1s autopkgtest [23:21:20]: starting date and time: 2025-03-15 23:21:20+0000 1s autopkgtest [23:21:20]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [23:21:20]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s6lzzm3j/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade subread --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-31.secgroup --name adt-plucky-amd64-subread-20250315-232119-juju-7f2275-prod-proposed-migration-environment-20-a5994e74-a955-4c9f-8a71-598582cfbf94 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 45s autopkgtest [23:22:04]: testbed dpkg architecture: amd64 45s autopkgtest [23:22:04]: testbed apt version: 2.9.31ubuntu1 46s autopkgtest [23:22:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 46s autopkgtest [23:22:05]: testbed release detected to be: None 47s autopkgtest [23:22:06]: updating testbed package index (apt update) 47s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 47s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 47s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 48s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 48s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 48s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 48s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 48s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 48s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 48s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 48s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 48s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 48s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 48s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 48s Fetched 1265 kB in 1s (1454 kB/s) 49s Reading package lists... 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 50s Calculating upgrade... 51s The following package was automatically installed and is no longer required: 51s libnl-genl-3-200 51s Use 'sudo apt autoremove' to remove it. 51s The following NEW packages will be installed: 51s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 51s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 51s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 51s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 51s The following packages will be upgraded: 51s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 51s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 51s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 51s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 51s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 51s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 51s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 51s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 51s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 51s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 51s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 51s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 51s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 51s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 51s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 51s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 51s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 51s parted pci.ids pciutils pinentry-curses python-apt-common python3 51s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 51s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 51s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 51s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 51s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 51s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 51s xz-utils 51s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 829 MB of archives. 51s After this operation, 325 MB of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 51s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 51s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 51s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 52s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 52s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 52s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 52s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 52s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 52s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 52s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 52s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 52s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 52s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 52s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 52s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 52s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 52s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 52s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 52s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 52s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 52s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 52s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 52s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 52s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 52s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 52s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 52s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 52s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 52s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 52s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 52s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 52s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 52s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 52s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 52s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 52s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 52s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 52s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 52s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 52s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 52s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 52s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 52s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 52s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 53s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 53s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 53s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 53s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 53s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 53s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 53s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 53s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 53s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 53s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 53s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 53s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 53s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 53s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 53s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 53s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 53s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 53s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 53s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 53s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 53s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 53s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 53s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 53s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 53s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 53s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 53s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 53s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 53s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 53s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 53s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 53s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 53s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 53s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 53s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 53s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 53s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 53s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 53s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 53s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 53s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 53s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 53s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 53s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 53s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 53s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 53s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 53s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 53s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 53s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 53s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 53s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 53s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 53s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 53s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 53s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 53s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 54s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 54s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 54s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 54s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 54s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 54s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 54s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 68s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 68s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 68s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 68s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 68s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 68s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 68s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 68s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 69s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 69s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 73s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 73s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 73s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 73s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 73s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 73s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 74s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 74s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 74s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 74s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 74s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 74s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 74s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 74s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 74s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 74s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 74s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 74s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 74s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 75s Preconfiguring packages ... 75s Fetched 829 MB in 24s (35.0 MB/s) 75s (Reading database ... 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(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 ... 109140 files and directories currently installed.) 75s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 75s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 75s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 75s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 76s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 76s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 76s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 76s Checking for services that may need to be restarted... 76s Checking init scripts... 76s Checking for services that may need to be restarted... 76s Checking init scripts... 76s Stopping some services possibly affected by the upgrade (will be restarted later): 76s cron: stopping...done. 76s 76s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 76s Setting up libc6:amd64 (2.41-1ubuntu1) ... 76s Checking for services that may need to be restarted... 76s Checking init scripts... 76s Restarting services possibly affected by the upgrade: 77s cron: restarting...done. 77s 77s Services restarted successfully. 77s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 80s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 80s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 80s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 80s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 80s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 80s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 80s Setting up apt (2.9.33) ... 81s (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 ... 109146 files and directories currently installed.) 81s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 81s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 81s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 81s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 81s Setting up python3-minimal (3.13.2-2) ... 81s (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 ... 109146 files and directories currently installed.) 81s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ... 81s Unpacking python3 (3.13.2-2) over (3.13.2-1) ... 81s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ... 81s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ... 81s Preparing to unpack .../2-media-types_13.0.0_all.deb ... 81s Unpacking media-types (13.0.0) over (12.0.0) ... 81s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ... 81s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 81s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ... 81s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 81s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ... 81s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 81s Setting up libtinfo6:amd64 (6.5+20250216-2) ... 82s (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 ... 109146 files and directories currently installed.) 82s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 82s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 82s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 82s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 82s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 82s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 82s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 82s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 82s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 82s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 82s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 82s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 82s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 82s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 82s Selecting previously unselected package libdebuginfod-common. 82s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 82s Unpacking libdebuginfod-common (0.192-4) ... 82s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 82s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 82s Setting up libsemanage-common (3.7-2.1build1) ... 82s (Reading database ... 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unpack .../29-xz-utils_5.6.4-1_amd64.deb ... 85s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ... 85s Preparing to unpack .../30-ubuntu-standard_1.549_amd64.deb ... 85s Unpacking ubuntu-standard (1.549) over (1.548) ... 85s Preparing to unpack .../31-libgprofng0_2.44-3ubuntu1_amd64.deb ... 85s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 85s Preparing to unpack .../32-libctf0_2.44-3ubuntu1_amd64.deb ... 85s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 85s Preparing to unpack .../33-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ... 85s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 85s Preparing to unpack .../34-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ... 85s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 85s Preparing to unpack .../35-libbinutils_2.44-3ubuntu1_amd64.deb ... 85s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 85s Preparing to unpack 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unpack .../80-python3-systemd_235-1build6_amd64.deb ... 96s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 96s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 96s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 96s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 96s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 96s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 96s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 96s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 96s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 97s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 97s Setting up media-types (13.0.0) ... 97s Installing new version of config file /etc/mime.types ... 97s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 97s Setting up ubuntu-kernel-accessories (1.549) ... 97s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 97s Setting up pci.ids (0.0~2025.03.09-1) ... 97s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 97s Setting up apt-utils (2.9.33) ... 97s Setting up libdebuginfod-common (0.192-4) ... 97s Setting up exfatprogs (1.2.8-1) ... 97s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 97s Setting up bpftool (7.6.0+6.14.0-10.10) ... 97s Setting up libestr0:amd64 (0.1.11-2) ... 97s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 97s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 97s Setting up dosfstools (4.2-1.2) ... 97s Setting up rsyslog (8.2412.0-2ubuntu2) ... 97s info: The user `syslog' is already a member of `adm'. 98s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 98s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 98s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 98s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 98s Setting up systemd (257.3-1ubuntu3) ... 98s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 98s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 98s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 99s Setting up libparted2t64:amd64 (3.6-5) ... 99s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 99s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 99s Setting up linux-headers-generic (6.14.0-10.10) ... 99s Setting up libjemalloc2:amd64 (5.3.0-3) ... 99s Setting up locales (2.41-1ubuntu1) ... 99s Installing new version of config file /etc/locale.alias ... 99s Generating locales (this might take a while)... 101s en_US.UTF-8... done 101s Generation complete. 101s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 101s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 101s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 101s Installing new version of config file /etc/apparmor.d/fusermount3 ... 101s Installing new version of config file /etc/apparmor.d/lsusb ... 101s Installing new version of config file /etc/apparmor.d/openvpn ... 102s Reloading AppArmor profiles 103s Setting up libftdi1-2:amd64 (1.5-8build1) ... 103s Setting up libglib2.0-data (2.84.0-1) ... 103s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 103s Setting up libncurses6:amd64 (6.5+20250216-2) ... 103s Setting up strace (6.13+ds-1ubuntu1) ... 103s Setting up xz-utils (5.6.4-1) ... 103s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 104s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 104s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 104s Setting up udev (257.3-1ubuntu3) ... 105s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 107s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 107s Setting up libpci3:amd64 (1:3.13.0-2) ... 107s Setting up whiptail (0.52.24-4ubuntu2) ... 107s Setting up python-apt-common (2.9.9build1) ... 107s Setting up pnp.ids (0.393-3) ... 107s Setting up libnl-3-200:amd64 (3.7.0-1) ... 107s Setting up python3.13-minimal (3.13.2-2) ... 107s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 107s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 107s Setting up libc-dev-bin (2.41-1ubuntu1) ... 107s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 107s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 107s Setting up rsync (3.4.1+ds1-3) ... 108s rsync.service is a disabled or a static unit not running, not starting it. 108s Setting up python3.13-gdbm (3.13.2-2) ... 108s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 108s Setting up systemd-resolved (257.3-1ubuntu3) ... 109s Setting up initramfs-tools-bin (0.146ubuntu1) ... 109s Setting up ncurses-term (6.5+20250216-2) ... 109s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 109s Setting up libpython3.13:amd64 (3.13.2-2) ... 109s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 109s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 109s Setting up systemd-sysv (257.3-1ubuntu3) ... 109s Setting up linux-headers-virtual (6.14.0-10.10) ... 109s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 109s Setting up python3.13 (3.13.2-2) ... 110s Setting up htop (3.4.0-2) ... 110s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 112s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 112s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 112s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 112s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 112s Setting up parted (3.6-5) ... 112s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 112s Setting up python3 (3.13.2-2) ... 112s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 112s Setting up python3-markupsafe (2.1.5-1build4) ... 112s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 114s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 114s Setting up hwdata (0.393-3) ... 114s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 114s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 114s No schema files found: doing nothing. 114s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 114s Setting up linux-perf (6.14.0-10.10) ... 114s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 114s Setting up pciutils (1:3.13.0-2) ... 114s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 114s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 114s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 114s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 115s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 115s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 115s Setting up curl (8.12.1-3ubuntu1) ... 115s Setting up linux-image-virtual (6.14.0-10.10) ... 115s Setting up initramfs-tools-core (0.146ubuntu1) ... 115s Setting up linux-tools-common (6.14.0-10.10) ... 115s Setting up python3-systemd (235-1build6) ... 115s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 115s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 115s Setting up linux-image-generic (6.14.0-10.10) ... 115s Setting up python3-dbus (1.3.2-5build5) ... 115s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 115s Setting up initramfs-tools (0.146ubuntu1) ... 115s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 115s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 115s update-initramfs: deferring update (trigger activated) 115s Setting up linux-generic (6.14.0-10.10) ... 115s Setting up ubuntu-minimal (1.549) ... 115s Setting up python3-apt (2.9.9build1) ... 115s Setting up python3-bcrypt (4.2.0-2.1build1) ... 115s Setting up python3-yaml (6.0.2-1build2) ... 115s Setting up libfwupd3:amd64 (2.0.6-4) ... 115s Setting up python3-lazr.uri (1.0.6-6) ... 115s Setting up binutils (2.44-3ubuntu1) ... 115s Setting up ubuntu-standard (1.549) ... 115s Setting up cloud-init-base (25.1-0ubuntu3) ... 117s Setting up linux-virtual (6.14.0-10.10) ... 117s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 117s Setting up python3-gi (3.50.0-4build1) ... 117s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 117s Setting up fwupd (2.0.6-4) ... 118s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 118s Setting up cloud-init (25.1-0ubuntu3) ... 118s Processing triggers for man-db (2.13.0-1) ... 119s Processing triggers for dbus (1.16.2-1ubuntu1) ... 120s Processing triggers for shared-mime-info (2.4-5) ... 120s Warning: program compiled against libxml 212 using older 209 120s Processing triggers for libc-bin (2.41-1ubuntu1) ... 120s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 120s /etc/kernel/postinst.d/initramfs-tools: 120s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 120s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 130s /etc/kernel/postinst.d/zz-update-grub: 130s Sourcing file `/etc/default/grub' 130s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 130s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 130s Generating grub configuration file ... 130s Found linux image: /boot/vmlinuz-6.14.0-10-generic 130s Found initrd image: /boot/initrd.img-6.14.0-10-generic 130s Found linux image: /boot/vmlinuz-6.12.0-16-generic 130s Found initrd image: /boot/initrd.img-6.12.0-16-generic 130s Found linux image: /boot/vmlinuz-6.11.0-8-generic 130s Found initrd image: /boot/initrd.img-6.11.0-8-generic 131s Warning: os-prober will not be executed to detect other bootable partitions. 131s Systems on them will not be added to the GRUB boot configuration. 131s Check GRUB_DISABLE_OS_PROBER documentation entry. 131s Adding boot menu entry for UEFI Firmware Settings ... 131s done 131s Processing triggers for initramfs-tools (0.146ubuntu1) ... 131s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 131s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Solving dependencies... 142s The following packages will be REMOVED: 142s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 142s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 142s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 142s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 142s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 142s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 142s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 142s linux-tools-6.12.0-16-generic* 143s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 143s After this operation, 545 MB disk space will be freed. 143s (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 ... 148643 files and directories currently installed.) 143s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 143s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 143s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 143s Removing libpython3.12t64:amd64 (3.12.9-1) ... 143s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 143s Removing libnsl2:amd64 (1.3.0-3build3) ... 143s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 143s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 144s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 145s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 146s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 148s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 148s /etc/kernel/postrm.d/initramfs-tools: 148s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 148s /etc/kernel/postrm.d/zz-update-grub: 148s Sourcing file `/etc/default/grub' 148s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 148s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 148s Generating grub configuration file ... 148s Found linux image: /boot/vmlinuz-6.14.0-10-generic 148s Found initrd image: /boot/initrd.img-6.14.0-10-generic 149s Found linux image: /boot/vmlinuz-6.12.0-16-generic 149s Found initrd image: /boot/initrd.img-6.12.0-16-generic 149s Warning: os-prober will not be executed to detect other bootable partitions. 149s Systems on them will not be added to the GRUB boot configuration. 149s Check GRUB_DISABLE_OS_PROBER documentation entry. 149s Adding boot menu entry for UEFI Firmware Settings ... 149s done 149s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 149s W: Removing the running kernel 149s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 149s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 149s /etc/kernel/postrm.d/initramfs-tools: 149s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 149s /etc/kernel/postrm.d/zz-update-grub: 149s Sourcing file `/etc/default/grub' 149s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 149s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 149s Generating grub configuration file ... 149s Found linux image: /boot/vmlinuz-6.14.0-10-generic 149s Found initrd image: /boot/initrd.img-6.14.0-10-generic 150s Warning: os-prober will not be executed to detect other bootable partitions. 150s Systems on them will not be added to the GRUB boot configuration. 150s Check GRUB_DISABLE_OS_PROBER documentation entry. 150s Adding boot menu entry for UEFI Firmware Settings ... 150s done 150s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 150s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 151s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 151s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 151s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 151s Processing triggers for libc-bin (2.41-1ubuntu1) ... 151s (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 ... 76972 files and directories currently installed.) 151s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 152s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 152s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 152s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 152s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 152s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 152s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 152s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 152s autopkgtest [23:23:51]: upgrading testbed (apt dist-upgrade and autopurge) 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 153s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 153s Starting 2 pkgProblemResolver with broken count: 0 153s Done 153s Entering ResolveByKeep 154s 154s Calculating upgrade... 154s The following packages will be upgraded: 154s libc-bin libc-dev-bin libc6 libc6-dev locales 154s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Need to get 10.5 MB of archives. 154s After this operation, 1024 B of additional disk space will be used. 154s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 155s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 155s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 155s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 155s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 155s Preconfiguring packages ... 155s Fetched 10.5 MB in 1s (10.2 MB/s) 155s (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 ... 76968 files and directories currently installed.) 155s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 155s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 155s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 155s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 155s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 156s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 156s Setting up libc6:amd64 (2.41-1ubuntu2) ... 156s (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 ... 76968 files and directories currently installed.) 156s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 156s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 156s Setting up libc-bin (2.41-1ubuntu2) ... 156s (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 ... 76968 files and directories currently installed.) 156s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 156s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 156s Setting up locales (2.41-1ubuntu2) ... 157s Generating locales (this might take a while)... 158s en_US.UTF-8... done 158s Generation complete. 158s Setting up libc-dev-bin (2.41-1ubuntu2) ... 158s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 158s Processing triggers for man-db (2.13.0-1) ... 159s Processing triggers for systemd (257.3-1ubuntu3) ... 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 161s Solving dependencies... 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s autopkgtest [23:24:00]: rebooting testbed after setup commands that affected boot 184s autopkgtest [23:24:23]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 186s autopkgtest [23:24:25]: @@@@@@@@@@@@@@@@@@@@ apt-source subread 189s Get:1 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (dsc) [2332 B] 189s Get:2 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (tar) [16.5 MB] 189s Get:3 http://ftpmaster.internal/ubuntu plucky/universe subread 2.0.7+dfsg-1 (diff) [19.6 kB] 190s gpgv: Signature made Sat Aug 31 10:04:54 2024 UTC 190s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 190s gpgv: issuer "emollier@debian.org" 190s gpgv: Can't check signature: No public key 190s dpkg-source: warning: cannot verify inline signature for ./subread_2.0.7+dfsg-1.dsc: no acceptable signature found 190s autopkgtest [23:24:29]: testing package subread version 2.0.7+dfsg-1 191s autopkgtest [23:24:30]: build not needed 194s autopkgtest [23:24:33]: test subread-tests: preparing testbed 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 195s The following NEW packages will be installed: 195s subread subread-data 195s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 195s Need to get 19.8 MB of archives. 195s After this operation, 21.2 MB of additional disk space will be used. 195s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 subread amd64 2.0.7+dfsg-1 [552 kB] 196s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 subread-data all 2.0.7+dfsg-1 [19.2 MB] 197s Fetched 19.8 MB in 1s (15.0 MB/s) 197s Selecting previously unselected package subread. 197s (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 ... 76968 files and directories currently installed.) 197s Preparing to unpack .../subread_2.0.7+dfsg-1_amd64.deb ... 197s Unpacking subread (2.0.7+dfsg-1) ... 197s Selecting previously unselected package subread-data. 197s Preparing to unpack .../subread-data_2.0.7+dfsg-1_all.deb ... 197s Unpacking subread-data (2.0.7+dfsg-1) ... 197s Setting up subread (2.0.7+dfsg-1) ... 197s Setting up subread-data (2.0.7+dfsg-1) ... 197s Processing triggers for man-db (2.13.0-1) ... 199s autopkgtest [23:24:38]: test subread-tests: [----------------------- 199s  199s 199s 199s 199s ************************************************** 199s ************************************************** 199s *** *** 199s *** This script will test the major functions *** 199s *** in our package, including the index build- *** 199s *** er, subread-align, subjunc, featureCounts *** 199s *** and exactSNP. *** 199s *** *** 199s *** Test will start in seconds. *** 199s *** *** 199s ************************************************** 199s ************************************************** 199s 200s 9test_all.sh: line 25: bc: command not found 201s test_all.sh: line 25: bc: command not found 203s test_all.sh: line 25: bc: command not found 204s test_all.sh: line 25: bc: command not found 205s test_all.sh: line 25: bc: command not found 206s test_all.sh: line 25: bc: command not found 207s test_all.sh: line 25: bc: command not found 208s test_all.sh: line 25: bc: command not found 209s test_all.sh: line 25: bc: command not found 209s [0,0Hrm: cannot remove 'test-tmp.log': No such file or directory 209s 209s ========== _____ _ _ ____ _____ ______ _____ 209s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 209s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 209s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 209s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 209s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 209s v2.0.7 209s 209s //================================= setting ==================================\\ 209s || || 209s || Index name : small1 || 209s || Index space : base space || 209s || Index split : no-split || 209s || Repeat threshold : 100 repeats || 209s || Gapped index : no || 209s || || 209s || Free / total memory : 3.6GB / 3.8GB || 209s || || 209s || Input files : 1 file in total || 209s || o chr901.fa || 209s || || 209s \\============================================================================// 209s 209s //================================= Running ==================================\\ 209s || || 209s || Check the integrity of provided reference sequences ... || 209s || There were 4 notes for reference sequences. || 209s || The notes can be found in the log file, '../small1.log'. || 209s || Scan uninformative subreads in reference sequences ... || 210s || 52 uninformative subreads were found. || 210s || These subreads were excluded from index building. || 210s || Estimate the index size... || 210s || 8%, 0 mins elapsed, rate=356.7k bps/s || 210s || 16%, 0 mins elapsed, rate=692.8k bps/s || 210s || 25%, 0 mins elapsed, rate=1010.0k bps/s || 210s || 33%, 0 mins elapsed, rate=1315.0k bps/s || 210s || 41%, 0 mins elapsed, rate=1599.8k bps/s || 210s || 50%, 0 mins elapsed, rate=1862.9k bps/s || 210s || 58%, 0 mins elapsed, rate=2118.5k bps/s || 210s || 66%, 0 mins elapsed, rate=2361.5k bps/s || 210s || 75%, 0 mins elapsed, rate=2592.7k bps/s || 210s || 83%, 0 mins elapsed, rate=2813.2k bps/s || 210s || 91%, 0 mins elapsed, rate=3043.4k bps/s || 210s || 3.0 GB of memory is needed for index building. || 212s || Build the index... || 212s || 8%, 0 mins elapsed, rate=41.2k bps/s || 212s || 16%, 0 mins elapsed, rate=81.4k bps/s || 212s || 25%, 0 mins elapsed, rate=120.7k bps/s || 212s || 33%, 0 mins elapsed, rate=159.0k bps/s || 212s || 41%, 0 mins elapsed, rate=196.5k bps/s || 212s || 50%, 0 mins elapsed, rate=233.1k bps/s || 212s || 58%, 0 mins elapsed, rate=268.4k bps/s || 212s || 66%, 0 mins elapsed, rate=302.9k bps/s || 212s || 75%, 0 mins elapsed, rate=336.5k bps/s || 212s || 83%, 0 mins elapsed, rate=369.3k bps/s || 213s || 91%, 0 mins elapsed, rate=400.9k bps/s || 213s || Save current index block... || 213s || [ 0.0% finished ] || 213s || [ 10.0% finished ] || 214s || [ 20.0% finished ] || 214s || [ 30.0% finished ] || 214s || [ 40.0% finished ] || 215s || [ 50.0% finished ] || 215s || [ 60.0% finished ] || 216s || [ 70.0% finished ] || 216s || [ 80.0% finished ] || 217s || [ 90.0% finished ] || 217s || [ 100.0% finished ] || 217s || || 217s || Total running time: 0.1 minutes. || 217s || Index ../small1 was successfully built. || 217s || || 217s \\============================================================================// 217s 219s 219s ========== _____ _ _ ____ _____ ______ _____ 219s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 219s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 219s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 219s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 219s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 219s v2.0.7 219s 219s //================================= setting ==================================\\ 219s || || 219s || Function : Read alignment (RNA-Seq) || 219s || Input file : test-noerror-r1.fq || 219s || Output file : test-tmp.sam (SAM) || 219s || Index name : small1 || 219s || || 219s || ------------------------------------ || 219s || || 219s || Threads : 1 || 219s || Phred offset : 64 || 219s || Min votes : 3 / 10 || 219s || Max mismatches : 3 || 219s || Max indel length : 5 || 219s || Report multi-mapping reads : no || 219s || Max alignments per multi-mapping read : 1 || 219s || || 219s \\============================================================================// 219s 219s //================= Running (15-Mar-2025 23:24:58, pid=1449) =================\\ 219s || || 219s || Check the input reads. || 219s || The input file contains base space reads. || 219s || Initialise the memory objects. || 219s || Estimate the mean read length. || 219s || The range of Phred scores observed in the data is [9,9] || 219s || Create the output SAM file. || 219s || Check the index. || 219s || Init the voting space. || 219s || Global environment is initialised. || 219s || Load the 1-th index block... || 250s || The index block has been loaded. || 250s || Start read mapping in chunk. || 250s || 33% completed, 0.5 mins elapsed, rate=60.1k reads per second || 251s || 74% completed, 0.5 mins elapsed, rate=0.5k reads per second || 251s || 83% completed, 0.5 mins elapsed, rate=0.5k reads per second || 251s || 91% completed, 0.5 mins elapsed, rate=0.6k reads per second || 251s || || 251s || Completed successfully. || 251s || || 251s \\==================================== ====================================// 251s 251s //================================ Summary =================================\\ 251s || || 251s || Total reads : 19998 || 251s || Mapped : 18785 (93.9%) || 251s || Uniquely mapped : 18785 || 251s || Multi-mapping : 0 || 251s || || 251s || Unmapped : 1213 || 251s || || 251s || Indels : 0 || 251s || || 251s || Running time : 0.5 minutes || 251s || || 251s \\============================================================================// 251s 251s 251s ========== _____ _ _ ____ _____ ______ _____ 251s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 251s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 251s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 251s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 251s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 251s v2.0.7 251s 251s //================================= setting ==================================\\ 251s || || 251s || Function : Read alignment (RNA-Seq) || 251s || Input file : test-noerror-r1.fq || 251s || Output file : test-tmp.sam (SAM) || 251s || Index name : small1 || 251s || || 251s || ------------------------------------ || 251s || || 251s || Threads : 1 || 251s || Phred offset : 64 || 251s || Min votes : 3 / 10 || 251s || Max mismatches : 3 || 251s || Max indel length : 5 || 251s || Report multi-mapping reads : no || 251s || Max alignments per multi-mapping read : 1 || 251s || || 251s \\============================================================================// 251s 251s //================= Running (15-Mar-2025 23:25:30, pid=1465) =================\\ 251s || || 251s || Check the input reads. || 251s || The input file contains base space reads. || 251s || Initialise the memory objects. || 251s || Estimate the mean read length. || 251s || The range of Phred scores observed in the data is [9,9] || 251s || Create the output SAM file. || 251s || Check the index. || 251s || Init the voting space. || 251s || Global environment is initialised. || 251s || Load the 1-th index block... || 283s || The index block has been loaded. || 283s || Start read mapping in chunk. || 283s || 33% completed, 0.5 mins elapsed, rate=57.5k reads per second || 283s || 74% completed, 0.5 mins elapsed, rate=0.5k reads per second || 283s || 83% completed, 0.5 mins elapsed, rate=0.5k reads per second || 284s || 91% completed, 0.5 mins elapsed, rate=0.6k reads per second || 284s || || 284s || Completed successfully. || 284s || || 284s \\==================================== ====================================// 284s 284s //================================ Summary =================================\\ 284s || || 284s || Total reads : 19998 || 284s || Mapped : 18785 (93.9%) || 284s || Uniquely mapped : 18785 || 284s || Multi-mapping : 0 || 284s || || 284s || Unmapped : 1213 || 284s || || 284s || Indels : 0 || 284s || || 284s || Running time : 0.5 minutes || 284s || || 284s \\============================================================================// 284s 284s 284s ========== _____ _ _ ____ _____ ______ _____ 284s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 284s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 284s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 284s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 284s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 284s v2.0.7 284s 284s //================================= setting ==================================\\ 284s || || 284s || Function : Read alignment (RNA-Seq) || 284s || Input file 1 : test-noerror-r1.fq || 284s || Input file 2 : test-noerror-r2.fq || 284s || Output file : test-tmp.sam (SAM) || 284s || Index name : small1 || 284s || || 284s || ------------------------------------ || 284s || || 284s || Threads : 1 || 284s || Phred offset : 64 || 284s || # of extracted subreads : 10 || 284s || Min read1 vote : 3 || 284s || Min read2 vote : 1 || 284s || Max fragment size : 600 || 284s || Min fragment size : 50 || 284s || Max mismatches : 3 || 284s || Max indel length : 5 || 284s || Report multi-mapping reads : no || 284s || Max alignments per multi-mapping read : 1 || 284s || || 284s \\============================================================================// 284s 284s //================= Running (15-Mar-2025 23:26:03, pid=1469) =================\\ 284s || || 284s || Check the input reads. || 284s || The input file contains base space reads. || 284s || Initialise the memory objects. || 284s || Estimate the mean read length. || 284s || The range of Phred scores observed in the data is [9,9] || 284s || Create the output SAM file. || 284s || Check the index. || 284s || Init the voting space. || 284s || Global environment is initialised. || 284s || Load the 1-th index block... || 316s || The index block has been loaded. || 316s || Start read mapping in chunk. || 316s || 33% completed, 0.5 mins elapsed, rate=22.4k fragments per second || 317s || Estimated fragment length : 495 bp || 317s || 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || 317s || 83% completed, 0.5 mins elapsed, rate=0.5k fragments per second || 317s || 91% completed, 0.6 mins elapsed, rate=0.6k fragments per second || 317s || || 317s || Completed successfully. || 317s || || 317s \\==================================== ====================================// 317s 317s //================================ Summary =================================\\ 317s || || 317s || Total fragments : 19998 || 317s || Mapped : 19491 (97.5%) || 317s || Uniquely mapped : 19491 || 317s || Multi-mapping : 0 || 317s || || 317s || Unmapped : 507 || 317s || || 317s || Properly paired : 19089 || 317s || Not properly paired : 402 || 317s || Singleton : 0 || 317s || Chimeric : 0 || 317s || Unexpected strandness : 0 || 317s || Unexpected fragment length : 385 || 317s || Unexpected read order : 17 || 317s || || 317s || Indels : 0 || 317s || || 317s || Running time : 0.6 minutes || 317s || || 317s \\============================================================================// 317s 317s 317s ========== _____ _ _ ____ _____ ______ _____ 317s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 317s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 317s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 317s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 317s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 317s v2.0.7 317s 317s //================================= setting ==================================\\ 317s || || 317s || Function : Read alignment (RNA-Seq) || 317s || Input file 1 : test-noerror-r1.fq || 317s || Input file 2 : test-noerror-r2.fq || 317s || Output file : test-tmp.sam (SAM) || 317s || Index name : small1 || 317s || || 317s || ------------------------------------ || 317s || || 317s || Threads : 1 || 317s || Phred offset : 64 || 317s || # of extracted subreads : 10 || 317s || Min read1 vote : 3 || 317s || Min read2 vote : 1 || 317s || Max fragment size : 600 || 317s || Min fragment size : 50 || 317s || Max mismatches : 3 || 317s || Max indel length : 5 || 317s || Report multi-mapping reads : no || 317s || Max alignments per multi-mapping read : 1 || 317s || || 317s \\============================================================================// 317s 317s //================= Running (15-Mar-2025 23:26:36, pid=1473) =================\\ 317s || || 317s || Check the input reads. || 317s || The input file contains base space reads. || 317s || Initialise the memory objects. || 317s || Estimate the mean read length. || 317s || The range of Phred scores observed in the data is [9,9] || 317s || Create the output SAM file. || 317s || Check the index. || 317s || Init the voting space. || 317s || Global environment is initialised. || 317s || Load the 1-th index block... || 349s || The index block has been loaded. || 349s || Start read mapping in chunk. || 349s || 33% completed, 0.5 mins elapsed, rate=23.3k fragments per second || 349s || Estimated fragment length : 495 bp || 349s || 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || 349s || 83% completed, 0.5 mins elapsed, rate=0.5k fragments per second || 350s || 91% completed, 0.5 mins elapsed, rate=0.6k fragments per second || 350s || || 350s || Completed successfully. || 350s || || 350s \\==================================== ====================================// 350s 350s //================================ Summary =================================\\ 350s || || 350s || Total fragments : 19998 || 350s || Mapped : 19491 (97.5%) || 350s || Uniquely mapped : 19491 || 350s || Multi-mapping : 0 || 350s || || 350s || Unmapped : 507 || 350s || || 350s || Properly paired : 19089 || 350s || Not properly paired : 402 || 350s || Singleton : 0 || 350s || Chimeric : 0 || 350s || Unexpected strandness : 0 || 350s || Unexpected fragment length : 385 || 350s || Unexpected read order : 17 || 350s || || 350s || Indels : 0 || 350s || || 350s || Running time : 0.5 minutes || 350s || || 350s \\============================================================================// 350s 350s 350s ========== _____ _ _ ____ _____ ______ _____ 350s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 350s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 350s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 350s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 350s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 350s v2.0.7 350s 350s //================================= setting ==================================\\ 350s || || 350s || Function : Read alignment (RNA-Seq) || 350s || Input file 1 : test-error-r1.fq || 350s || Input file 2 : test-error-r2.fq || 350s || Output file : test-tmp.sam (SAM) || 350s || Index name : small1 || 350s || || 350s || ------------------------------------ || 350s || || 350s || Threads : 1 || 350s || Phred offset : 64 || 350s || # of extracted subreads : 10 || 350s || Min read1 vote : 3 || 350s || Min read2 vote : 1 || 350s || Max fragment size : 600 || 350s || Min fragment size : 50 || 350s || Max mismatches : 3 || 350s || Max indel length : 5 || 350s || Report multi-mapping reads : no || 350s || Max alignments per multi-mapping read : 1 || 350s || || 350s \\============================================================================// 350s 350s //================= Running (15-Mar-2025 23:27:09, pid=1477) =================\\ 350s || || 350s || Check the input reads. || 350s || The input file contains base space reads. || 350s || Initialise the memory objects. || 350s || Estimate the mean read length. || 350s || The range of Phred scores observed in the data is [-14,-14] || 350s || Create the output SAM file. || 350s || Check the index. || 350s || Init the voting space. || 350s || Global environment is initialised. || 350s || Load the 1-th index block... || 382s || The index block has been loaded. || 382s || Start read mapping in chunk. || 382s || 33% completed, 0.5 mins elapsed, rate=32.8k fragments per second || 382s || Estimated fragment length : 497 bp || 382s || 74% completed, 0.5 mins elapsed, rate=0.5k fragments per second || 383s || 83% completed, 0.5 mins elapsed, rate=0.5k fragments per second || 383s || 91% completed, 0.5 mins elapsed, rate=0.6k fragments per second || 383s || || 383s || Completed successfully. || 383s || || 383s \\==================================== ====================================// 383s 383s //================================ Summary =================================\\ 383s || || 383s || Total fragments : 20000 || 383s || Mapped : 18937 (94.7%) || 383s || Uniquely mapped : 18937 || 383s || Multi-mapping : 0 || 383s || || 383s || Unmapped : 1063 || 383s || || 383s || Properly paired : 14143 || 383s || Not properly paired : 4794 || 383s || Singleton : 4504 || 383s || Chimeric : 0 || 383s || Unexpected strandness : 0 || 383s || Unexpected fragment length : 274 || 383s || Unexpected read order : 16 || 383s || || 383s || Indels : 15 || 383s || || 383s || Running time : 0.5 minutes || 383s || || 383s \\============================================================================// 383s 383s 383s ========== _____ _ _ ____ _____ ______ _____ 383s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 383s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 383s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 383s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 383s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 383s v2.0.7 383s 383s //================================= setting ==================================\\ 383s || || 383s || Function : Read alignment (RNA-Seq) || 383s || Input file 1 : test-err-mut-r1.fq.gz || 383s || Input file 2 : test-err-mut-r2.fq.gz || 383s || Output file : test-tmp.sam (SAM) || 383s || Index name : small1 || 383s || || 383s || ------------------------------------ || 383s || || 383s || Threads : 1 || 383s || Phred offset : 64 || 383s || # of extracted subreads : 10 || 383s || Min read1 vote : 3 || 383s || Min read2 vote : 1 || 383s || Max fragment size : 600 || 383s || Min fragment size : 50 || 383s || Max mismatches : 3 || 383s || Max indel length : 5 || 383s || Report multi-mapping reads : no || 383s || Max alignments per multi-mapping read : 1 || 383s || Read group name : MyTestGroup || 383s || || 383s \\============================================================================// 383s 383s //================= Running (15-Mar-2025 23:27:42, pid=1481) =================\\ 383s || || 383s ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. 383s ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. 383s 76f6c2a84c5097b13435bbeac4a8acd8 ../small1.00.b.array 383s 39cd407b95c866d7db864ce69a7d08fb ../small1.00.b.tab 383s ************************************************* 383s *** SINGLE-END READS NO ERROR ****** 383s ************************************************* 383s 383s unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 383s accuracy= 1.0 ; sensitivity= 0.9393439343934393 383s paired_match= 0 ; paired= 0.0 383s ************************************************* 383s *** SINGLE-END READS NO ERROR NO DUP ****** 383s ************************************************* 383s 383s unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 383s accuracy= 1.0 ; sensitivity= 0.9393439343934393 383s paired_match= 0 ; paired= 0.0 383s 383s ************************************************* 383s *** READS WITH NO ERROR ****** 383s ************************************************* 383s 383s unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 383s accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 383s paired_match= 38926 ; paired= 1.0 383s 383s ************************************************* 383s *** READS NO ERROR, NO DUPLICATED REPORT ****** 383s ************************************************* 383s 383s unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 383s accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 383s paired_match= 38926 ; paired= 1.0 383s 383s ************************************************* 383s *** READS WITH ONLY SEQUENCING ERROR ****** 383s ************************************************* 383s 383s unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 383s accuracy= 0.9980221756068325 ; sensitivity= 0.83425 383s paired_match= 28800 ; paired= 0.8647609896709104 383s 383s ************************************************* 383s *** READS WITH SEQUENCING ERROR AND MUTATION *** 383s *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** 383s ************************************************* 383s 383s unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 383s accuracy= 0.9980221756068325 ; sensitivity= 0.83425 383s paired_match= 28800 ; paired= 0.8647609896709104 383s 383s ========== _____ _ _ ____ _____ ______ _____ 383s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 383s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 383s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 383s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 383s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 383s v2.0.7 383s 383s //================================= setting ==================================\\ 383s || || 383s || Index name : small1 || 383s || Index space : base space || 383s || Memory : 8000 Mbytes || 383s || Repeat threshold : 100 repeats || 383s || Gapped index : yes || 383s || || 383s || Free / total memory : 3.5GB / 3.8GB || 383s || || 383s || Input files : 1 file in total || 383s || o chr901.fa || 383s || || 383s \\============================================================================// 383s 383s //================================= Running ==================================\\ 383s || || 383s || Check the integrity of provided reference sequences ... || 383s || There were 4 notes for reference sequences. || 383s || The notes can be found in the log file, '../small1.log'. || 383s || Scan uninformative subreads in reference sequences ... || 384s || 2 uninformative subreads were found. || 384s || These subreads were excluded from index building. || 384s || Estimate the index size... || 384s || 8%, 0 mins elapsed, rate=2619.7k bps/s || 384s || 16%, 0 mins elapsed, rate=4657.3k bps/s || 384s || 25%, 0 mins elapsed, rate=6287.4k bps/s || 384s || 33%, 0 mins elapsed, rate=7621.1k bps/s || 384s || 41%, 0 mins elapsed, rate=8732.5k bps/s || 384s || 50%, 0 mins elapsed, rate=9672.9k bps/s || 384s || 58%, 0 mins elapsed, rate=10295.2k bps/s || 384s || 66%, 0 mins elapsed, rate=11177.6k bps/s || 384s || 75%, 0 mins elapsed, rate=11788.9k bps/s || 384s || 83%, 0 mins elapsed, rate=12328.2k bps/s || 384s || 91%, 0 mins elapsed, rate=12807.7k bps/s || 384s || 0.8 GB of memory is needed for index building. || 384s || Build the index... || 384s || 8%, 0 mins elapsed, rate=366.1k bps/s || 384s || 16%, 0 mins elapsed, rate=704.5k bps/s || 384s || 25%, 0 mins elapsed, rate=1022.3k bps/s || 384s || 33%, 0 mins elapsed, rate=1320.2k bps/s || 384s || 41%, 0 mins elapsed, rate=1599.8k bps/s || 384s || 50%, 0 mins elapsed, rate=1856.1k bps/s || 384s || 58%, 0 mins elapsed, rate=2103.3k bps/s || 384s || 66%, 0 mins elapsed, rate=2336.8k bps/s || 384s || 75%, 0 mins elapsed, rate=2548.9k bps/s || 384s || 83%, 0 mins elapsed, rate=2757.6k bps/s || 384s || 91%, 0 mins elapsed, rate=2955.6k bps/s || 384s || Save current index block... || 384s || [ 0.0% finished ] || 384s || [ 10.0% finished ] || 384s || [ 20.0% finished ] || 384s || [ 30.0% finished ] || 384s || [ 40.0% finished ] || 385s || [ 50.0% finished ] || 385s || [ 60.0% finished ] || 385s || [ 70.0% finished ] || 385s || [ 80.0% finished ] || 385s || [ 90.0% finished ] || 385s || [ 100.0% finished ] || 385s || || 385s || Total running time: 0.0 minutes. || 385s || Index ../small1 was successfully built. || 385s || || 385s \\============================================================================// 385s 385s 385s ========== _____ _ _ ____ _____ ______ _____ 385s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 385s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 385s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 385s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 385s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 385s v2.0.7 385s 385s //================================= setting ==================================\\ 385s || || 385s || Function : Read alignment + Junction detection (RNA-Seq) || 385s || Input file 1 : junction-reads-A.fq || 385s || Input file 2 : junction-reads-B.fq || 385s || Output file : junctions.sam (SAM) || 385s || Index name : small1 || 385s || || 385s || ------------------------------------ || 385s || || 385s || Threads : 1 || 385s || Phred offset : 33 || 385s || # of extracted subreads : 14 || 385s || Min read1 vote : 1 || 385s || Min read2 vote : 1 || 385s || Max fragment size : 600 || 385s || Min fragment size : 50 || 385s || Max mismatches : 3 || 385s || Max indel length : 5 || 385s || Report multi-mapping reads : no || 385s || Max alignments per multi-mapping read : 1 || 385s || || 385s \\============================================================================// 385s 385s //================= Running (15-Mar-2025 23:27:44, pid=1488) =================\\ 385s || || 385s || Check the input reads. || 385s || The input file contains base space reads. || 385s || Initialise the memory objects. || 385s || Estimate the mean read length. || 385s || The range of Phred scores observed in the data is [2,41] || 385s || Create the output SAM file. || 385s || Check the index. || 385s || Init the voting space. || 385s || Global environment is initialised. || 385s || Load the 1-th index block... || 389s || The index block has been loaded. || 389s || Start read mapping in chunk. || 389s || 41% completed, 0.1 mins elapsed, rate=20.1k fragments per second || 390s || Estimated fragment length : 173 bp || 390s || 77% completed, 0.1 mins elapsed, rate=2.5k fragments per second || 390s || 87% completed, 0.1 mins elapsed, rate=2.8k fragments per second || 390s || 97% completed, 0.1 mins elapsed, rate=3.0k fragments per second || 390s || || 390s || Completed successfully. || 390s || || 390s \\==================================== ====================================// 390s 390s //================================ Summary =================================\\ 390s || || 390s || Total fragments : 16052 || 390s || Mapped : 15291 (95.3%) || 390s || Uniquely mapped : 15291 || 390s || Multi-mapping : 0 || 390s || || 390s || Unmapped : 761 || 390s || || 390s || Properly paired : 13894 || 390s || Not properly paired : 1397 || 390s || Singleton : 962 || 390s || Chimeric : 0 || 390s || Unexpected strandness : 36 || 390s || Unexpected fragment length : 335 || 390s || Unexpected read order : 64 || 390s || || 390s || Junctions : 419 || 390s || Indels : 177 || 390s || || 390s || Running time : 0.1 minutes || 390s || || 390s \\============================================================================// 390s 390s 390s ========== _____ _ _ ____ _____ ______ _____ 390s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 390s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 390s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 390s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 390s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 390s v2.0.7 390s 390s //================================= setting ==================================\\ 390s || || 390s || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || 390s || Input file 1 : junction-reads-A.fq || 390s || Input file 2 : junction-reads-B.fq || 390s || Output file : junctionsNfusions.bam (BAM) || 390s || Index name : small1 || 390s || || 390s || ------------------------------------ || 390s || || 390s || Threads : 1 || 390s || Phred offset : 33 || 390s || # of extracted subreads : 28 || 390s || Min read1 vote : 1 || 390s || Min read2 vote : 1 || 390s || Max fragment size : 600 || 390s || Min fragment size : 50 || 390s || Max mismatches : 3 || 390s || Max indel length : 5 || 390s || Report multi-mapping reads : no || 390s || Max alignments per multi-mapping read : 1 || 390s || || 390s \\============================================================================// 390s 390s //================= Running (15-Mar-2025 23:27:49, pid=1490) =================\\ 390s || || 390s || Check the input reads. || 390s || The input file contains base space reads. || 390s || Initialise the memory objects. || 390s || Estimate the mean read length. || 390s || The range of Phred scores observed in the data is [2,41] || 390s || Create the output BAM file. || 390s || Check the index. || 390s || Init the voting space. || 390s || Global environment is initialised. || 391s || Load the 1-th index block... || 394s || The index block has been loaded. || 394s || Start read mapping in chunk. || 395s || 41% completed, 0.1 mins elapsed, rate=11.9k fragments per second || 395s || Estimated fragment length : 174 bp || 396s || 77% completed, 0.1 mins elapsed, rate=2.3k fragments per second || 396s || 87% completed, 0.1 mins elapsed, rate=2.5k fragments per second || 396s || 97% completed, 0.1 mins elapsed, rate=2.7k fragments per second || 396s || || 396s || Completed successfully. || 396s || || 396s \\==================================== ====================================// 396s 396s //================================ Summary =================================\\ 396s || || 396s || Total fragments : 16052 || 396s || Mapped : 15273 (95.1%) || 396s || Uniquely mapped : 15273 || 396s || Multi-mapping : 0 || 396s || || 396s || Unmapped : 779 || 396s || || 396s || Properly paired : 13793 || 396s || Not properly paired : 1480 || 396s || Singleton : 1013 || 396s || Chimeric : 0 || 396s || Unexpected strandness : 37 || 396s || Unexpected fragment length : 368 || 396s || Unexpected read order : 62 || 396s || || 396s || Junctions : 437 || 396s || Fusions : 33 || 396s || Indels : 180 || 396s || || 396s || Running time : 0.1 minutes || 396s || || 396s \\============================================================================// 396s 396s 396s ========== _____ _ _ ____ _____ ______ _____ 396s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 396s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 396s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 396s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 396s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 396s v2.0.7 396s 396s //========================== featureCounts setting ===========================\\ 396s || || 396s || Input files : 1 SAM file || 396s || || 396s || test-minimum.sam || 396s || || 396s || Output file : test-minimum.FC || 396s || Summary : test-minimum.FC.summary || 396s || Paired-end : yes || 396s || Count read pairs : no || 396s || Annotation : test-minimum.GTF (GTF) || 396s || Dir for temp files : result || 396s || || 396s || Threads : 1 || 396s || Level : meta-feature level || 396s || Multimapping reads : not counted || 396s || Multi-overlapping reads : not counted || 396s || Min overlapping bases : 1 || 396s || || 396s \\============================================================================// 396s 396s //================================= Running ==================================\\ 396s || || 396s || Load annotation file test-minimum.GTF ... || 396s || Features : 23 || 396s || Meta-features : 7 || 396s || Chromosomes/contigs : 3 || 396s || || 396s || Process SAM file test-minimum.sam... || 396s || Paired-end reads are included. || 396s || The reads are assigned on the single-end mode. || 396s || Total alignments : 998 || 396s || Successfully assigned alignments : 389 (39.0%) || 396s || Running time : 0.00 minutes || 396s || || 396s || Write the final count table. || 396s || Write the read assignment summary. || 396s || || 396s || Summary of counting results can be found in file "result/test-minimum.FC. || 396s || summary" || 396s || || 396s \\============================================================================// 396s 396s 396s ================================================================================ 396s FeatureCounts Basic Test 396s http://subread.sourceforge.net/ 396s ================================================================================ 396s 396s ================================================================================ 396s Basic Test finished. 396s The results are in result/test-minimum.FC 396s ================================================================================ 396s 396s 396s 396s 396s ================================================================================ 396s FeatureCounts Chromosome Name Aliases Tests 396s http://subread.sourceforge.net/ 396s ================================================================================ 396s 396s Testing chromosome aliases ... [PASS] 396s 396s 396s ================================================================================ 396s FeatureCounts Chromosome Name Inference Tests 396s http://subread.sourceforge.net/ 396s ================================================================================ 396s 396s Testing automatic inference of chromosome names ... [PASS] 396s 396s mkdir: unrecognized option '--countReadPairs' 396s Try 'mkdir --help' for more information. 396s 396s ================================================================================ 396s FeatureCounts Corner Case Tests 396s http://subread.sourceforge.net/ 396s ================================================================================ 396s 396s Testing indel reads ... [PASS] 396s Testing junction reads ... [PASS] 396s Testing paired-end reads (fragment counting) ... [PASS] 396s Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] 396s Testing multi-overlapping reads ... [PASS] 396s Testing feature-level summarization ... [PASS] 396s Testing gene-level summarization ... [PASS] 396s Testing multi-mapping reads ... [PASS] 396s Testing multi-mapping reads (primary only) ... [PASS] 396s Testing both ends mapped ... [PASS] 396s Testing disallowing chimeric fragments ... [PASS] 396s Testing Allowing multi-mapped reads ... [PASS] 396s Testing not sorting input file ... [PASS] 396s Testing minimum overlapping length ... [PASS] 396s Testing minimum overlapping fraction ... [PASS] 396s Testing Largest Overlapping ... [PASS] 396s Testing paired-end distance ... [PASS] 396s Testing Read to position (5' end) ... [PASS] 396s Testing Read to position (3' end) ... [PASS] 396s Testing Read extension to the 3' end ... [PASS] 396s Testing Read extension to the 5' end ... [PASS] 397s Testing Low maxOPs value ... [PASS] 397s Testing minimum mapping quality ... [PASS] 397s Testing Ignoring duplicated reads ... [PASS] 397s Testing Fraction counting ... [PASS] 397s Testing Advanced fractions ... [PASS] 397s Testing Junction counting ... [PASS,PASS] 397s Skipping Junction counting (with genome). 397s Testing GTF format annotations ... [PASS] 397s Testing SAF format annotations ... [PASS] 397s Testing SAM format input ... [PASS] 397s Testing BAM format input ... [PASS] 397s Testing unstranded read summarization ... [PASS] 397s Testing stranded read summarization ... [PASS] 397s Testing reversely stranded read summarization ... [PASS] 397s Testing Ignoring duplicate fragments ... [PASS] 397s Testing Junction reads only ... [PASS] 397s Testing Exonic reads only ... [PASS] 397s 397s Testing intron_between ... [PASS] 397s Testing intron_between ... [PASS] 397s Testing intron_between ... [PASS] 397s Testing intron_between ... [PASS] 397s Testing across_genes ... [PASS] 397s Testing across_genes ... [PASS] 397s Testing across_genes ... [PASS] 397s Testing across_genes ... [PASS] 397s Testing across_intron ... [PASS] 397s Testing across_intron ... [PASS] 397s Testing across_intron ... [PASS] 397s Testing across_intron ... [PASS] 397s ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b 397s Check the input format ... 399s 399s ========== _____ _ _ ____ _____ ______ _____ 399s ===== / ____| | | | _ \| __ \| ____| /\ | __ \ 399s ===== | (___ | | | | |_) | |__) | |__ / \ | | | | 399s ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | 399s ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | 399s ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ 399s v2.0.7 399s 399s //============================= exactSNP setting =============================\\ 399s || || 399s || Input file : test-in.BAM (BAM) || 399s || Output file : test-out.VCF || 399s || Reference genome : chr901.fa || 399s || Temp path : || 399s || || 399s || Threads : 1 || 399s || Min supporting reads : 1 || 399s || Min pct. of supporting reads : 0.0% || 399s || Min base quality score : 13 || 399s || Number of trimmed bases : 3 || 399s || || 399s || Q value cutoff : 10E-12.0 || 399s || P value upper bound : 0.00500 || 399s || Flanking windows size : 5 || 399s || || 399s \\============================================================================// 399s 399s //====================== Running (15-Mar-2025 23:27:58) ======================\\ 399s || || 399s || Split BAM file into result/temp-snps-002082-FA163EC85920-* ... || 403s || processed block chr901@999950 by thread 1/1 [block number=1/1] || 403s  403s || || 403s || Completed successfully. || 403s || || 403s \\============================================================================// 403s 403s //================================= Summary ==================================\\ 403s || || 403s || Processed reads : 50204 || 403s || Reported SNPs : 416 || 403s || Reported indels : 22 || 403s || || 403s || Running time : 0.1 minutes || 403s || || 403s \\============================================================================// 403s 403s 403s ************************************************** 403s ************************************************** 403s *** *** 403s *** Test finished. *** 403s *** *** 403s *** Should there be any error, please visit *** 403s *** http://subread.sourceforge.net/ for more *** 403s *** information. *** 403s *** *** 403s ************************************************** 403s ************************************************** 403s 403s  403s 403s autopkgtest [23:28:02]: test subread-tests: -----------------------] 403s subread-tests PASS 403s autopkgtest [23:28:02]: test subread-tests: - - - - - - - - - - results - - - - - - - - - - 404s autopkgtest [23:28:03]: @@@@@@@@@@@@@@@@@@@@ summary 404s subread-tests PASS 421s nova [W] Skipping flock for amd64 421s Creating nova instance adt-plucky-amd64-subread-20250315-232119-juju-7f2275-prod-proposed-migration-environment-20-a5994e74-a955-4c9f-8a71-598582cfbf94 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 421s nova [W] Timed out waiting for 3fb7bcab-207c-4a2b-a088-c945a260683e to get deleted.