0s autopkgtest [17:57:25]: starting date and time: 2024-11-13 17:57:25+0000 0s autopkgtest [17:57:25]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [17:57:25]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._2nwnipz/out --timeout-copy=6000 --setup-commands '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,keyserver.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:python3-defaults,src:python3-stdlib-extensions --apt-upgrade macs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- lxd -r lxd-armhf-10.145.243.141 lxd-armhf-10.145.243.141:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [17:58:18]: testbed dpkg architecture: armhf 55s autopkgtest [17:58:20]: testbed apt version: 2.9.8 55s autopkgtest [17:58:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [106 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [647 kB] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 64s Fetched 1943 kB in 1s (1978 kB/s) 64s Reading package lists... 81s tee: /proc/self/fd/2: Permission denied 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 107s The following packages were automatically installed and are no longer required: 107s libperl5.38t64 perl-modules-5.38 python3-netifaces 107s Use 'apt autoremove' to remove them. 107s The following NEW packages will be installed: 107s libperl5.40 perl-modules-5.40 python3.13-gdbm systemd-cryptsetup 107s The following packages will be upgraded: 107s apport apport-core-dump-handler base-files base-passwd bash-completion 107s dhcpcd-base distro-info-data dpkg dpkg-dev fwupd gcc-14-base info 107s install-info iproute2 libarchive13t64 libatomic1 libattr1 107s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 107s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 107s libblockdev3 libbpf1 libbsd0 libbytesize-common libbytesize1 libdb5.3t64 107s libdpkg-perl libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevdev2 107s libfastjson4 libflashrom1 libftdi1-2 libfwupd2 libgcc-s1 libgnutls30t64 107s libgpgme11t64 libinih1 libjson-c5 libjson-glib-1.0-0 libjson-glib-1.0-common 107s libkeyutils1 libldap-common libldap2 liblocale-gettext-perl libmaxminddb0 107s libmnl0 libnetfilter-conntrack3 libnetplan1 libnghttp2-14 libnspr4 107s libnss-systemd libnvme1t64 libpam-systemd libpipeline1 libplymouth5 107s libpng16-16t64 libpopt0 libpython3-stdlib libpython3.12-minimal 107s libpython3.12-stdlib libsgutils2-1.46-2 libssh2-1t64 libstdc++6 107s libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl 107s libtraceevent1 libtraceevent1-plugin libudev1 libudisks2-0 liburcu8t64 107s libutempter0 libuv1t64 libx11-6 libx11-data libxau6 libxmlb2 mawk 107s motd-news-config nano netplan-generator netplan.io openssh-client 107s openssh-server openssh-sftp-server pci.ids perl perl-base plymouth 107s plymouth-theme-ubuntu-text python3 python3-apport python3-certifi 107s python3-cffi-backend python3-configobj python3-gdbm python3-gi python3-idna 107s python3-jaraco.functools python3-json-pointer python3-jsonpatch 107s python3-lazr.restfulclient python3-lazr.uri python3-minimal 107s python3-more-itertools python3-netplan python3-oauthlib 107s python3-problem-report python3-typeguard python3-urllib3 python3-wadllib 107s python3-zipp python3.12 python3.12-gdbm python3.12-minimal sg3-utils 107s sg3-utils-udev ssh-import-id systemd systemd-resolved systemd-sysv 107s systemd-timesyncd tzdata udev udisks2 ufw usbutils vim-common vim-tiny xxd 107s 140 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 45.4 MB of archives. 107s After this operation, 43.1 MB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu3 [5190 B] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu3 [75.1 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg armhf 1.22.11ubuntu3 [1247 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-7 [3214 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-7 [4139 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-7 [263 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-7 [1674 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 108s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 108s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 108s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf base-passwd armhf 3.6.5 [53.2 kB] 108s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 108s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 108s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf tzdata all 2024b-1ubuntu2 [274 kB] 108s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12 armhf 3.12.7-3 [661 kB] 108s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1934 kB] 108s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-minimal armhf 3.12.7-3 [2012 kB] 108s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-minimal armhf 3.12.7-3 [822 kB] 108s Get:20 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 108s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libnss-systemd armhf 256.5-2ubuntu4 [155 kB] 108s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-timesyncd armhf 256.5-2ubuntu4 [40.7 kB] 108s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-resolved armhf 256.5-2ubuntu4 [309 kB] 108s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd-shared armhf 256.5-2ubuntu4 [2129 kB] 108s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd0 armhf 256.5-2ubuntu4 [428 kB] 108s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-sysv armhf 256.5-2ubuntu4 [11.9 kB] 108s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libpam-systemd armhf 256.5-2ubuntu4 [226 kB] 108s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf systemd armhf 256.5-2ubuntu4 [3442 kB] 109s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf udev armhf 256.5-2ubuntu4 [1949 kB] 109s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libudev1 armhf 256.5-2ubuntu4 [188 kB] 109s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf python3-problem-report all 2.30.0-0ubuntu5 [25.0 kB] 109s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apport all 2.30.0-0ubuntu5 [93.2 kB] 109s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gi armhf 3.50.0-3 [227 kB] 109s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf apport-core-dump-handler all 2.30.0-0ubuntu5 [17.9 kB] 109s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf apport all 2.30.0-0ubuntu5 [83.0 kB] 109s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libbsd0 armhf 0.12.2-2 [36.8 kB] 109s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libedit2 armhf 3.1-20240808-1 [79.0 kB] 109s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-sftp-server armhf 1:9.7p1-7ubuntu5 [35.4 kB] 109s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-server armhf 1:9.7p1-7ubuntu5 [505 kB] 109s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-client armhf 1:9.7p1-7ubuntu5 [889 kB] 109s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-8ubuntu1 [7846 B] 109s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-8ubuntu1 [51.5 kB] 109s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-8ubuntu1 [711 kB] 109s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-8ubuntu1 [40.8 kB] 109s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libattr1 armhf 1:2.5.2-2 [10.5 kB] 109s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 109s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 109s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf mawk armhf 1.3.4.20240905-1 [116 kB] 109s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf dhcpcd-base armhf 1:10.1.0-2 [188 kB] 109s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 109s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 109s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 109s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libbpf1 armhf 1:1.5.0-1 [158 kB] 109s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libmnl0 armhf 1.0.5-3 [10.7 kB] 109s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 109s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libfastjson4 armhf 1.2304.0-2 [20.2 kB] 109s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-c5 armhf 0.18+ds-1 [33.2 kB] 109s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 109s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf netplan-generator armhf 1.1.1-1 [60.4 kB] 109s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cffi-backend armhf 1.17.1-2 [68.7 kB] 109s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf python3-netplan armhf 1.1.1-1 [24.1 kB] 109s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf netplan.io armhf 1.1.1-1 [66.4 kB] 109s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libnetplan1 armhf 1.1.1-1 [122 kB] 109s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libpopt0 armhf 1.19+dfsg-2 [25.4 kB] 109s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 109s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 109s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 109s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf bash-completion all 1:2.14.0-2 [210 kB] 109s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 109s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm-common all 2.4.123-1 [8436 B] 109s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm2 armhf 2.4.123-1 [36.5 kB] 109s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 109s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libmaxminddb0 armhf 1.11.0-1 [16.8 kB] 109s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libnetfilter-conntrack3 armhf 1.1.0-1 [38.4 kB] 109s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-14 armhf 1.64.0-1 [68.9 kB] 109s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 109s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libpng16-16t64 armhf 1.6.44-2 [168 kB] 109s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libplymouth5 armhf 24.004.60-1ubuntu11 [140 kB] 109s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.3-1ubuntu1 [18.1 kB] 109s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.3-1ubuntu1 [52.1 kB] 109s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf liburcu8t64 armhf 0.14.1-1 [56.6 kB] 109s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libuv1t64 armhf 1.48.0-7 [83.3 kB] 109s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-data all 2:1.8.10-2 [116 kB] 109s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-6 armhf 2:1.8.10-2 [587 kB] 109s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libxau6 armhf 1:1.0.11-1 [6558 B] 109s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 109s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf pci.ids all 0.0~2024.10.24-1 [279 kB] 109s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu11 [9920 B] 109s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth armhf 24.004.60-1ubuntu11 [142 kB] 109s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-gdbm armhf 3.12.7-3 [28.7 kB] 109s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 109s Get:92 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 109s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf ufw all 0.36.2-8 [170 kB] 109s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf usbutils armhf 1:018-1 [76.1 kB] 109s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg-dev all 1.22.11ubuntu3 [1088 kB] 109s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf libdpkg-perl all 1.22.11ubuntu3 [279 kB] 109s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive13t64 armhf 3.7.4-1.1 [331 kB] 109s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 109s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libflashrom1 armhf 1.4.0-3ubuntu1 [141 kB] 109s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 109s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 110s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 110s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libxmlb2 armhf 0.3.21-1 [57.7 kB] 110s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 110s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.1-1 [17.4 kB] 110s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.1-1 [22.4 kB] 110s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.1-1 [34.3 kB] 110s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.1-1 [6552 B] 110s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize1 armhf 2.11-1ubuntu1 [12.0 kB] 110s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize-common all 2.11-1ubuntu1 [3584 B] 110s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.1-1 [13.4 kB] 110s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libnvme1t64 armhf 1.11-1 [73.8 kB] 110s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.1-1 [17.6 kB] 110s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.1-1 [16.5 kB] 110s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.1-1 [8952 B] 110s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.1-1 [44.2 kB] 110s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.23.2-5ubuntu4 [123 kB] 110s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 110s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-common all 2.6.8+dfsg-1~exp4ubuntu3 [32.3 kB] 110s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4ubuntu3 [173 kB] 110s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libnspr4 armhf 2:4.35-1.1ubuntu2 [94.1 kB] 110s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 110s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1t64 armhf 1.11.1-1 [116 kB] 110s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf udisks2 armhf 2.10.1-11ubuntu1 [278 kB] 110s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf libudisks2-0 armhf 2.10.1-11ubuntu1 [142 kB] 110s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 110s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf python3-certifi all 2024.8.30+dfsg-1 [9742 B] 110s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 110s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf python3-idna all 3.8-2 [47.0 kB] 110s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3-more-itertools all 10.5.0-1 [56.2 kB] 110s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jaraco.functools all 4.1.0-1 [11.8 kB] 110s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 110s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonpatch all 1.32-4 [12.2 kB] 111s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 111s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf python3-wadllib all 2.0.0-1 [36.7 kB] 111s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-2 [89.8 kB] 111s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.restfulclient all 0.14.6-2 [50.9 kB] 111s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf python3-typeguard all 4.4.1-1 [29.0 kB] 111s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf python3-urllib3 all 2.0.7-2ubuntu0.1 [93.1 kB] 111s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.21.0-1 [10.2 kB] 111s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 111s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 111s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-cryptsetup armhf 256.5-2ubuntu4 [122 kB] 111s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf ssh-import-id all 5.11-0ubuntu3 [10.1 kB] 111s Preconfiguring packages ... 111s Fetched 45.4 MB in 4s (12.6 MB/s) 112s (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 ... 59386 files and directories currently installed.) 112s Preparing to unpack .../motd-news-config_13.5ubuntu3_all.deb ... 112s Unpacking motd-news-config (13.5ubuntu3) over (13.3ubuntu6) ... 112s Preparing to unpack .../base-files_13.5ubuntu3_armhf.deb ... 112s Unpacking base-files (13.5ubuntu3) over (13.3ubuntu6) ... 112s Setting up base-files (13.5ubuntu3) ... 112s Installing new version of config file /etc/issue ... 112s Installing new version of config file /etc/issue.net ... 112s Installing new version of config file /etc/lsb-release ... 113s motd-news.service is a disabled or a static unit not running, not starting it. 113s (Reading database ... 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'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 131s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 131s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 131s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 131s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 131s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 131s loop8: Failed to write 'change' to '/sys/devices/virtual/block/loop8/uevent': Permission denied 132s Setting up systemd-sysv (256.5-2ubuntu4) ... 132s Setting up openssh-server (1:9.7p1-7ubuntu5) ... 133s Setting up plymouth (24.004.60-1ubuntu11) ... 133s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 134s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 134s Setting up libfwupd2:armhf (1.9.26-2) ... 134s Setting up libnss-systemd:armhf (256.5-2ubuntu4) ... 134s Setting up python3 (3.12.7-1) ... 134s Setting up python3-zipp (3.21.0-1) ... 134s Setting up dpkg-dev (1.22.11ubuntu3) ... 134s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu11) ... 134s update-initramfs: deferring update (trigger activated) 134s Setting up python3-oauthlib (3.2.2-2) ... 135s Setting up python3-configobj (5.0.9-1) ... 135s Setting up python3-certifi (2024.8.30+dfsg-1) ... 135s Setting up python3-gi (3.50.0-3) ... 135s Setting up python3-idna (3.8-2) ... 135s Setting up python3-urllib3 (2.0.7-2ubuntu0.1) ... 136s Setting up python3-json-pointer (2.4-2) ... 136s Setting up libpam-systemd:armhf (256.5-2ubuntu4) ... 136s Setting up fwupd (1.9.26-2) ... 136s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 136s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 136s fwupd.service is a disabled or a static unit not running, not starting it. 136s Setting up python3-cffi-backend:armhf (1.17.1-2) ... 136s Setting up python3-more-itertools (10.5.0-1) ... 137s Setting up python3-jaraco.functools (4.1.0-1) ... 137s Setting up python3-gdbm:armhf (3.12.7-1) ... 137s Setting up python3-problem-report (2.30.0-0ubuntu5) ... 137s Setting up ssh-import-id (5.11-0ubuntu3) ... 137s Setting up python3-jsonpatch (1.32-4) ... 137s Setting up python3-typeguard (4.4.1-1) ... 137s Setting up ufw (0.36.2-8) ... 138s Setting up python3-lazr.uri (1.0.6-4) ... 139s Setting up python3-apport (2.30.0-0ubuntu5) ... 139s Setting up python3-wadllib (2.0.0-1) ... 139s Setting up python3-netplan (1.1.1-1) ... 139s Setting up python3-lazr.restfulclient (0.14.6-2) ... 140s Setting up netplan.io (1.1.1-1) ... 140s Setting up apport-core-dump-handler (2.30.0-0ubuntu5) ... 140s Setting up apport (2.30.0-0ubuntu5) ... 140s Installing new version of config file /etc/apport/crashdb.conf ... 141s apport-autoreport.service is a disabled or a static unit not running, not starting it. 141s Processing triggers for dbus (1.14.10-4ubuntu5) ... 141s Processing triggers for shared-mime-info (2.4-5) ... 142s Processing triggers for install-info (7.1.1-1) ... 142s Processing triggers for initramfs-tools (0.142ubuntu34) ... 142s Processing triggers for libc-bin (2.40-1ubuntu3) ... 142s Processing triggers for rsyslog (8.2406.0-1ubuntu2) ... 142s Processing triggers for man-db (2.12.1-3) ... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s The following packages will be REMOVED: 145s libperl5.38t64* perl-modules-5.38* python3-netifaces* 146s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 146s After this operation, 41.7 MB disk space will be freed. 146s (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 ... 61506 files and directories currently installed.) 146s Removing libperl5.38t64:armhf (5.38.2-5) ... 146s Removing perl-modules-5.38 (5.38.2-5) ... 146s Removing python3-netifaces:armhf (0.11.0-2build3) ... 146s Processing triggers for man-db (2.12.1-3) ... 146s Processing triggers for libc-bin (2.40-1ubuntu3) ... 148s autopkgtest [17:59:53]: rebooting testbed after setup commands that affected boot 216s autopkgtest [18:01:01]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct 2 16:39:14 UTC 2 243s autopkgtest [18:01:28]: @@@@@@@@@@@@@@@@@@@@ apt-source macs 261s Get:1 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (dsc) [2152 B] 261s Get:2 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (tar) [197 MB] 261s Get:3 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (diff) [1268 kB] 262s gpgv: Signature made Sat Sep 7 23:10:03 2024 UTC 262s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 262s gpgv: Can't check signature: No public key 262s dpkg-source: warning: cannot verify inline signature for ./macs_3.0.2-1.dsc: no acceptable signature found 266s autopkgtest [18:01:51]: testing package macs version 3.0.2-1 269s autopkgtest [18:01:54]: build not needed 283s autopkgtest [18:02:08]: test run-unit-test: preparing testbed 294s Reading package lists... 294s Building dependency tree... 294s Reading state information... 295s Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 296s The following additional packages will be installed: 296s libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs python3-cykhash 296s python3-decorator python3-hmmlearn python3-joblib python3-numpy 296s python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl 296s Suggested packages: 296s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 296s python-scipy-doc python3-dap python-sklearn-doc ipython3 296s Recommended packages: 296s python3-pytest python3-simplejson python3-psutil g++ | c++-compiler 296s python3-pil python3-matplotlib 296s The following NEW packages will be installed: 296s autopkgtest-satdep libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs 296s python3-cykhash python3-decorator python3-hmmlearn python3-joblib 296s python3-numpy python3-scipy python3-sklearn python3-sklearn-lib 296s python3-threadpoolctl 296s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 296s Need to get 32.6 MB/32.6 MB of archives. 296s After this operation, 114 MB of additional disk space will be used. 296s Get:1 /tmp/autopkgtest.0vaE8I/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 296s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 296s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 296s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 296s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 296s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 296s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 296s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cykhash armhf 2.0.0-3build1 [455 kB] 296s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 296s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 297s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.3.2-5 [206 kB] 297s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB] 297s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-6 [3751 kB] 297s Get:14 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 297s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-hmmlearn armhf 0.3.2-2 [120 kB] 297s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf macs armhf 3.0.2-1 [3102 kB] 298s Fetched 32.6 MB in 2s (18.8 MB/s) 298s Selecting previously unselected package libblas3:armhf. 298s (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 ... 59566 files and directories currently installed.) 298s Preparing to unpack .../00-libblas3_3.12.0-3build2_armhf.deb ... 298s Unpacking libblas3:armhf (3.12.0-3build2) ... 298s Selecting previously unselected package libgfortran5:armhf. 298s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 298s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 298s Selecting previously unselected package libgomp1:armhf. 298s Preparing to unpack .../02-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 298s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 298s Selecting previously unselected package liblapack3:armhf. 298s Preparing to unpack .../03-liblapack3_3.12.0-3build2_armhf.deb ... 298s Unpacking liblapack3:armhf (3.12.0-3build2) ... 298s Selecting previously unselected package liblbfgsb0:armhf. 298s Preparing to unpack .../04-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 298s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 298s Selecting previously unselected package python3-numpy. 298s Preparing to unpack .../05-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 298s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 298s Selecting previously unselected package python3-cykhash. 298s Preparing to unpack .../06-python3-cykhash_2.0.0-3build1_armhf.deb ... 298s Unpacking python3-cykhash (2.0.0-3build1) ... 298s Selecting previously unselected package python3-decorator. 298s Preparing to unpack .../07-python3-decorator_5.1.1-5_all.deb ... 298s Unpacking python3-decorator (5.1.1-5) ... 298s Selecting previously unselected package python3-scipy. 298s Preparing to unpack .../08-python3-scipy_1.13.1-5_armhf.deb ... 298s Unpacking python3-scipy (1.13.1-5) ... 299s Selecting previously unselected package python3-joblib. 299s Preparing to unpack .../09-python3-joblib_1.3.2-5_all.deb ... 299s Unpacking python3-joblib (1.3.2-5) ... 299s Selecting previously unselected package python3-threadpoolctl. 299s Preparing to unpack .../10-python3-threadpoolctl_3.1.0-1_all.deb ... 299s Unpacking python3-threadpoolctl (3.1.0-1) ... 299s Selecting previously unselected package python3-sklearn-lib:armhf. 299s Preparing to unpack .../11-python3-sklearn-lib_1.4.2+dfsg-6_armhf.deb ... 299s Unpacking python3-sklearn-lib:armhf (1.4.2+dfsg-6) ... 299s Selecting previously unselected package python3-sklearn. 299s Preparing to unpack .../12-python3-sklearn_1.4.2+dfsg-6_all.deb ... 299s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 299s Selecting previously unselected package python3-hmmlearn. 299s Preparing to unpack .../13-python3-hmmlearn_0.3.2-2_armhf.deb ... 299s Unpacking python3-hmmlearn (0.3.2-2) ... 299s Selecting previously unselected package macs. 299s Preparing to unpack .../14-macs_3.0.2-1_armhf.deb ... 299s Unpacking macs (3.0.2-1) ... 299s Selecting previously unselected package autopkgtest-satdep. 299s Preparing to unpack .../15-1-autopkgtest-satdep.deb ... 299s Unpacking autopkgtest-satdep (0) ... 299s Setting up python3-joblib (1.3.2-5) ... 300s Setting up python3-threadpoolctl (3.1.0-1) ... 300s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 300s Setting up python3-cykhash (2.0.0-3build1) ... 300s Setting up python3-decorator (5.1.1-5) ... 300s Setting up libblas3:armhf (3.12.0-3build2) ... 300s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 300s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 300s Setting up liblapack3:armhf (3.12.0-3build2) ... 300s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 300s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 302s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 302s Setting up python3-scipy (1.13.1-5) ... 306s Setting up python3-sklearn-lib:armhf (1.4.2+dfsg-6) ... 306s Setting up python3-sklearn (1.4.2+dfsg-6) ... 309s Setting up python3-hmmlearn (0.3.2-2) ... 309s Setting up macs (3.0.2-1) ... 309s Setting up autopkgtest-satdep (0) ... 309s Processing triggers for man-db (2.12.1-3) ... 310s Processing triggers for libc-bin (2.40-1ubuntu3) ... 321s (Reading database ... 63125 files and directories currently installed.) 321s Removing autopkgtest-satdep (0) ... 327s autopkgtest [18:02:52]: test run-unit-test: [----------------------- 329s + pkg=macs 329s + '[' /tmp/autopkgtest.0vaE8I/autopkgtest_tmp = '' ']' 329s + cp -a /usr/share/doc/macs/examples/aluY.chr1.bed.gz /usr/share/doc/macs/examples/gerp.chr1.bed.gz /tmp/autopkgtest.0vaE8I/autopkgtest_tmp 329s + cd /tmp/autopkgtest.0vaE8I/autopkgtest_tmp 329s + gunzip aluY.chr1.bed.gz gerp.chr1.bed.gz 329s + macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 329s INFO @ 13 Nov 2024 18:02:54: [27 MB] 329s # Command line: callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 329s # ARGUMENTS LIST: 329s # name = test 329s # format = AUTO 329s # ChIP-seq file = ['aluY.chr1.bed'] 329s # control file = None 329s # effective genome size = 2.91e+09 329s # band width = 300 329s # model fold = [5, 50] 329s # qvalue cutoff = 1.00e-02 329s # The maximum gap between significant sites is assigned as the read length/tag size. 329s # The minimum length of peaks is assigned as the predicted fragment length "d". 329s # Larger dataset will be scaled towards smaller dataset. 329s # Range for calculating regional lambda is: 10000 bps 329s # Broad region calling is off 329s # Paired-End mode is off 329s 329s INFO @ 13 Nov 2024 18:02:54: [27 MB] #1 read tag files... 329s INFO @ 13 Nov 2024 18:02:54: [27 MB] #1 read treatment tags... 329s INFO @ 13 Nov 2024 18:02:54: [27 MB] Detected format is: BED 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 tag size is determined as 294 bps 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 tag size = 294.0 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 total tags in treatment: 11628 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 user defined the maximum tags... 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 tags after filtering in treatment: 11628 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 Redundant rate of treatment: 0.00 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #1 finished! 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #2 Build Peak Model... 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #2 Skipped... 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #2 Use 200 as fragment length 329s INFO @ 13 Nov 2024 18:02:54: [28 MB] #3 Call peaks... 329s INFO @ 13 Nov 2024 18:02:54: [29 MB] #3 Pre-compute pvalue-qvalue table... 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #3 In the peak calling step, the following will be performed simultaneously: 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_treat_pileup.bdg 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... test_control_lambda.bdg 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #3 Pileup will be based on sequencing depth in treatment. 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #3 Call peaks for each chromosome... 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #4 Write output xls file... test_peaks.xls 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #4 Write peak in narrowPeak format file... test_peaks.narrowPeak 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] #4 Write summits bed file... test_summits.bed 330s INFO @ 13 Nov 2024 18:02:55: [31 MB] Done! 330s + macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 330s INFO @ 13 Nov 2024 18:02:55: [27 MB] 330s # Command line: callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 330s # ARGUMENTS LIST: 330s # name = NA 330s # format = AUTO 330s # ChIP-seq file = ['gerp.chr1.bed'] 330s # control file = None 330s # effective genome size = 2.91e+09 330s # band width = 300 330s # model fold = [5, 50] 330s # qvalue cutoff for narrow/strong regions = 5.00e-02 330s # qvalue cutoff for broad/weak regions = 1.00e-01 330s # The maximum gap between significant sites is assigned as the read length/tag size. 330s # The minimum length of peaks is assigned as the predicted fragment length "d". 330s # Larger dataset will be scaled towards smaller dataset. 330s # Range for calculating regional lambda is: 10000 bps 330s # Broad region calling is on 330s # Paired-End mode is off 330s 330s INFO @ 13 Nov 2024 18:02:55: [27 MB] #1 read tag files... 330s INFO @ 13 Nov 2024 18:02:55: [27 MB] #1 read treatment tags... 330s INFO @ 13 Nov 2024 18:02:55: [27 MB] Detected format is: BED 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 tag size is determined as 181 bps 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 tag size = 181.0 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 total tags in treatment: 88292 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 user defined the maximum tags... 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 tags after filtering in treatment: 88292 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 Redundant rate of treatment: 0.00 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #1 finished! 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #2 Build Peak Model... 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #2 Skipped... 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #2 Use 200 as fragment length 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #3 Call peaks... 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... 330s INFO @ 13 Nov 2024 18:02:55: [35 MB] #3 Pre-compute pvalue-qvalue table... 330s INFO @ 13 Nov 2024 18:02:55: [49 MB] #3 Call peaks for each chromosome... 330s INFO @ 13 Nov 2024 18:02:55: [49 MB] #4 Write output xls file... NA_peaks.xls 330s INFO @ 13 Nov 2024 18:02:55: [49 MB] #4 Write broad peak in broadPeak format file... NA_peaks.broadPeak 330s INFO @ 13 Nov 2024 18:02:55: [49 MB] #4 Write broad peak in bed12/gappedPeak format file... NA_peaks.gappedPeak 330s INFO @ 13 Nov 2024 18:02:55: [49 MB] Done! 331s autopkgtest [18:02:56]: test run-unit-test: -----------------------] 335s run-unit-test PASS 335s autopkgtest [18:03:00]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 339s autopkgtest [18:03:04]: @@@@@@@@@@@@@@@@@@@@ summary 339s run-unit-test PASS