed=0	#hits=2891/32000000	speed=2.47MT/s
634s   * #variants=75122	#multi_allelic=0	#not_processed=0	#hits=3110/33000000	speed=2.43MT/s
634s   * #variants=77058	#multi_allelic=0	#not_processed=0	#hits=3209/34000000	speed=2.46MT/s
635s   * #variants=78989	#multi_allelic=0	#not_processed=0	#hits=3218/35000000	speed=2.46MT/s
635s   * #variants=80903	#multi_allelic=0	#not_processed=0	#hits=3250/36000000	speed=2.49MT/s
635s   * #variants=82811	#multi_allelic=0	#not_processed=0	#hits=3463/37000000	speed=2.44MT/s
636s   * #variants=84694	#multi_allelic=0	#not_processed=0	#hits=4035/38000000	speed=2.38MT/s
636s   * #variants=85485	#multi_allelic=0	#not_processed=0	#hits=4036/38425275	speed=2.46MT/s
636s 
636s Running time: 25 seconds
638s 
638s QTLtools
638s   * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS
638s   * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch
638s   * Webpage : https://qtltools.github.io/qtltools/
638s   * Version : 1.3.1
638s   * Date    : 19/04/2024 - 01:59:43
638s   * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452
638s 
638s MAPPING QTL IN TRANS
638s   * TASK: Permute randomly chosen phenotypes 1000 times and test
638s   * Cis-window size is 5000000 bp
638s   * #bins = 1000
638s   * threshold = 1e-05
638s 
638s Initialize random number generator
638s   * Built-in seed is 15112011
638s   * First Integer = 30553
638s   * First Double = 0.0126695
638s 
638s Read sample list from [genotypes.chr22.vcf.gz]
638s   * #samples = 358
638s 
638s Checking sample list in [genes.simulated.chr22.bed.gz]
638s   * #samples = 358
638s 
638s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0
638s   * 358 samples included
639s   * 608 phenotypes included
639s   * 275 phenotypes is on the negative strand
639s 
639s Normal transform phenotypes
639s 
639s Calculate correlation threshold
639s   * thres = 1e-05
639s   * corr = 0.2311
639s 
639s Sweep through genotype data in [genotypes.chr22.vcf.gz]
639s   * #variants=1177	#multi_allelic=0	#not_processed=0	#hits=28/1000000	speed=2.60MT/s
639s   * #variants=2383	#multi_allelic=0	#not_processed=0	#hits=38/2000000	speed=2.56MT/s
640s   * #variants=3633	#multi_allelic=0	#not_processed=0	#hits=53/3000000	speed=2.53MT/s
640s   * #variants=4928	#multi_allelic=0	#not_processed=0	#hits=53/4000000	speed=2.53MT/s
641s   * #variants=6269	#multi_allelic=0	#not_processed=0	#hits=71/5000000	speed=2.51MT/s
641s   * #variants=7675	#multi_allelic=0	#not_processed=0	#hits=72/6000000	speed=2.50MT/s
641s   * #variants=9151	#multi_allelic=0	#not_processed=0	#hits=88/7000000	speed=2.49MT/s
642s   * #variants=10663	#multi_allelic=0	#not_processed=0	#hits=96/8000000	speed=2.45MT/s
642s   * #variants=12202	#multi_allelic=0	#not_processed=0	#hits=96/9000000	speed=2.46MT/s
643s   * #variants=13804	#multi_allelic=0	#not_processed=0	#hits=96/10000000	speed=2.44MT/s
643s   * #variants=15381	#multi_allelic=0	#not_processed=0	#hits=120/11000000	speed=2.44MT/s
644s   * #variants=16946	#multi_allelic=0	#not_processed=0	#hits=123/12000000	speed=2.45MT/s
644s   * #variants=18483	#multi_allelic=0	#not_processed=0	#hits=129/13000000	speed=2.47MT/s
644s   * #variants=19995	#multi_allelic=0	#not_processed=0	#hits=131/14000000	speed=2.44MT/s
645s   * #variants=21489	#multi_allelic=0	#not_processed=0	#hits=132/15000000	speed=2.46MT/s
645s   * #variants=22947	#multi_allelic=0	#not_processed=0	#hits=151/16000000	speed=2.47MT/s
646s   * #variants=24445	#multi_allelic=0	#not_processed=0	#hits=168/17000000	speed=2.47MT/s
646s   * #variants=25965	#multi_allelic=0	#not_processed=0	#hits=175/18000000	speed=2.45MT/s
646s   * #variants=27472	#multi_allelic=0	#not_processed=0	#hits=179/19000000	speed=2.46MT/s
647s   * #variants=28933	#multi_allelic=0	#not_processed=0	#hits=181/20000000	speed=2.48MT/s
647s   * #variants=30325	#multi_allelic=0	#not_processed=0	#hits=181/21000000	speed=2.49MT/s
648s   * #variants=31617	#multi_allelic=0	#not_processed=0	#hits=182/22000000	speed=2.53MT/s
648s   * #variants=32875	#multi_allelic=0	#not_processed=0	#hits=190/23000000	speed=2.54MT/s
648s   * #variants=34127	#multi_allelic=0	#not_processed=0	#hits=192/24000000	speed=2.54MT/s
649s   * #variants=35392	#multi_allelic=0	#not_processed=0	#hits=206/25000000	speed=2.52MT/s
649s   * #variants=36652	#multi_allelic=0	#not_processed=0	#hits=206/26000000	speed=2.54MT/s
650s   * #variants=37940	#multi_allelic=0	#not_processed=0	#hits=213/27000000	speed=2.53MT/s
650s   * #variants=39255	#multi_allelic=0	#not_processed=0	#hits=238/28000000	speed=2.53MT/s
650s   * #variants=40602	#multi_allelic=0	#not_processed=0	#hits=239/29000000	speed=2.51MT/s
651s   * #variants=41998	#multi_allelic=0	#not_processed=0	#hits=245/30000000	speed=2.49MT/s
651s   * #variants=43398	#multi_allelic=0	#not_processed=0	#hits=245/31000000	speed=2.49MT/s
652s   * #variants=44803	#multi_allelic=0	#not_processed=0	#hits=260/32000000	speed=2.48MT/s
652s   * #variants=46187	#multi_allelic=0	#not_processed=0	#hits=261/33000000	speed=2.49MT/s
652s   * #variants=47545	#multi_allelic=0	#not_processed=0	#hits=268/34000000	speed=2.52MT/s
653s   * #variants=48904	#multi_allelic=0	#not_processed=0	#hits=280/35000000	speed=2.54MT/s
653s   * #variants=50309	#multi_allelic=0	#not_processed=0	#hits=306/36000000	speed=2.49MT/s
654s   * #variants=51731	#multi_allelic=0	#not_processed=0	#hits=314/37000000	speed=2.49MT/s
654s   * #variants=53171	#multi_allelic=0	#not_processed=0	#hits=320/38000000	speed=2.49MT/s
654s   * #variants=54621	#multi_allelic=0	#not_processed=0	#hits=323/39000000	speed=2.48MT/s
655s   * #variants=56099	#multi_allelic=0	#not_processed=0	#hits=323/40000000	speed=1.88MT/s
655s   * #variants=57584	#multi_allelic=0	#not_processed=0	#hits=340/41000000	speed=2.17MT/s
656s   * #variants=59032	#multi_allelic=0	#not_processed=0	#hits=344/42000000	speed=2.46MT/s
656s   * #variants=60437	#multi_allelic=0	#not_processed=0	#hits=345/43000000	speed=2.49MT/s
657s   * #variants=61810	#multi_allelic=0	#not_processed=0	#hits=357/44000000	speed=2.49MT/s
657s   * #variants=63129	#multi_allelic=0	#not_processed=0	#hits=384/45000000	speed=2.50MT/s
657s   * #variants=64409	#multi_allelic=0	#not_processed=0	#hits=391/46000000	speed=2.51MT/s
658s   * #variants=65679	#multi_allelic=0	#not_processed=0	#hits=430/47000000	speed=2.54MT/s
658s   * #variants=66953	#multi_allelic=0	#not_processed=0	#hits=436/48000000	speed=2.55MT/s
659s   * #variants=68247	#multi_allelic=0	#not_processed=0	#hits=446/49000000	speed=2.53MT/s
659s   * #variants=69595	#multi_allelic=0	#not_processed=0	#hits=460/50000000	speed=2.51MT/s
659s   * #variants=70918	#multi_allelic=0	#not_processed=0	#hits=481/51000000	speed=2.50MT/s
660s   * #variants=72211	#multi_allelic=0	#not_processed=0	#hits=492/52000000	speed=2.52MT/s
660s   * #variants=73449	#multi_allelic=0	#not_processed=0	#hits=492/53000000	speed=2.56MT/s
661s   * #variants=74662	#multi_allelic=0	#not_processed=0	#hits=500/54000000	speed=2.54MT/s
661s   * #variants=75863	#multi_allelic=0	#not_processed=0	#hits=506/55000000	speed=2.56MT/s
661s   * #variants=77058	#multi_allelic=0	#not_processed=0	#hits=513/56000000	speed=2.56MT/s
662s   * #variants=78253	#multi_allelic=0	#not_processed=0	#hits=515/57000000	speed=2.55MT/s
662s   * #variants=79446	#multi_allelic=0	#not_processed=0	#hits=530/58000000	speed=2.51MT/s
663s   * #variants=80634	#multi_allelic=0	#not_processed=0	#hits=581/59000000	speed=2.53MT/s
663s   * #variants=81817	#multi_allelic=0	#not_processed=0	#hits=594/60000000	speed=2.53MT/s
663s   * #variants=82993	#multi_allelic=0	#not_processed=0	#hits=598/61000000	speed=2.53MT/s
664s   * #variants=84160	#multi_allelic=0	#not_processed=0	#hits=599/62000000	speed=2.55MT/s
664s   * #variants=85304	#multi_allelic=0	#not_processed=0	#hits=609/63000000	speed=2.58MT/s
664s   * #variants=85485	#multi_allelic=0	#not_processed=0	#hits=609/63157827	speed=2.77MT/s
664s 
664s Running time: 26 seconds
674s autopkgtest [02:00:19]: test run-sample-analysis: -----------------------]
680s run-sample-analysis  PASS
680s autopkgtest [02:00:25]: test run-sample-analysis:  - - - - - - - - - - results - - - - - - - - - -
686s autopkgtest [02:00:31]: @@@@@@@@@@@@@@@@@@@@ summary
686s run-sample-analysis  PASS