0s autopkgtest [10:39:39]: starting date and time: 2025-11-01 10:39:39+0000 0s autopkgtest [10:39:39]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [10:39:39]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.clc8sr61/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:scipy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scipy/1.16.3-1 -- lxd -r lxd-armhf-10.145.243.229 lxd-armhf-10.145.243.229:autopkgtest/ubuntu/resolute/armhf 20s autopkgtest [10:39:59]: testbed dpkg architecture: armhf 22s autopkgtest [10:40:01]: testbed apt version: 3.1.6ubuntu2 26s autopkgtest [10:40:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [10:40:06]: testbed release detected to be: None 35s autopkgtest [10:40:14]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 37s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [87.8 kB] 37s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [87.8 kB] 37s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [87.8 kB] 37s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2408 kB] 38s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 38s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 38s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [50.0 kB] 38s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [196 kB] 38s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 38s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1696 kB] 39s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [29.0 kB] 39s Get:13 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [311 kB] 39s Get:14 http://ftpmaster.internal/ubuntu resolute/restricted Sources [12.5 kB] 39s Get:15 http://ftpmaster.internal/ubuntu resolute/main Sources [1414 kB] 39s Get:16 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.1 MB] 43s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 43s Get:18 http://ftpmaster.internal/ubuntu resolute/restricted armhf Packages [1232 B] 43s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 46s Get:20 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [183 kB] 47s Fetched 44.5 MB in 10s (4356 kB/s) 48s Reading package lists... 54s autopkgtest [10:40:33]: upgrading testbed (apt dist-upgrade and autopurge) 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 57s The following NEW packages will be installed: 57s python3.14-gdbm 57s The following packages will be upgraded: 57s apparmor apt base-files bind9-dnsutils bind9-host bind9-libs binutils 57s binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils 57s cloud-init cloud-init-base distro-info-data dpkg dpkg-dev eject fdisk 57s gcc-15-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnu-coreutils grep 57s libapparmor1 libapt-pkg7.0 libatomic1 libaudit-common libaudit1 libbinutils 57s libblkid1 libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 libdpkg-perl 57s libdrm-common libdrm2 libelf1t64 libfdisk1 libfribidi0 libgcc-s1 57s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpg-error-l10n 57s libgpg-error0 libhogweed6t64 libjson-c5 liblastlog2-2 libmount1 57s libnettle8t64 libnewt0.52 libnftables1 libnl-3-200 libnl-route-3-200 57s libp11-kit0 libpython3.13-minimal libpython3.13-stdlib librtmp1 libseccomp2 57s libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe2 57s libsmartcols1 libstdc++6 libuchardet0 libuuid1 libxml2-16 login 57s lto-disabled-list mount nano nftables publicsuffix python-apt-common 57s python3-apt python3-bcrypt python3-blinker python3-cffi-backend python3-dbus 57s python3-gdbm python3-inflect python3-jwt python3-lazr.uri python3-markupsafe 57s python3-more-itertools python3-oauthlib python3-openssl python3-pyparsing 57s python3-yaml python3-zipp python3.13 python3.13-gdbm python3.13-minimal 57s sensible-utils sudo-rs tzdata ubuntu-pro-client ubuntu-pro-client-l10n 57s usb.ids util-linux uuid-runtime whiptail 57s 105 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 28.4 MB of archives. 57s After this operation, 1137 kB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf base-files armhf 14ubuntu4 [75.4 kB] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libatomic1 armhf 15.2.0-7ubuntu1 [7818 B] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-base armhf 15.2.0-7ubuntu1 [58.4 kB] 57s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-s1 armhf 15.2.0-7ubuntu1 [40.5 kB] 57s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++6 armhf 15.2.0-7ubuntu1 [731 kB] 58s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libapt-pkg7.0 armhf 3.1.11 [1157 kB] 58s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg armhf 1.22.21ubuntu4 [1245 kB] 58s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf grep armhf 3.12-1 [165 kB] 58s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf eject armhf 2.41.2-4ubuntu1 [65.9 kB] 58s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf fdisk armhf 2.41.2-4ubuntu1 [164 kB] 58s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libblkid1 armhf 2.41.2-4ubuntu1 [174 kB] 58s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libmount1 armhf 2.41.2-4ubuntu1 [206 kB] 58s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libsmartcols1 armhf 2.41.2-4ubuntu1 [143 kB] 58s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf mount armhf 2.41.2-4ubuntu1 [166 kB] 58s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf uuid-runtime armhf 2.41.2-4ubuntu1 [67.6 kB] 58s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libuuid1 armhf 2.41.2-4ubuntu1 [43.8 kB] 58s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libfdisk1 armhf 2.41.2-4ubuntu1 [222 kB] 58s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf bsdutils armhf 1:2.41.2-4ubuntu1 [98.2 kB] 58s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf util-linux armhf 2.41.2-4ubuntu1 [1146 kB] 58s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf bsdextrautils armhf 2.41.2-4ubuntu1 [101 kB] 58s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libselinux1 armhf 3.8.1-1build2 [81.3 kB] 58s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libseccomp2 armhf 2.6.0-2ubuntu3 [53.5 kB] 58s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf apt armhf 3.1.11 [1434 kB] 58s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf gnu-coreutils armhf 9.7-3ubuntu1 [1209 kB] 58s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit-common all 1:4.0.5-1build2 [6596 B] 58s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libcap-ng0 armhf 0.8.5-4build3 [14.0 kB] 58s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit1 armhf 1:4.0.5-1build2 [51.7 kB] 58s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf login armhf 1:4.16.0-2+really2.41.2-4ubuntu1 [109 kB] 58s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13 armhf 3.13.9-1 [753 kB] 58s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-minimal armhf 3.13.9-1 [2058 kB] 58s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-stdlib armhf 3.13.9-1 [1957 kB] 59s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-minimal armhf 3.13.9-1 [873 kB] 59s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf tzdata all 2025b-5ubuntu1 [198 kB] 59s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf liblastlog2-2 armhf 2.41.2-4ubuntu1 [34.6 kB] 59s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage-common all 3.8.1-1build1 [7916 B] 59s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libsepol2 armhf 3.9-2 [286 kB] 59s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage2 armhf 3.8.1-1build1 [89.2 kB] 59s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libgpg-error-l10n all 1.56-2 [9066 B] 59s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libgpg-error0 armhf 1.56-2 [69.2 kB] 59s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf sensible-utils all 0.0.26 [27.0 kB] 59s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf distro-info-data all 0.68 [7378 B] 59s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-girepository-2.0 armhf 1.86.0-6 [25.3 kB] 59s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-glib-2.0 armhf 2.86.1-1 [182 kB] 59s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libglib2.0-0t64 armhf 2.86.1-1 [1482 kB] 59s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libgirepository-1.0-1 armhf 1.86.0-6 [111 kB] 59s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libapparmor1 armhf 5.0.0~alpha1-0ubuntu8.1 [52.9 kB] 59s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libelf1t64 armhf 0.193-3 [50.9 kB] 59s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libfribidi0 armhf 1.0.16-3 [24.1 kB] 59s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libglib2.0-data all 2.86.1-1 [56.7 kB] 59s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libnettle8t64 armhf 3.10.2-1 [189 kB] 59s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf libhogweed6t64 armhf 3.10.2-1 [188 kB] 59s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf libjson-c5 armhf 0.18+ds-1.1 [33.3 kB] 59s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf libnewt0.52 armhf 0.52.25-1ubuntu2 [39.9 kB] 59s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf libp11-kit0 armhf 0.25.9-2 [265 kB] 59s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf libxml2-16 armhf 2.14.5+dfsg-0.2build1 [527 kB] 59s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf python-apt-common all 3.0.0ubuntu2 [21.7 kB] 59s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf python3-apt armhf 3.0.0ubuntu2 [189 kB] 59s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cffi-backend armhf 2.0.0-2 [99.1 kB] 59s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf python3-dbus armhf 1.4.0-1build1 [113 kB] 59s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf python3-yaml armhf 6.0.2-2 [181 kB] 59s Get:61 http://ftpmaster.internal/ubuntu resolute/main armhf sudo-rs armhf 0.2.8-1ubuntu5.1 [548 kB] 59s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-pro-client-l10n armhf 37.1ubuntu0 [19.8 kB] 59s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-pro-client armhf 37.1ubuntu0 [260 kB] 59s Get:64 http://ftpmaster.internal/ubuntu resolute/main armhf whiptail armhf 0.52.25-1ubuntu2 [17.1 kB] 59s Get:65 http://ftpmaster.internal/ubuntu resolute/main armhf apparmor armhf 5.0.0~alpha1-0ubuntu8.1 [631 kB] 59s Get:66 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-dnsutils armhf 1:9.20.11-1ubuntu3 [156 kB] 59s Get:67 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-host armhf 1:9.20.11-1ubuntu3 [46.5 kB] 59s Get:68 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-libs armhf 1:9.20.11-1ubuntu3 [1202 kB] 59s Get:69 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm-common all 2.4.127-1ubuntu1 [9716 B] 59s Get:70 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm2 armhf 2.4.127-1ubuntu1 [37.8 kB] 59s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf nftables armhf 1.1.5-2 [73.2 kB] 59s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf libnftables1 armhf 1.1.5-2 [329 kB] 59s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf libnl-route-3-200 armhf 3.11.0-2 [173 kB] 60s Get:74 http://ftpmaster.internal/ubuntu resolute/main armhf libnl-3-200 armhf 3.11.0-2 [51.2 kB] 60s Get:75 http://ftpmaster.internal/ubuntu resolute/main armhf libuchardet0 armhf 0.0.8-2 [74.1 kB] 60s Get:76 http://ftpmaster.internal/ubuntu resolute/main armhf nano armhf 8.6-1 [279 kB] 60s Get:77 http://ftpmaster.internal/ubuntu resolute/main armhf publicsuffix all 20251016.1743-0.1 [136 kB] 60s Get:78 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-gdbm armhf 3.13.9-1 [30.9 kB] 60s Get:79 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-gdbm armhf 3.14.0-4 [31.3 kB] 60s Get:80 http://ftpmaster.internal/ubuntu resolute/main armhf python3-gdbm armhf 3.13.9-1 [8884 B] 60s Get:81 http://ftpmaster.internal/ubuntu resolute/main armhf usb.ids all 2025.09.15-1 [224 kB] 60s Get:82 http://ftpmaster.internal/ubuntu resolute/main armhf libctf0 armhf 2.45-8ubuntu1 [75.7 kB] 60s Get:83 http://ftpmaster.internal/ubuntu resolute/main armhf libctf-nobfd0 armhf 2.45-8ubuntu1 [78.9 kB] 60s Get:84 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-arm-linux-gnueabihf armhf 2.45-8ubuntu1 [1022 kB] 60s Get:85 http://ftpmaster.internal/ubuntu resolute/main armhf libbinutils armhf 2.45-8ubuntu1 [411 kB] 60s Get:86 http://ftpmaster.internal/ubuntu resolute/main armhf binutils armhf 2.45-8ubuntu1 [3234 B] 60s Get:87 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-common armhf 2.45-8ubuntu1 [221 kB] 60s Get:88 http://ftpmaster.internal/ubuntu resolute/main armhf libsframe2 armhf 2.45-8ubuntu1 [13.3 kB] 60s Get:89 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init-base all 25.4~1gcb12e00e-0ubuntu1 [625 kB] 60s Get:90 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init all 25.4~1gcb12e00e-0ubuntu1 [2114 B] 60s Get:91 http://ftpmaster.internal/ubuntu resolute/main armhf python3-blinker all 1.9.0-2 [10.8 kB] 60s Get:92 http://ftpmaster.internal/ubuntu resolute/main armhf python3-jwt all 2.10.1-3 [21.1 kB] 60s Get:93 http://ftpmaster.internal/ubuntu resolute/main armhf python3-oauthlib all 3.3.1-1 [93.5 kB] 60s Get:94 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg-dev all 1.22.21ubuntu4 [1088 kB] 60s Get:95 http://ftpmaster.internal/ubuntu resolute/main armhf libdpkg-perl all 1.22.21ubuntu4 [280 kB] 60s Get:96 http://ftpmaster.internal/ubuntu resolute/main armhf lto-disabled-list all 71 [12.5 kB] 60s Get:97 http://ftpmaster.internal/ubuntu resolute/main armhf libbrotli1 armhf 1.1.0-2build6 [320 kB] 60s Get:98 http://ftpmaster.internal/ubuntu resolute/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-3 [52.1 kB] 60s Get:99 http://ftpmaster.internal/ubuntu resolute/main armhf python3-more-itertools all 10.8.0-1 [63.5 kB] 60s Get:100 http://ftpmaster.internal/ubuntu resolute/main armhf python3-inflect all 7.5.0-1 [33.9 kB] 60s Get:101 http://ftpmaster.internal/ubuntu resolute/main armhf python3-lazr.uri all 1.0.6-7 [13.8 kB] 60s Get:102 http://ftpmaster.internal/ubuntu resolute/main armhf python3-markupsafe armhf 3.0.3-1 [12.1 kB] 60s Get:103 http://ftpmaster.internal/ubuntu resolute/main armhf python3-openssl all 25.1.0-1 [46.4 kB] 60s Get:104 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pyparsing all 3.1.3-1 [87.0 kB] 60s Get:105 http://ftpmaster.internal/ubuntu resolute/main armhf python3-zipp all 3.23.0-1 [10.4 kB] 60s Get:106 http://ftpmaster.internal/ubuntu resolute/main armhf python3-bcrypt armhf 4.3.0-2 [251 kB] 61s Preconfiguring packages ... 61s Fetched 28.4 MB in 4s (7953 kB/s) 61s (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 ... 61081 files and directories currently installed.) 61s Preparing to unpack .../base-files_14ubuntu4_armhf.deb ... 61s Unpacking base-files (14ubuntu4) over (14ubuntu3) ... 61s Setting up base-files (14ubuntu4) ... 61s Installing new version of config file /etc/issue ... 61s Installing new version of config file /etc/issue.net ... 61s Installing new version of config file /etc/lsb-release ... 62s motd-news.service is a disabled or a static unit not running, not starting it. 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_armhf.deb ... 62s Unpacking libatomic1:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 62s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_armhf.deb ... 62s Unpacking gcc-15-base:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 62s Setting up gcc-15-base:armhf (15.2.0-7ubuntu1) ... 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_armhf.deb ... 62s Unpacking libgcc-s1:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 62s Setting up libgcc-s1:armhf (15.2.0-7ubuntu1) ... 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_armhf.deb ... 62s Unpacking libstdc++6:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 62s Setting up libstdc++6:armhf (15.2.0-7ubuntu1) ... 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../libapt-pkg7.0_3.1.11_armhf.deb ... 62s Unpacking libapt-pkg7.0:armhf (3.1.11) over (3.1.6ubuntu2) ... 63s Setting up libapt-pkg7.0:armhf (3.1.11) ... 63s (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 ... 61082 files and directories currently installed.) 63s Preparing to unpack .../dpkg_1.22.21ubuntu4_armhf.deb ... 63s Unpacking dpkg (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 63s Setting up dpkg (1.22.21ubuntu4) ... 63s (Reading database ... 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.../38-python3.13-gdbm_3.13.9-1_armhf.deb ... 71s Unpacking python3.13-gdbm (3.13.9-1) over (3.13.7-1) ... 71s Selecting previously unselected package python3.14-gdbm. 71s Preparing to unpack .../39-python3.14-gdbm_3.14.0-4_armhf.deb ... 71s Unpacking python3.14-gdbm (3.14.0-4) ... 71s Preparing to unpack .../40-python3-gdbm_3.13.9-1_armhf.deb ... 71s Unpacking python3-gdbm:armhf (3.13.9-1) over (3.13.5-1) ... 71s Preparing to unpack .../41-usb.ids_2025.09.15-1_all.deb ... 71s Unpacking usb.ids (2025.09.15-1) over (2025.07.26-1) ... 71s Preparing to unpack .../42-libctf0_2.45-8ubuntu1_armhf.deb ... 71s Unpacking libctf0:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 71s Preparing to unpack .../43-libctf-nobfd0_2.45-8ubuntu1_armhf.deb ... 71s Unpacking libctf-nobfd0:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 71s Preparing to unpack .../44-binutils-arm-linux-gnueabihf_2.45-8ubuntu1_armhf.deb ... 71s Unpacking binutils-arm-linux-gnueabihf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 71s Preparing to unpack .../45-libbinutils_2.45-8ubuntu1_armhf.deb ... 71s Unpacking libbinutils:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 71s Preparing to unpack .../46-binutils_2.45-8ubuntu1_armhf.deb ... 71s Unpacking binutils (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 71s Preparing to unpack .../47-binutils-common_2.45-8ubuntu1_armhf.deb ... 71s Unpacking binutils-common:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 71s Preparing to unpack .../48-libsframe2_2.45-8ubuntu1_armhf.deb ... 71s Unpacking libsframe2:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 71s Preparing to unpack .../49-cloud-init-base_25.4~1gcb12e00e-0ubuntu1_all.deb ... 72s Unpacking cloud-init-base (25.4~1gcb12e00e-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 72s Preparing to unpack .../50-cloud-init_25.4~1gcb12e00e-0ubuntu1_all.deb ... 72s Unpacking cloud-init (25.4~1gcb12e00e-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 72s Preparing to unpack .../51-python3-blinker_1.9.0-2_all.deb ... 72s Unpacking python3-blinker (1.9.0-2) over (1.9.0-1) ... 72s Preparing to unpack .../52-python3-jwt_2.10.1-3_all.deb ... 72s Unpacking python3-jwt (2.10.1-3) over (2.10.1-2) ... 72s Preparing to unpack .../53-python3-oauthlib_3.3.1-1_all.deb ... 72s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 72s Preparing to unpack .../54-dpkg-dev_1.22.21ubuntu4_all.deb ... 72s Unpacking dpkg-dev (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 72s Preparing to unpack .../55-libdpkg-perl_1.22.21ubuntu4_all.deb ... 72s Unpacking libdpkg-perl (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 72s Preparing to unpack .../56-lto-disabled-list_71_all.deb ... 72s Unpacking lto-disabled-list (71) over (69) ... 72s Preparing to unpack .../57-libbrotli1_1.1.0-2build6_armhf.deb ... 72s Unpacking libbrotli1:armhf (1.1.0-2build6) over (1.1.0-2build5) ... 72s Preparing to unpack .../58-librtmp1_2.4+20151223.gitfa8646d.1-3_armhf.deb ... 72s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-3) over (2.4+20151223.gitfa8646d.1-2build8) ... 72s Preparing to unpack .../59-python3-more-itertools_10.8.0-1_all.deb ... 72s Unpacking python3-more-itertools (10.8.0-1) over (10.7.0-1) ... 73s Preparing to unpack .../60-python3-inflect_7.5.0-1_all.deb ... 73s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 73s Preparing to unpack .../61-python3-lazr.uri_1.0.6-7_all.deb ... 73s Unpacking python3-lazr.uri (1.0.6-7) over (1.0.6-6) ... 73s Preparing to unpack .../62-python3-markupsafe_3.0.3-1_armhf.deb ... 73s Unpacking python3-markupsafe (3.0.3-1) over (2.1.5-1build4) ... 73s Preparing to unpack .../63-python3-openssl_25.1.0-1_all.deb ... 73s Unpacking python3-openssl (25.1.0-1) over (25.0.0-1) ... 73s Preparing to unpack .../64-python3-pyparsing_3.1.3-1_all.deb ... 73s Unpacking python3-pyparsing (3.1.3-1) over (3.1.2-1) ... 73s Preparing to unpack .../65-python3-zipp_3.23.0-1_all.deb ... 73s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 73s Preparing to unpack .../66-python3-bcrypt_4.3.0-2_armhf.deb ... 73s Unpacking python3-bcrypt (4.3.0-2) over (4.2.0-2.1build1) ... 73s Setting up python3-more-itertools (10.8.0-1) ... 73s Setting up lto-disabled-list (71) ... 73s Setting up libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) ... 73s Setting up libnewt0.52:armhf (0.52.25-1ubuntu2) ... 73s Setting up libnftables1:armhf (1.1.5-2) ... 73s Setting up nftables (1.1.5-2) ... 74s Setting up bsdextrautils (2.41.2-4ubuntu1) ... 74s Setting up python3-jwt (2.10.1-3) ... 74s Setting up distro-info-data (0.68) ... 74s Setting up libxml2-16:armhf (2.14.5+dfsg-0.2build1) ... 74s Setting up libsframe2:armhf (2.45-8ubuntu1) ... 74s Setting up python3-openssl (25.1.0-1) ... 74s Setting up python3-bcrypt (4.3.0-2) ... 74s Setting up libbrotli1:armhf (1.1.0-2build6) ... 74s Setting up binutils-common:armhf (2.45-8ubuntu1) ... 74s Setting up libctf-nobfd0:armhf (2.45-8ubuntu1) ... 74s Setting up python3-yaml (6.0.2-2) ... 75s Setting up python3-lazr.uri (1.0.6-7) ... 75s Setting up python3-zipp (3.23.0-1) ... 75s Setting up python3-markupsafe (3.0.3-1) ... 75s Setting up libelf1t64:armhf (0.193-3) ... 75s Setting up tzdata (2025b-5ubuntu1) ... 75s 75s Current default time zone: 'Etc/UTC' 75s Local time is now: Sat Nov 1 10:40:54 UTC 2025. 75s Universal Time is now: Sat Nov 1 10:40:54 UTC 2025. 75s Run 'dpkg-reconfigure tzdata' if you wish to change it. 75s 75s Setting up eject (2.41.2-4ubuntu1) ... 75s Setting up libpython3.13-minimal:armhf (3.13.9-1) ... 75s Setting up apparmor (5.0.0~alpha1-0ubuntu8.1) ... 75s Installing new version of config file /etc/apparmor.d/fusermount3 ... 75s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 75s 75s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 75s 75s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 75s 76s Reloading AppArmor profiles 76s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "bwrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "bfdd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "alsamixer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "babeld". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "bgpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "dnstracer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "eigrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "fabricd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "dig". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Unable to replace "fusermount3". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "iotop-c". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "isisd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "hostname". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "gs". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ldpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "john". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "irssi". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lsblk". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "compressor". /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "locale". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lsusb". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "linux-boot-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "mbsync". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "mosquitto". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "nhrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "notify-send". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "nslookup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ospf6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "nc.openbsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ospfd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "pathd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "pim6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "os-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "pbrd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "pimd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "qpdf". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ripd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ripngd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "openvpn". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 76s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 76s 77s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "proftpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "staticd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "systemd-detect-virt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "tinyproxy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "ssh-keyscan". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "mx-extract". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "rygel". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "/usr/sbin/chronyd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "cmds". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "tnftp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "dumpcap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "tshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "vrrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "who". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "wg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "wg-quick". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "znc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s Error: At least one profile failed to load 77s Setting up python3-inflect (7.5.0-1) ... 77s Setting up libnettle8t64:armhf (3.10.2-1) ... 77s Setting up libglib2.0-data (2.86.1-1) ... 77s Setting up python3-pyparsing (3.1.3-1) ... 77s Setting up python3.14-gdbm (3.14.0-4) ... 77s Setting up libfribidi0:armhf (1.0.16-3) ... 77s Setting up libp11-kit0:armhf (0.25.9-2) ... 77s Setting up libatomic1:armhf (15.2.0-7ubuntu1) ... 77s Setting up usb.ids (2025.09.15-1) ... 77s Setting up libdpkg-perl (1.22.21ubuntu4) ... 77s Setting up libfdisk1:armhf (2.41.2-4ubuntu1) ... 77s Setting up nano (8.6-1) ... 77s Installing new version of config file /etc/nanorc ... 77s Setting up whiptail (0.52.25-1ubuntu2) ... 77s Setting up python-apt-common (3.0.0ubuntu2) ... 77s Setting up libhogweed6t64:armhf (3.10.2-1) ... 77s Setting up mount (2.41.2-4ubuntu1) ... 77s Setting up sensible-utils (0.0.26) ... 77s Setting up uuid-runtime (2.41.2-4ubuntu1) ... 78s uuidd.service is a disabled or a static unit not running, not starting it. 78s Setting up libuchardet0:armhf (0.0.8-2) ... 78s Setting up libnl-3-200:armhf (3.11.0-2) ... 78s Setting up python3.13-minimal (3.13.9-1) ... 79s Setting up libbinutils:armhf (2.45-8ubuntu1) ... 79s Setting up libgpg-error-l10n (1.56-2) ... 79s Setting up libdrm-common (2.4.127-1ubuntu1) ... 79s Setting up libpython3.13-stdlib:armhf (3.13.9-1) ... 79s Setting up libjson-c5:armhf (0.18+ds-1.1) ... 79s Setting up publicsuffix (20251016.1743-0.1) ... 79s Setting up sudo-rs (0.2.8-1ubuntu5.1) ... 79s Setting up python3-cffi-backend:armhf (2.0.0-2) ... 79s Setting up python3.13-gdbm (3.13.9-1) ... 79s Setting up login (1:4.16.0-2+really2.41.2-4ubuntu1) ... 79s Setting up python3-blinker (1.9.0-2) ... 79s Setting up libctf0:armhf (2.45-8ubuntu1) ... 79s Setting up bind9-libs:armhf (1:9.20.11-1ubuntu3) ... 79s Setting up python3.13 (3.13.9-1) ... 80s Setting up python3-gdbm:armhf (3.13.9-1) ... 80s Setting up python3-apt (3.0.0ubuntu2) ... 80s Setting up fdisk (2.41.2-4ubuntu1) ... 80s Setting up libnl-route-3-200:armhf (3.11.0-2) ... 80s Setting up libglib2.0-0t64:armhf (2.86.1-1) ... 80s No schema files found: doing nothing. 80s Setting up python3-oauthlib (3.3.1-1) ... 81s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-3) ... 81s Setting up gir1.2-glib-2.0:armhf (2.86.1-1) ... 81s Setting up libdrm2:armhf (2.4.127-1ubuntu1) ... 81s Setting up libgirepository-1.0-1:armhf (1.86.0-6) ... 81s Setting up bind9-host (1:9.20.11-1ubuntu3) ... 81s Setting up binutils-arm-linux-gnueabihf (2.45-8ubuntu1) ... 81s Setting up ubuntu-pro-client (37.1ubuntu0) ... 81s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 81s 81s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 81s 81s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 81s 82s Setting up ubuntu-pro-client-l10n (37.1ubuntu0) ... 82s Setting up python3-dbus (1.4.0-1build1) ... 82s Setting up binutils (2.45-8ubuntu1) ... 82s Setting up cloud-init-base (25.4~1gcb12e00e-0ubuntu1) ... 82s Encountered debconf setting for cloud-init-base/datasources. 84s Setting up dpkg-dev (1.22.21ubuntu4) ... 84s Setting up gir1.2-girepository-2.0:armhf (1.86.0-6) ... 84s Setting up bind9-dnsutils (1:9.20.11-1ubuntu3) ... 84s Setting up cloud-init (25.4~1gcb12e00e-0ubuntu1) ... 84s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 84s Processing triggers for systemd (257.9-0ubuntu2) ... 84s Processing triggers for man-db (2.13.1-1) ... 86s Processing triggers for plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu1) ... 86s Processing triggers for procps (2:4.0.4-8ubuntu3) ... 86s Processing triggers for install-info (7.1.1-1ubuntu1) ... 86s Processing triggers for libc-bin (2.42-0ubuntu3) ... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s Solving dependencies... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s autopkgtest [10:41:11]: rebooting testbed after setup commands that affected boot 133s autopkgtest [10:41:52]: testbed running kernel: Linux 6.8.0-86-generic #87~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 29 09:26:46 UTC 2 157s autopkgtest [10:42:16]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 174s Get:1 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (dsc) [2291 B] 174s Get:2 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (tar) [22.3 MB] 174s Get:3 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (diff) [9656 B] 174s gpgv: Signature made Tue Oct 21 17:53:35 2025 UTC 174s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 174s gpgv: Can't check signature: No public key 174s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build3.dsc: no acceptable signature found 174s autopkgtest [10:42:33]: testing package tombo version 1.5.1-7build3 176s autopkgtest [10:42:35]: build not needed 182s autopkgtest [10:42:41]: test run-unit-test: preparing testbed 183s Reading package lists... 184s Building dependency tree... 184s Reading state information... 184s Solving dependencies... 184s The following NEW packages will be installed: 184s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 184s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 184s libjs-underscore liblapack3 liblzf1 libqhull-r8.0 libsz2 python3-decorator 184s python3-h5py python3-h5py-serial python3-mappy python3-numpy 184s python3-numpy-dev python3-packaging python3-scipy python3-tqdm 184s sphinx-rtd-theme-common tombo tombo-doc 185s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 185s Need to get 62.7 MB of archives. 185s After this operation, 212 MB of additional disk space will be used. 185s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-lato all 2.015-1 [2781 kB] 185s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 185s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-6build1 [133 kB] 185s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-7ubuntu1 [334 kB] 185s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-6build1 [2091 kB] 185s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 186s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 186s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 186s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libaec0 armhf 1.1.4-2 [21.1 kB] 186s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libsz2 armhf 1.1.4-2 [5322 B] 186s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-310 armhf 1.14.5+repack-3build1 [1411 kB] 186s Get:12 http://ftpmaster.internal/ubuntu resolute/universe armhf libhdf5-hl-310 armhf 1.14.5+repack-3build1 [58.9 kB] 186s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 186s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 186s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 186s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf liblzf1 armhf 3.6-4 [6554 B] 186s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 186s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 186s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py-serial armhf 3.13.0-1ubuntu1 [1109 kB] 186s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-h5py all 3.13.0-1ubuntu1 [8230 B] 186s Get:21 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-mappy armhf 2.27+dfsg-1build3 [205 kB] 186s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf python3-packaging all 25.0-1 [52.8 kB] 186s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-tqdm all 4.67.1-5 [92.1 kB] 186s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 186s Get:25 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf python3-scipy armhf 1.16.3-1 [18.2 MB] 187s Get:26 http://ftpmaster.internal/ubuntu resolute/universe armhf tombo armhf 1.5.1-7build3 [507 kB] 188s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 188s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf tombo-doc all 1.5.1-7build3 [21.7 MB] 190s Fetched 62.7 MB in 5s (13.2 MB/s) 190s Selecting previously unselected package fonts-lato. 190s (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 ... 61071 files and directories currently installed.) 190s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 190s Unpacking fonts-lato (2.015-1) ... 190s Selecting previously unselected package python3-numpy-dev:armhf. 190s Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 190s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 190s Selecting previously unselected package libblas3:armhf. 190s Preparing to unpack .../02-libblas3_3.12.1-6build1_armhf.deb ... 190s Unpacking libblas3:armhf (3.12.1-6build1) ... 190s Selecting previously unselected package libgfortran5:armhf. 190s Preparing to unpack .../03-libgfortran5_15.2.0-7ubuntu1_armhf.deb ... 190s Unpacking libgfortran5:armhf (15.2.0-7ubuntu1) ... 190s Selecting previously unselected package liblapack3:armhf. 190s Preparing to unpack .../04-liblapack3_3.12.1-6build1_armhf.deb ... 190s Unpacking liblapack3:armhf (3.12.1-6build1) ... 190s Selecting previously unselected package python3-numpy. 190s Preparing to unpack .../05-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 190s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 190s Selecting previously unselected package fonts-font-awesome. 190s Preparing to unpack .../06-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 190s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 190s Selecting previously unselected package fonts-mathjax. 190s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 190s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 190s Selecting previously unselected package libaec0:armhf. 190s Preparing to unpack .../08-libaec0_1.1.4-2_armhf.deb ... 190s Unpacking libaec0:armhf (1.1.4-2) ... 190s Selecting previously unselected package libsz2:armhf. 190s Preparing to unpack .../09-libsz2_1.1.4-2_armhf.deb ... 190s Unpacking libsz2:armhf (1.1.4-2) ... 190s Selecting previously unselected package libhdf5-310:armhf. 190s Preparing to unpack .../10-libhdf5-310_1.14.5+repack-3build1_armhf.deb ... 190s Unpacking libhdf5-310:armhf (1.14.5+repack-3build1) ... 190s Selecting previously unselected package libhdf5-hl-310:armhf. 190s Preparing to unpack .../11-libhdf5-hl-310_1.14.5+repack-3build1_armhf.deb ... 190s Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3build1) ... 190s Selecting previously unselected package libjs-jquery. 191s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 191s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 191s Selecting previously unselected package libjs-underscore. 191s Preparing to unpack .../13-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 191s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 191s Selecting previously unselected package libjs-sphinxdoc. 191s Preparing to unpack .../14-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 191s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 191s Selecting previously unselected package liblzf1:armhf. 191s Preparing to unpack .../15-liblzf1_3.6-4_armhf.deb ... 191s Unpacking liblzf1:armhf (3.6-4) ... 191s Selecting previously unselected package libqhull-r8.0:armhf. 191s Preparing to unpack .../16-libqhull-r8.0_2020.2-6build1_armhf.deb ... 191s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 191s Selecting previously unselected package python3-decorator. 191s Preparing to unpack .../17-python3-decorator_5.2.1-2_all.deb ... 191s Unpacking python3-decorator (5.2.1-2) ... 191s Selecting previously 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using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 193s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 195s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 195s Setting up tombo-doc (1.5.1-7build3) ... 195s Setting up libhdf5-310:armhf (1.14.5+repack-3build1) ... 195s Setting up libhdf5-hl-310:armhf (1.14.5+repack-3build1) ... 195s Setting up python3-scipy (1.16.3-1) ... 199s Setting up python3-h5py-serial (3.13.0-1ubuntu1) ... 199s Setting up python3-h5py (3.13.0-1ubuntu1) ... 199s Setting up tombo (1.5.1-7build3) ... 200s Processing triggers for man-db (2.13.1-1) ... 200s Processing triggers for libc-bin (2.42-0ubuntu3) ... 209s autopkgtest [10:43:08]: test run-unit-test: [----------------------- 211s ********* Testing help commands ********** 211s usage: tombo [-h] [-v] 211s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 211s 211s ********** Tombo ********* 211s 211s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 211s 211s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 211s 211s Tombo command groups (additional help available within each command group): 211s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 211s preprocess Pre-process nanopore reads for Tombo processing. 211s filter Apply filter to Tombo index file for specified criterion. 211s detect_modifications Perform statistical testing to detect non-standard nucleotides. 211s text_output Output Tombo results in text files. 211s build_model Create canonical and alternative base Tombo models. 211s plot Save plots to visualize raw nanopore signal or testing results. 211s 211s options: 211s -h, --help show this help message and exit 211s -v, --version show Tombo version and exit. 211s usage: tombo resquiggle [--dna] [--rna] 211s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 211s [--q-score Q_SCORE] 211s [--signal-matching-score SIGNAL_MATCHING_SCORE] 211s [--processes PROCESSES] 211s [--corrected-group CORRECTED_GROUP] 211s [--basecall-group BASECALL_GROUP] 211s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 211s [--overwrite] 211s [--failed-reads-filename FAILED_READS_FILENAME] 211s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 211s [--print-advanced-arguments] [--quiet] [--help] 211s fast5s_basedir reference 211s 211s Required Arguments: 211s fast5s_basedir Directory containing fast5 files. All files ending in 211s "fast5" found recursively within this base directory 211s will be processed. 211s reference Reference genome/transcriptome FASTA file or minimap2 211s index (with "map-ont" preset) for mapping. 211s 211s Model Parameters: 211s --dna Explicitly select canonical DNA model. Default: 211s Automatically determine from FAST5s 211s --rna Explicitly select canonical RNA model. Default: 211s Automatically determine from FAST5s 211s 211s Read Filtering Argument: 211s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 211s Filter reads based on observations per base percentile 211s thresholds. Format thresholds as "percentile:thresh 211s [pctl2:thresh2 ...]". For example to filter reads with 211s 99th pctl > 200 obs/base or max > 5k obs/base use 211s "99:200 100:5000". 211s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 211s Default: 0.000000 211s --signal-matching-score SIGNAL_MATCHING_SCORE 211s Observed to expected signal matching score (higher 211s score indicates poor matching). Sample type defaults: 211s RNA : 2 || DNA : 1.1 211s 211s Multiprocessing Arguments: 211s --processes PROCESSES 211s Number of processes. Default: 1 211s 211s FAST5 Data Arguments: 211s --corrected-group CORRECTED_GROUP 211s FAST5 group created by resquiggle command. Default: 211s RawGenomeCorrected_000 211s --basecall-group BASECALL_GROUP 211s FAST5 group obtain original basecalls (under Analyses 211s group). Default: Basecall_1D_000 211s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 211s FAST5 subgroup(s) (under /Analyses/[--basecall- 211s group]/) containing basecalls and created within 211s [--corrected-group] containing re-squiggle results. 211s Default: ['BaseCalled_template'] 211s --overwrite Overwrite previous corrected group in FAST5 files. 211s Note: only effects --corrected-group or --new- 211s corrected-group. 211s 211s Input/Output Arguments: 211s --failed-reads-filename FAILED_READS_FILENAME 211s Output failed read filenames with assoicated error. 211s Default: Do not store failed reads. 211s --num-most-common-errors NUM_MOST_COMMON_ERRORS 211s Dynamically show this many most common errors so far 211s through run. Default: 0; Just show progress 211s 211s Advanced Arguments: 211s --print-advanced-arguments 211s Print advanced re-squiggle arguments and exit. 211s 211s Miscellaneous Arguments: 211s --quiet, -q Don't print status information. 211s --help, -h Print this help message and exit 212s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 212s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 212s [--basecall-group BASECALL_GROUP] 212s [--basecall-subgroup BASECALL_SUBGROUP] 212s [--overwrite] 212s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 212s [--processes PROCESSES] 212s [--quiet] [--help] 212s 212s Required Arguments: 212s --fast5-basedir FAST5_BASEDIR 212s Directory containing fast5 files. 212s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 212s FASTQ filenames containing basecalls to be added to 212s raw FAST5 files. 212s 212s FAST5 Data Arguments: 212s --basecall-group BASECALL_GROUP 212s FAST5 group obtain original basecalls (under Analyses 212s group). Default: Basecall_1D_000 212s --basecall-subgroup BASECALL_SUBGROUP 212s FAST5 subgroup (under /Analyses/[--basecall-group]/) 212s under which to store basecalls from FASTQs. Default: 212s BaseCalled_template 212s --overwrite Overwrite previous corrected group in FAST5 files. 212s Note: only effects --corrected-group or --new- 212s corrected-group. 212s 212s Sequencing Summary Argument: 212s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 212s Sequencing summary filenames produced by albacore. 212s These can make annotation of raw FAST5 files with 212s FASTQ sequence much faster. 212s 212s Multiprocessing Argument: 212s --processes PROCESSES 212s Number of processes. Default: 1 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo filter clear_filters 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s [--corrected-group CORRECTED_GROUP] 212s [--quiet] [--help] 212s 212s Required Argument: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s 212s FAST5 Data Argument: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 212s [--corrected-group CORRECTED_GROUP] [--quiet] 212s [--help] 212s 212s Required Argument: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s 212s Read Filtering Argument: 212s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 212s Filter reads based on observations per base percentile 212s thresholds. Format thresholds as "percentile:thresh 212s [pctl2:thresh2 ...]". For example to filter reads with 212s 99th pctl > 200 obs/base or max > 5k obs/base use 212s "99:200 100:5000". 212s 212s FAST5 Data Argument: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo filter level_coverage 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s [--percent-to-filter PERCENT_TO_FILTER] 212s [--corrected-group CORRECTED_GROUP] 212s [--quiet] [--help] 212s 212s Required Arguments: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s 212s Read Filtering Argument: 212s --percent-to-filter PERCENT_TO_FILTER 212s Percentage of all reads to filter. Reads are randomly 212s selected weighted according to the approximate 212s coverage at the mapped genomic location. This can be 212s useful in modeling and testing. Default: 10.000000 212s 212s FAST5 Data Arguments: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo filter q_score 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s [--q-score Q_SCORE] 212s [--corrected-group CORRECTED_GROUP] 212s [--basecall-group BASECALL_GROUP] [--quiet] 212s [--help] 212s 212s Required Arguments: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s 212s Read Filtering Argument: 212s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 212s Default: 7.000000 212s 212s FAST5 Data Arguments: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s --basecall-group BASECALL_GROUP 212s FAST5 group obtain original basecalls (under Analyses 212s group). Default: Basecall_1D_000 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo filter raw_signal_matching 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s --signal-matching-score SIGNAL_MATCHING_SCORE 212s [--corrected-group CORRECTED_GROUP] 212s [--quiet] [--help] 212s 212s Required Arguments: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s --signal-matching-score SIGNAL_MATCHING_SCORE 212s Observed to expected signal matching score (higher 212s score indicates poor matching). Sample type defaults: 212s RNA : 2 || DNA : 1.1 212s 212s FAST5 Data Arguments: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo filter genome_locations 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 212s [--include-partial-overlap] 212s [--corrected-group CORRECTED_GROUP] 212s [--quiet] [--help] 212s 212s Required Arguments: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 212s Filter out reads not falling completely within include 212s regions. Omit start and end coordinates to include an 212s entire chromosome/sequence record. Format regions as 212s "chrm[:start-end] [chrm2[:start2-end2] ...]". 212s 212s Filter Argument: 212s --include-partial-overlap 212s Include reads that partially overlap the specified 212s region. Default: Only include reads completely 212s contained in a specified region 212s 212s FAST5 Data Argument: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo detect_modifications de_novo 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s --statistics-file-basename STATISTICS_FILE_BASENAME 212s [--dna] [--rna] 212s [--fishers-method-context FISHERS_METHOD_CONTEXT] 212s [--minimum-test-reads MINIMUM_TEST_READS] 212s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 212s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 212s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 212s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 212s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 212s [--processes PROCESSES] 212s [--corrected-group CORRECTED_GROUP] 212s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 212s [--quiet] [--help] 212s 212s Required Argument: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s --statistics-file-basename STATISTICS_FILE_BASENAME 212s File base name to save base by base statistics from 212s testing. Filenames will be [--statistics-file- 212s basename].[--alternate-bases]?.tombo.stats 212s 212s Comparison Model Arguments: 212s --dna Explicitly select canonical DNA model. Default: 212s Automatically determine from FAST5s 212s --rna Explicitly select canonical RNA model. Default: 212s Automatically determine from FAST5s 212s 212s Significance Test Arguments: 212s --fishers-method-context FISHERS_METHOD_CONTEXT 212s Number of context bases up and downstream over which 212s to compute Fisher's method combined p-values. Note: 212s Not applicable for alternative model likelihood ratio 212s tests. Default: 1. 212s --minimum-test-reads MINIMUM_TEST_READS 212s Number of reads required at a position to perform 212s significance testing or contribute to model 212s estimation. Default: 1 212s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 212s P-value threshold when computing fraction of 212s significant reads at each genomic position. If two 212s values are provided, statistics between these values 212s are not considered. Default thresholds: DNA:0.15-0.5 , 212s RNA:0.05-0.4 212s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 212s Dampen fraction modified estimates for low coverage 212s sites. Two parameters are unmodified and modified 212s pseudo read counts. This is equivalent to a beta prior 212s on the fraction estimate. Set to "0 0" to disable 212s dampened fraction estimation. Default: [2, 0] 212s 212s Output Argument: 212s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 212s Base for binary files containing per-read statistics 212s from statistical testing. Filenames will be [--per- 212s read-statistics-basename].[--alternate- 212s bases]?.tombo.per_read_stats 212s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 212s Number of the most significant sites to store for 212s faster access. If a longer list of most significant 212s sites is required the list must be re-computed from 212s all batches. Very large values can increase RAM usage. 212s Default: 100000 212s 212s Multiprocessing Arguments: 212s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 212s Size of regions over which to multiprocesses statistic 212s computation. For very deep samples a smaller value is 212s recommmended in order to control memory consumption. 212s Default: 10000 212s --processes PROCESSES 212s Number of processes. Default: 1 212s 212s FAST5 Data Arguments: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 212s FAST5 subgroup(s) (under /Analyses/[--basecall- 212s group]/) containing basecalls and created within 212s [--corrected-group] containing re-squiggle results. 212s Default: ['BaseCalled_template'] 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo detect_modifications alternative_model 212s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 212s [--statistics-file-basename STATISTICS_FILE_BASENAME] 212s [--alternate-bases {CpG,dam,5mC,dcm,6mA} [{CpG,dam,5mC,dcm,6mA} ...]] 212s [--print-available-models] 212s [--dna] [--rna] 212s [--minimum-test-reads MINIMUM_TEST_READS] 212s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 212s [--standard-log-likelihood-ratio] 212s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 212s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 212s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 212s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 212s [--processes PROCESSES] 212s [--corrected-group CORRECTED_GROUP] 212s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 212s [--quiet] [--help] 212s 212s Required Argument: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s --statistics-file-basename STATISTICS_FILE_BASENAME 212s File base name to save base by base statistics from 212s testing. Filenames will be [--statistics-file- 212s basename].[--alternate-bases]?.tombo.stats 212s --alternate-bases {CpG,dam,5mC,dcm,6mA} [{CpG,dam,5mC,dcm,6mA} ...] 212s Default non-standard base model for testing (not 212s required if user created --alternate-model-filenames 212s is provided). 212s 212s Comparison Arguments: 212s --print-available-models 212s Print available alternative models and exit. 212s --dna Explicitly select canonical DNA model. Default: 212s Automatically determine from FAST5s 212s --rna Explicitly select canonical RNA model. Default: 212s Automatically determine from FAST5s 212s 212s Significance Test Arguments: 212s --minimum-test-reads MINIMUM_TEST_READS 212s Number of reads required at a position to perform 212s significance testing or contribute to model 212s estimation. Default: 1 212s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 212s Log likelihood ratio threshold when computing fraction 212s of significant reads at each genomic position. If two 212s values are provided, statistics between these values 212s are not considered. Default thresholds: DNA:-1.5-2.5 , 212s RNA:-2.5-2.5 212s --standard-log-likelihood-ratio 212s Use a standard log likelihood ratio (LLR) statistic. 212s Default is to use an outlier-robust LLR-like 212s statistic. Detail in full online documentation. 212s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 212s Dampen fraction modified estimates for low coverage 212s sites. Two parameters are unmodified and modified 212s pseudo read counts. This is equivalent to a beta prior 212s on the fraction estimate. Set to "0 0" to disable 212s dampened fraction estimation. Default: [2, 0] 212s 212s Output Argument: 212s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 212s Base for binary files containing per-read statistics 212s from statistical testing. Filenames will be [--per- 212s read-statistics-basename].[--alternate- 212s bases]?.tombo.per_read_stats 212s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 212s Number of the most significant sites to store for 212s faster access. If a longer list of most significant 212s sites is required the list must be re-computed from 212s all batches. Very large values can increase RAM usage. 212s Default: 100000 212s 212s Multiprocessing Arguments: 212s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 212s Size of regions over which to multiprocesses statistic 212s computation. For very deep samples a smaller value is 212s recommmended in order to control memory consumption. 212s Default: 10000 212s --processes PROCESSES 212s Number of processes. Default: 1 212s 212s FAST5 Data Arguments: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 212s FAST5 subgroup(s) (under /Analyses/[--basecall- 212s group]/) containing basecalls and created within 212s [--corrected-group] containing re-squiggle results. 212s Default: ['BaseCalled_template'] 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 212s usage: tombo detect_modifications model_sample_compare 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s --statistics-file-basename STATISTICS_FILE_BASENAME 212s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 212s [--sample-only-estimates] 212s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 212s [--dna] [--rna] 212s [--fishers-method-context FISHERS_METHOD_CONTEXT] 212s [--minimum-test-reads MINIMUM_TEST_READS] 212s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 212s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 212s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 212s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 212s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 212s [--processes PROCESSES] 212s [--corrected-group CORRECTED_GROUP] 212s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 212s [--quiet] [--help] 212s 212s Required Argument: 212s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 212s Directories containing fast5 files. 212s --statistics-file-basename STATISTICS_FILE_BASENAME 212s File base name to save base by base statistics from 212s testing. Filenames will be [--statistics-file- 212s basename].[--alternate-bases]?.tombo.stats 212s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 212s Set of directories containing fast5 files for control 212s reads, containing only canonical nucleotides. 212s 212s Model Prior Arguments: 212s --sample-only-estimates 212s Only use canonical sample to estimate expected signal 212s level and spread. Default: Use canonical model to 212s improve estimtates (esp. for low coverage regions) 212s using baysian posterior estimates. 212s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 212s Prior weights (one each for mean and spread) applied 212s to canonical base model for estimating posterior model 212s parameters for sample comparison. Default: [5, 40] 212s --dna Explicitly select canonical DNA model. Default: 212s Automatically determine from FAST5s 212s --rna Explicitly select canonical RNA model. Default: 212s Automatically determine from FAST5s 212s 212s Significance Test Arguments: 212s --fishers-method-context FISHERS_METHOD_CONTEXT 212s Number of context bases up and downstream over which 212s to compute Fisher's method combined p-values. Note: 212s Not applicable for alternative model likelihood ratio 212s tests. Default: 1. 212s --minimum-test-reads MINIMUM_TEST_READS 212s Number of reads required at a position to perform 212s significance testing or contribute to model 212s estimation. Default: 1 212s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 212s P-value threshold when computing fraction of 212s significant reads at each genomic position. If two 212s values are provided, statistics between these values 212s are not considered. Default thresholds: DNA:0.15-0.5 , 212s RNA:0.05-0.4 212s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 212s Dampen fraction modified estimates for low coverage 212s sites. Two parameters are unmodified and modified 212s pseudo read counts. This is equivalent to a beta prior 212s on the fraction estimate. Set to "0 0" to disable 212s dampened fraction estimation. Default: [2, 0] 212s 212s Output Argument: 212s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 212s Base for binary files containing per-read statistics 212s from statistical testing. Filenames will be [--per- 212s read-statistics-basename].[--alternate- 212s bases]?.tombo.per_read_stats 212s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 212s Number of the most significant sites to store for 212s faster access. If a longer list of most significant 212s sites is required the list must be re-computed from 212s all batches. Very large values can increase RAM usage. 212s Default: 100000 212s 212s Multiprocessing Arguments: 212s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 212s Size of regions over which to multiprocesses statistic 212s computation. For very deep samples a smaller value is 212s recommmended in order to control memory consumption. 212s Default: 10000 212s --processes PROCESSES 212s Number of processes. Default: 1 212s 212s FAST5 Data Arguments: 212s --corrected-group CORRECTED_GROUP 212s FAST5 group created by resquiggle command. Default: 212s RawGenomeCorrected_000 212s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 212s FAST5 subgroup(s) (under /Analyses/[--basecall- 212s group]/) containing basecalls and created within 212s [--corrected-group] containing re-squiggle results. 212s Default: ['BaseCalled_template'] 212s 212s Miscellaneous Arguments: 212s --quiet, -q Don't print status information. 212s --help, -h Print this help message and exit 213s usage: tombo detect_modifications level_sample_compare 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s --statistics-file-basename STATISTICS_FILE_BASENAME 213s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 213s [--fishers-method-context FISHERS_METHOD_CONTEXT] 213s [--minimum-test-reads MINIMUM_TEST_READS] 213s [--statistic-type {ks,u,t}] 213s [--store-p-value] 213s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 213s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 213s [--processes PROCESSES] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Argument: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s --statistics-file-basename STATISTICS_FILE_BASENAME 213s File base name to save base by base statistics from 213s testing. Filenames will be [--statistics-file- 213s basename].[--alternate-bases]?.tombo.stats 213s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for 213s alternate set of reads. 213s 213s Significance Test Arguments: 213s --fishers-method-context FISHERS_METHOD_CONTEXT 213s Number of context bases up and downstream over which 213s to compute Fisher's method combined p-values. Note: 213s Not applicable for alternative model likelihood ratio 213s tests. Default: 1. 213s --minimum-test-reads MINIMUM_TEST_READS 213s Number of reads required at a position to perform 213s significance testing or contribute to model 213s estimation. Default: 50 213s --statistic-type {ks,u,t} 213s Type of statistical test to apply. Default: "ks" 213s --store-p-value Store p-value instead of effect-size statistic. 213s Statistics are D-statistic (KS-test), deviation from 213s even common language effect size (u-test), and Cohen's 213s D (t-test). 213s 213s Output Argument: 213s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 213s Number of the most significant sites to store for 213s faster access. If a longer list of most significant 213s sites is required the list must be re-computed from 213s all batches. Very large values can increase RAM usage. 213s Default: 100000 213s 213s Multiprocessing Arguments: 213s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 213s Size of regions over which to multiprocesses statistic 213s computation. For very deep samples a smaller value is 213s recommmended in order to control memory consumption. 213s Default: 10000 213s --processes PROCESSES 213s Number of processes. Default: 1 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo detect_modifications aggregate_per_read_stats 213s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 213s --statistics-filename STATISTICS_FILENAME 213s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 213s [--minimum-test-reads MINIMUM_TEST_READS] 213s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 213s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 213s [--processes PROCESSES] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Argument: 213s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 213s Binary file containing per-read statistics from 213s statistical testing. 213s --statistics-filename STATISTICS_FILENAME 213s File to save/load genomic base anchored statistics. 213s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 213s P-value or log likelihood ratio threshold when 213s computing fraction of significant reads at each 213s genomic position. If two values are provided, 213s statistics between these values are not considered. 213s 213s Significance Test Arguments: 213s --minimum-test-reads MINIMUM_TEST_READS 213s Number of reads required at a position to perform 213s significance testing or contribute to model 213s estimation. Default: 1 213s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 213s Dampen fraction modified estimates for low coverage 213s sites. Two parameters are unmodified and modified 213s pseudo read counts. This is equivalent to a beta prior 213s on the fraction estimate. Set to "0 0" to disable 213s dampened fraction estimation. Default: [2, 0] 213s 213s Output Argument: 213s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 213s Number of the most significant sites to store for 213s faster access. If a longer list of most significant 213s sites is required the list must be re-computed from 213s all batches. Very large values can increase RAM usage. 213s Default: 100000 213s 213s Multiprocessing Arguments: 213s --processes PROCESSES 213s Number of processes. Default: 1 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo text_output browser_files 213s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 213s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 213s [--statistics-filename STATISTICS_FILENAME] 213s [--genome-fasta GENOME_FASTA] 213s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 213s [--browser-file-basename BROWSER_FILE_BASENAME] 213s [--file-types {coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} [{coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} ...]] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Data Arguments: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for control 213s reads, containing only canonical nucleotides. 213s --statistics-filename STATISTICS_FILENAME 213s File to save/load genomic base anchored statistics. 213s 213s Statistic Motif Filter Arguments: 213s --genome-fasta GENOME_FASTA 213s FASTA file used to re-squiggle. For faster sequence 213s access. 213s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 213s Ground truth, motif centered, modified base 213s descriptions for output filtering. Format descriptions 213s as: "motif:mod_pos:name". The mod_pos indicates the 213s modified base within the motif (1-based index). 213s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 213s output for identification of E. coli dam and dcm 213s methylation. 213s 213s Output Arguments: 213s --browser-file-basename BROWSER_FILE_BASENAME 213s Basename for output browser files. Two files (plus and 213s minus strand) will be produced for each --file-types 213s supplied. Filenames formatted as "[browser-file- 213s basename].[file- 213s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 213s Default: tombo_results 213s --file-types {coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} [{coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} ...] 213s Data types of genome browser files to produce. 213s Produced coverage files are in bedGraph format, while 213s all other file types will be in wiggle format 213s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 213s Default: "coverage" 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo text_output signif_sequence_context 213s --statistics-filename STATISTICS_FILENAME 213s [--genome-fasta GENOME_FASTA] 213s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 213s [--num-regions NUM_REGIONS] 213s [--num-bases NUM_BASES] 213s [--sequences-filename SEQUENCES_FILENAME] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Argument: 213s --statistics-filename STATISTICS_FILENAME 213s File to save/load genomic base anchored statistics. 213s 213s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 213s --genome-fasta GENOME_FASTA 213s FASTA file used to re-squiggle. For faster sequence 213s access. 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s 213s Region Selection Arguments: 213s --num-regions NUM_REGIONS 213s Number of regions to plot. Default: 100 213s --num-bases NUM_BASES 213s Number of bases to plot/output. Default: 15 213s 213s Output Arguments: 213s --sequences-filename SEQUENCES_FILENAME 213s File for sequences from selected regions. Sequences 213s will be stored in FASTA format. Default: 213s tombo_results.significant_regions.fasta. 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo plot max_coverage 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 213s [--plot-standard-model] 213s [--plot-alternate-model {CpG,dam,6mA,5mC,dcm}] 213s [--overplot-threshold OVERPLOT_THRESHOLD] 213s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 213s [--num-regions NUM_REGIONS] 213s [--num-bases NUM_BASES] 213s [--pdf-filename PDF_FILENAME] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Argument: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s 213s Comparison Arguments: 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for control 213s reads, containing only canonical nucleotides. 213s --plot-standard-model 213s Add default standard model distribution to the plot. 213s --plot-alternate-model {CpG,dam,6mA,5mC,dcm} 213s Add alternative model distribution to the plot. 213s 213s Overplotting Arguments: 213s --overplot-threshold OVERPLOT_THRESHOLD 213s Coverage level to trigger alternative plot type 213s instead of raw signal. Default: 50 213s --overplot-type {Downsample,Boxplot,Quantile,Density} 213s Plot type for regions with higher coverage. Default: 213s Downsample 213s 213s Plotting Region Arguments: 213s --num-regions NUM_REGIONS 213s Number of regions to plot. Default: 10 213s --num-bases NUM_BASES 213s Number of bases to plot/output. Default: 21 213s 213s Output Argument: 213s --pdf-filename PDF_FILENAME 213s PDF filename to store plot(s). Default: 213s tombo_results.max_coverage.pdf 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo plot genome_locations 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 213s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 213s [--plot-standard-model] 213s [--plot-alternate-model {5mC,6mA,dam,dcm,CpG}] 213s [--overplot-threshold OVERPLOT_THRESHOLD] 213s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 213s [--num-bases NUM_BASES] 213s [--pdf-filename PDF_FILENAME] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Arguments: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 213s Genomic locations at which to plot signal. Format 213s locations as "chrm:position[:strand] 213s [chrm2:position2[:strand2] ...]" (strand not 213s applicable for all applications) 213s 213s Comparison Arguments: 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for control 213s reads, containing only canonical nucleotides. 213s --plot-standard-model 213s Add default standard model distribution to the plot. 213s --plot-alternate-model {5mC,6mA,dam,dcm,CpG} 213s Add alternative model distribution to the plot. 213s 213s Overplotting Arguments: 213s --overplot-threshold OVERPLOT_THRESHOLD 213s Coverage level to trigger alternative plot type 213s instead of raw signal. Default: 50 213s --overplot-type {Downsample,Boxplot,Quantile,Density} 213s Plot type for regions with higher coverage. Default: 213s Downsample 213s 213s Plotting Region Argument: 213s --num-bases NUM_BASES 213s Number of bases to plot/output. Default: 21 213s 213s Output Argument: 213s --pdf-filename PDF_FILENAME 213s PDF filename to store plot(s). Default: 213s tombo_results.genome_locations.pdf 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo plot motif_centered 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s --motif MOTIF --genome-fasta GENOME_FASTA 213s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 213s [--plot-standard-model] 213s [--plot-alternate-model {dcm,dam,5mC,6mA,CpG}] 213s [--overplot-threshold OVERPLOT_THRESHOLD] 213s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 213s [--num-regions NUM_REGIONS] 213s [--num-bases NUM_BASES] [--deepest-coverage] 213s [--pdf-filename PDF_FILENAME] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Arguments: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s --motif MOTIF Motif of interest at which to plot signal and 213s statsitics. Supports IUPAC single letter codes (use T 213s for RNA). 213s --genome-fasta GENOME_FASTA 213s FASTA file used to re-squiggle. For faster sequence 213s access. 213s 213s Comparison Arguments: 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for control 213s reads, containing only canonical nucleotides. 213s --plot-standard-model 213s Add default standard model distribution to the plot. 213s --plot-alternate-model {dcm,dam,5mC,6mA,CpG} 213s Add alternative model distribution to the plot. 213s 213s Overplotting Arguments: 213s --overplot-threshold OVERPLOT_THRESHOLD 213s Coverage level to trigger alternative plot type 213s instead of raw signal. Default: 50 213s --overplot-type {Downsample,Boxplot,Quantile,Density} 213s Plot type for regions with higher coverage. Default: 213s Downsample 213s 213s Plotting Region Arguments: 213s --num-regions NUM_REGIONS 213s Number of regions to plot. Default: 10 213s --num-bases NUM_BASES 213s Number of bases to plot/output. Default: 21 213s --deepest-coverage Plot the deepest coverage regions. 213s 213s Output Argument: 213s --pdf-filename PDF_FILENAME 213s PDF filename to store plot(s). Default: 213s tombo_results.motif_centered.pdf 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo plot max_difference 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s [--overplot-threshold OVERPLOT_THRESHOLD] 213s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 213s [--num-regions NUM_REGIONS] 213s [--num-bases NUM_BASES] 213s [--pdf-filename PDF_FILENAME] 213s [--sequences-filename SEQUENCES_FILENAME] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Arguments: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for control 213s reads, containing only canonical nucleotides. 213s 213s Overplotting Arguments: 213s --overplot-threshold OVERPLOT_THRESHOLD 213s Coverage level to trigger alternative plot type 213s instead of raw signal. Default: 50 213s --overplot-type {Downsample,Boxplot,Quantile,Density} 213s Plot type for regions with higher coverage. Default: 213s Downsample 213s 213s Plotting Region Arguments: 213s --num-regions NUM_REGIONS 213s Number of regions to plot. Default: 10 213s --num-bases NUM_BASES 213s Number of bases to plot/output. Default: 21 213s 213s Output Arguments: 213s --pdf-filename PDF_FILENAME 213s PDF filename to store plot(s). Default: 213s tombo_results.max_difference.pdf 213s --sequences-filename SEQUENCES_FILENAME 213s File for sequences from selected regions. Sequences 213s will be stored in FASTA format. Default: None. 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo plot most_significant 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s --statistics-filename STATISTICS_FILENAME 213s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 213s [--plot-standard-model] 213s [--plot-alternate-model {CpG,dam,6mA,dcm,5mC}] 213s [--overplot-threshold OVERPLOT_THRESHOLD] 213s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 213s [--num-regions NUM_REGIONS] 213s [--num-bases NUM_BASES] 213s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 213s [--pdf-filename PDF_FILENAME] 213s [--sequences-filename SEQUENCES_FILENAME] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Arguments: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s --statistics-filename STATISTICS_FILENAME 213s File to save/load genomic base anchored statistics. 213s 213s Comparison Arguments: 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for control 213s reads, containing only canonical nucleotides. 213s --plot-standard-model 213s Add default standard model distribution to the plot. 213s --plot-alternate-model {CpG,dam,6mA,dcm,5mC} 213s Add alternative model distribution to the plot. 213s 213s Overplotting Arguments: 213s --overplot-threshold OVERPLOT_THRESHOLD 213s Coverage level to trigger alternative plot type 213s instead of raw signal. Default: 50 213s --overplot-type {Downsample,Boxplot,Quantile,Density} 213s Plot type for regions with higher coverage. Default: 213s Downsample 213s 213s Plotting Region Arguments: 213s --num-regions NUM_REGIONS 213s Number of regions to plot. Default: 10 213s --num-bases NUM_BASES 213s Number of bases to plot/output. Default: 21 213s 213s Statistical Argument: 213s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 213s Dampen fraction modified estimates for low coverage 213s sites. Two parameters are unmodified and modified 213s pseudo read counts. This is equivalent to a beta prior 213s on the fraction estimate. Set to "0 0" to disable 213s dampened fraction estimation. Default: [2, 0] 213s 213s Output Arguments: 213s --pdf-filename PDF_FILENAME 213s PDF filename to store plot(s). Default: 213s tombo_results.significant_difference.pdf 213s --sequences-filename SEQUENCES_FILENAME 213s File for sequences from selected regions. Sequences 213s will be stored in FASTA format. Default: None. 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 213s usage: tombo plot motif_with_stats 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s --motif MOTIF 213s --statistics-filename STATISTICS_FILENAME 213s --genome-fasta GENOME_FASTA 213s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 213s [--plot-standard-model] 213s [--plot-alternate-model {CpG,dam,5mC,6mA,dcm}] 213s [--overplot-threshold OVERPLOT_THRESHOLD] 213s [--num-regions NUM_REGIONS] 213s [--num-context NUM_CONTEXT] 213s [--num-statistics NUM_STATISTICS] 213s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 213s [--pdf-filename PDF_FILENAME] 213s [--corrected-group CORRECTED_GROUP] 213s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 213s [--quiet] [--help] 213s 213s Required Arguments: 213s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 213s Directories containing fast5 files. 213s --motif MOTIF Motif of interest at which to plot signal and 213s statsitics. Supports IUPAC single letter codes (use T 213s for RNA). 213s --statistics-filename STATISTICS_FILENAME 213s File to save/load genomic base anchored statistics. 213s --genome-fasta GENOME_FASTA 213s FASTA file used to re-squiggle. For faster sequence 213s access. 213s 213s Comparison Arguments: 213s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 213s Set of directories containing fast5 files for control 213s reads, containing only canonical nucleotides. 213s --plot-standard-model 213s Add default standard model distribution to the plot. 213s --plot-alternate-model {CpG,dam,5mC,6mA,dcm} 213s Add alternative model distribution to the plot. 213s 213s Overplotting Argument: 213s --overplot-threshold OVERPLOT_THRESHOLD 213s Coverage level to trigger alternative plot type 213s instead of raw signal. Default: 50 213s 213s Plotting Region Arguments: 213s --num-regions NUM_REGIONS 213s Number of regions to plot. Default: 3 213s --num-context NUM_CONTEXT 213s Number of context bases around motif. Default: 5 213s --num-statistics NUM_STATISTICS 213s Number of motif centered regions to include in 213s statistic distributions. Default: 200 213s 213s Statistical Argument: 213s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 213s Dampen fraction modified estimates for low coverage 213s sites. Two parameters are unmodified and modified 213s pseudo read counts. This is equivalent to a beta prior 213s on the fraction estimate. Set to "0 0" to disable 213s dampened fraction estimation. Default: [2, 0] 213s 213s Output Argument: 213s --pdf-filename PDF_FILENAME 213s PDF filename to store plot(s). Default: 213s tombo_results.motif_statistics.pdf 213s 213s FAST5 Data Arguments: 213s --corrected-group CORRECTED_GROUP 213s FAST5 group created by resquiggle command. Default: 213s RawGenomeCorrected_000 213s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 213s FAST5 subgroup(s) (under /Analyses/[--basecall- 213s group]/) containing basecalls and created within 213s [--corrected-group] containing re-squiggle results. 213s Default: ['BaseCalled_template'] 213s 213s Miscellaneous Arguments: 213s --quiet, -q Don't print status information. 213s --help, -h Print this help message and exit 214s usage: tombo plot per_read 214s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 214s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 214s [--genome-fasta GENOME_FASTA] 214s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 214s [--num-reads NUM_READS] [--num-bases NUM_BASES] 214s [--box-center] [--pdf-filename PDF_FILENAME] 214s [--corrected-group CORRECTED_GROUP] 214s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 214s [--quiet] [--help] 214s 214s Required Arguments: 214s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 214s Genomic locations at which to plot signal. Format 214s locations as "chrm:position[:strand] 214s [chrm2:position2[:strand2] ...]" (strand not 214s applicable for all applications) 214s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 214s Binary file containing per-read statistics from 214s statistical testing. 214s 214s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 214s --genome-fasta GENOME_FASTA 214s FASTA file used to re-squiggle. For faster sequence 214s access. 214s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s Directories containing fast5 files. 214s 214s Plotting Region Arguments: 214s --num-reads NUM_READS 214s Number of reads to plot. Default: 100 214s --num-bases NUM_BASES 214s Number of bases to plot/output. Default: 51 214s --box-center Plot a box around the central base. 214s 214s Output Argument: 214s --pdf-filename PDF_FILENAME 214s PDF filename to store plot(s). Default: 214s tombo_results.per_read_stats.pdf 214s 214s FAST5 Data Arguments: 214s --corrected-group CORRECTED_GROUP 214s FAST5 group created by resquiggle command. Default: 214s RawGenomeCorrected_000 214s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 214s FAST5 subgroup(s) (under /Analyses/[--basecall- 214s group]/) containing basecalls and created within 214s [--corrected-group] containing re-squiggle results. 214s Default: ['BaseCalled_template'] 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo plot roc 214s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 214s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 214s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 214s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 214s [--genome-fasta GENOME_FASTA] 214s [--pdf-filename PDF_FILENAME] 214s [--statistics-per-block STATISTICS_PER_BLOCK] 214s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 214s [--quiet] [--help] 214s 214s Required Argument: 214s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 214s Files to load genomic base anchored statistics. 214s 214s Ground Truth Arguments (provide bed files or motifs): 214s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 214s Modification description and bed format files 214s containing single base locations of ground truth 214s modified sites. Bed files should contain 6 fields 214s including strand. Format descriptions as 214s "mod_name:locs.bed". Example: "CpG 214s bisulfite":bisulfite_locs.bed 214s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 214s Bed format files containing single base locations of 214s ground truth unmodified sites. Bed files should 214s contain 6 fields including strand. 214s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 214s Ground truth, motif centered, modified base 214s descriptions for computing ROC and PR curves. Each 214s statistics file is associated with a set of motif 214s descriptions. Format descriptions as: 214s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 214s mod_pos indicates the alternate-base within the motif 214s (1-based index). Example: CCWGG:2:"dcm 214s 5mC"::GATC:2:"dam 6mA" would assess the performance of 214s a single Tombo statistics file for identification of 214s E. coli dam and dcm methylation. 214s --genome-fasta GENOME_FASTA 214s FASTA file used to re-squiggle. For faster sequence 214s access. 214s 214s Output Arguments: 214s --pdf-filename PDF_FILENAME 214s PDF filename to store plot(s). Default: 214s tombo_results.roc.pdf 214s 214s Down-sampling Arguments: 214s --statistics-per-block STATISTICS_PER_BLOCK 214s Number of randomly selected per-read, per-base 214s statistics to extract from each genomic block for 214s plotting. Default: Include all stats 214s --total-statistics-limit TOTAL_STATISTICS_LIMIT 214s Total per-read statistics to be extracted for 214s plotting. Avoids memory overflow for large runs. 214s Default: 5000000 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo plot per_read_roc 214s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 214s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 214s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 214s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 214s [--genome-fasta GENOME_FASTA] 214s [--statistics-per-block STATISTICS_PER_BLOCK] 214s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 214s [--pdf-filename PDF_FILENAME] [--quiet] 214s [--help] 214s 214s Required Argument: 214s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 214s Binary files containing per-read statistics from 214s statistical testing. 214s 214s Ground Truth Arguments (provide bed files or motifs): 214s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 214s Modification description and bed format files 214s containing single base locations of ground truth 214s modified sites. Bed files should contain 6 fields 214s including strand. Format descriptions as 214s "mod_name:locs.bed". Example: "CpG 214s bisulfite":bisulfite_locs.bed 214s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 214s Bed format files containing single base locations of 214s ground truth unmodified sites. Bed files should 214s contain 6 fields including strand. 214s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 214s Ground truth, motif centered, modified base 214s descriptions for computing ROC and PR curves. Each 214s statistics file is associated with a set of motif 214s descriptions. Format descriptions as: 214s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 214s mod_pos indicates the alternate-base within the motif 214s (1-based index). Example: CCWGG:2:"dcm 214s 5mC"::GATC:2:"dam 6mA" would assess the performance of 214s a single Tombo statistics file for identification of 214s E. coli dam and dcm methylation. 214s --genome-fasta GENOME_FASTA 214s FASTA file used to re-squiggle. For faster sequence 214s access. 214s 214s Down-sampling Arguments: 214s --statistics-per-block STATISTICS_PER_BLOCK 214s Number of randomly selected per-read, per-base 214s statistics to extract from each genomic block for 214s plotting. Default: 100000 214s --total-statistics-limit TOTAL_STATISTICS_LIMIT 214s Total per-read statistics to be extracted for 214s plotting. Avoids memory overflow for large runs. 214s Default: 5000000 214s 214s Output Arguments: 214s --pdf-filename PDF_FILENAME 214s PDF filename to store plot(s). Default: 214s tombo_results.per_reads_roc.pdf 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s [--upstream-bases {0,1,2,3,4}] 214s [--downstream-bases {0,1,2,3,4}] [--read-mean] 214s [--num-kmer-threshold NUM_KMER_THRESHOLD] 214s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 214s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 214s [--corrected-group CORRECTED_GROUP] 214s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 214s [--quiet] [--help] 214s 214s Required Argument: 214s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s Directories containing fast5 files. 214s 214s Data Processing Arguments: 214s --upstream-bases {0,1,2,3,4} 214s Upstream bases in k-mer. Default: 1 214s --downstream-bases {0,1,2,3,4} 214s Downstream bases in k-mer. Default: 2 214s --read-mean Plot k-mer means across whole reads as opposed to 214s individual k-mer event levels. 214s --num-kmer-threshold NUM_KMER_THRESHOLD 214s Observations of each k-mer required to include a read 214s in read level averages. Default: 1 214s 214s Plotting Region Arguments: 214s --num-reads NUM_READS 214s Number of reads to plot. Default: 100 214s 214s Output Arguments: 214s --pdf-filename PDF_FILENAME 214s PDF filename to store plot(s). Default: 214s tombo_results.kmer_distribution.pdf 214s --r-data-filename R_DATA_FILENAME 214s Filename to save R data structure. Default: Don't save 214s --dont-plot Don't plot result. Useful to produce only R data file. 214s 214s FAST5 Data Arguments: 214s --corrected-group CORRECTED_GROUP 214s FAST5 group created by resquiggle command. Default: 214s RawGenomeCorrected_000 214s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 214s FAST5 subgroup(s) (under /Analyses/[--basecall- 214s group]/) containing basecalls and created within 214s [--corrected-group] containing re-squiggle results. 214s Default: ['BaseCalled_template'] 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo plot cluster_most_significant 214s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 214s --statistics-filename STATISTICS_FILENAME 214s [--genome-fasta GENOME_FASTA] 214s [--processes PROCESSES] 214s [--num-regions NUM_REGIONS] 214s [--num-bases NUM_BASES] 214s [--slide-span SLIDE_SPAN] 214s [--pdf-filename PDF_FILENAME] 214s [--r-data-filename R_DATA_FILENAME] 214s [--corrected-group CORRECTED_GROUP] 214s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 214s [--quiet] [--help] 214s 214s Required Arguments: 214s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s Directories containing fast5 files. 214s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 214s Set of directories containing fast5 files for control 214s reads, containing only canonical nucleotides. 214s --statistics-filename STATISTICS_FILENAME 214s File to save/load genomic base anchored statistics. 214s 214s FASTA Sequence Argument: 214s --genome-fasta GENOME_FASTA 214s FASTA file used to re-squiggle. For faster sequence 214s access. 214s 214s Multiprocessing Argument: 214s --processes PROCESSES 214s Number of processes. Default: 1 214s 214s Plotting Region Arguments: 214s --num-regions NUM_REGIONS 214s Number of regions to plot. Default: 10 214s --num-bases NUM_BASES 214s Number of bases to plot/output. Default: 21 214s --slide-span SLIDE_SPAN 214s Number of bases offset over which to search when 214s computing distances for signal cluster plotting. 214s Default: 0 (exact position) 214s 214s Output Arguments: 214s --pdf-filename PDF_FILENAME 214s PDF filename to store plot(s). Default: 214s tombo_results.signal_clusters.pdf 214s --r-data-filename R_DATA_FILENAME 214s Filename to save R data structure. Default: Don't save 214s 214s FAST5 Data Arguments: 214s --corrected-group CORRECTED_GROUP 214s FAST5 group created by resquiggle command. Default: 214s RawGenomeCorrected_000 214s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 214s FAST5 subgroup(s) (under /Analyses/[--basecall- 214s group]/) containing basecalls and created within 214s [--corrected-group] containing re-squiggle results. 214s Default: ['BaseCalled_template'] 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 214s 214s Required Arguments: 214s fast5s_basedir Directory containing fast5 files. All files ending in 214s "fast5" found recursively within this base directory will be 214s processed. 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo build_model event_resquiggle 214s [--minimap2-executable MINIMAP2_EXECUTABLE] 214s [--minimap2-index MINIMAP2_INDEX] 214s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 214s [--graphmap-executable GRAPHMAP_EXECUTABLE] 214s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 214s [--normalization-type {median,pA,pA_raw,none}] 214s [--pore-model-filename PORE_MODEL_FILENAME] 214s [--outlier-threshold OUTLIER_THRESHOLD] 214s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 214s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 214s [--timeout TIMEOUT] 214s [--cpts-limit CPTS_LIMIT] 214s [--skip-index] [--overwrite] 214s [--failed-reads-filename FAILED_READS_FILENAME] 214s [--include-event-stdev] 214s [--corrected-group CORRECTED_GROUP] 214s [--basecall-group BASECALL_GROUP] 214s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 214s [--processes PROCESSES] 214s [--align-processes ALIGN_PROCESSES] 214s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 214s [--resquiggle-processes RESQUIGGLE_PROCESSES] 214s [--quiet] [--help] 214s fast5s_basedir reference_fasta 214s 214s Required Arguments: 214s fast5s_basedir Directory containing fast5 files. All files ending in 214s "fast5" found recursively within this base directory 214s will be processed. 214s reference_fasta Reference genome/transcriptome FASTA file for mapping. 214s 214s Mapper Arguments (One mapper is required): 214s --minimap2-executable MINIMAP2_EXECUTABLE 214s Path to minimap2 executable. 214s --minimap2-index MINIMAP2_INDEX 214s Path to minimap2 index (with map-ont preset) file 214s corresponding to the [genome_fasta] provided. 214s --bwa-mem-executable BWA_MEM_EXECUTABLE 214s Path to bwa-mem executable. 214s --graphmap-executable GRAPHMAP_EXECUTABLE 214s Path to graphmap executable. 214s --alignment-batch-size ALIGNMENT_BATCH_SIZE 214s Number of reads included in each alignment call. Note: 214s A new system mapping call is made for each batch 214s (including loading of the genome), so it is advised to 214s use larger values for larger genomes. Default: 1000 214s 214s Signal Processing Arguments: 214s --normalization-type {median,pA,pA_raw,none} 214s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 214s as in the ONT events (using offset, range and 214s digitization), "pA": k-mer-based correction for pA 214s drift as in nanopolish (requires [--pore-model- 214s filename]), "median": median and MAD from raw signal. 214s Default: median 214s --pore-model-filename PORE_MODEL_FILENAME 214s File containing kmer model parameters (level_mean and 214s level_stdv) used in order to compute kmer-based 214s corrected pA values. E.g. https://github.com/jts/nanop 214s olish/blob/master/etc/r9- 214s models/template_median68pA.5mers.model 214s --outlier-threshold OUTLIER_THRESHOLD 214s Windosrize the signal at this number of scale values. 214s Negative value disables outlier clipping. Default: 214s 5.000000 214s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 214s Specify the 2 parameters for segmentation 1) running 214s neighboring windows width 2) minimum raw observations 214s per genomic base. Sample type defaults: RNA : 12 6 || 214s DNA : 5 3 214s 214s Read Filtering Arguments: 214s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 214s Filter reads based on observations per base percentile 214s thresholds. Format thresholds as "percentile:thresh 214s [pctl2:thresh2 ...]". For example to filter reads with 214s 99th pctl > 200 obs/base or max > 5k obs/base use 214s "99:200 100:5000". 214s --timeout TIMEOUT Timeout in seconds for processing a single read. 214s Default: No timeout. 214s --cpts-limit CPTS_LIMIT 214s Maximum number of changepoints to find within a single 214s indel group. Default: No limit. 214s 214s Input/Output Arguments: 214s --skip-index Skip creation of tombo index. This drastically slows 214s downstream tombo commands. Default stores tombo index 214s named ".[--fast5-basedir].[--corrected- 214s group].tombo.index" to be loaded automatically for 214s downstream commands. 214s --overwrite Overwrite previous corrected group in FAST5 files. 214s Note: only effects --corrected-group or --new- 214s corrected-group. 214s --failed-reads-filename FAILED_READS_FILENAME 214s Output failed read filenames with assoicated error. 214s Default: Do not store failed reads. 214s --include-event-stdev 214s Include corrected event standard deviation in output 214s FAST5 data. 214s 214s FAST5 Data Arguments: 214s --corrected-group CORRECTED_GROUP 214s FAST5 group created by resquiggle command. Default: 214s RawGenomeCorrected_000 214s --basecall-group BASECALL_GROUP 214s FAST5 group obtain original basecalls (under Analyses 214s group). Default: Basecall_1D_000 214s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 214s FAST5 subgroup(s) (under /Analyses/[--basecall- 214s group]/) containing basecalls and created within 214s [--corrected-group] containing re-squiggle results. 214s Default: ['BaseCalled_template'] 214s 214s Multiprocessing Arguments: 214s --processes PROCESSES 214s Number of processes. Default: 2 214s --align-processes ALIGN_PROCESSES 214s Number of processes to use for parsing and aligning 214s original basecalls. Each process will independently 214s load the genome into memory, so use caution with 214s larger genomes (e.g. human). Default: 1 214s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 214s Number of threads to use for aligner system call. 214s Default: [--processes] / (2 * [--align-processes)] 214s --resquiggle-processes RESQUIGGLE_PROCESSES 214s Number of processes to use for resquiggle algorithm. 214s Default: [--processes] / 2 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo build_model estimate_reference 214s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s --tombo-model-filename TOMBO_MODEL_FILENAME 214s [--estimate-mean] 214s [--kmer-specific-sd] 214s [--upstream-bases {0,1,2,3,4}] 214s [--downstream-bases {0,1,2,3,4}] 214s [--minimum-test-reads MINIMUM_TEST_READS] 214s [--coverage-threshold COVERAGE_THRESHOLD] 214s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 214s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 214s [--processes PROCESSES] 214s [--corrected-group CORRECTED_GROUP] 214s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 214s [--quiet] [--help] 214s 214s Required Arguments: 214s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s Directories containing fast5 files. 214s --tombo-model-filename TOMBO_MODEL_FILENAME 214s Filename to save Tombo model. 214s 214s Modeling Arguments: 214s --estimate-mean Use the mean instead of median for model level 214s estimation. Note: This can cause poor fits due to 214s outliers 214s --kmer-specific-sd Estimate standard deviation for each k-mers 214s individually. 214s --upstream-bases {0,1,2,3,4} 214s Upstream bases in k-mer. Default: 1 214s --downstream-bases {0,1,2,3,4} 214s Downstream bases in k-mer. Default: 2 214s 214s Filtering Arguments: 214s --minimum-test-reads MINIMUM_TEST_READS 214s Number of reads required at a position to perform 214s significance testing or contribute to model 214s estimation. Default: 10 214s --coverage-threshold COVERAGE_THRESHOLD 214s Maximum mean coverage per region when estimating k-mer 214s model (limits compute time for deep samples). Default: 214s 100 214s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 214s Number of each k-mer observations required in order to 214s produce a reference (genomic locations for standard 214s reference and per-read for alternative reference). 214s Default: 5 214s 214s Multiprocessing Arguments: 214s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 214s Size of regions over which to multiprocesses statistic 214s computation. For very deep samples a smaller value is 214s recommmended in order to control memory consumption. 214s Default: 10000 214s --processes PROCESSES 214s Number of processes. Default: 1 214s 214s FAST5 Data Arguments: 214s --corrected-group CORRECTED_GROUP 214s FAST5 group created by resquiggle command. Default: 214s RawGenomeCorrected_000 214s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 214s FAST5 subgroup(s) (under /Analyses/[--basecall- 214s group]/) containing basecalls and created within 214s [--corrected-group] containing re-squiggle results. 214s Default: ['BaseCalled_template'] 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s usage: tombo build_model estimate_alt_reference 214s --alternate-model-filename ALTERNATE_MODEL_FILENAME 214s --alternate-model-name ALTERNATE_MODEL_NAME 214s --alternate-model-base {A,C,G,T} 214s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 214s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 214s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 214s [--control-density-filename CONTROL_DENSITY_FILENAME] 214s [--dna] [--rna] 214s [--tombo-model-filename TOMBO_MODEL_FILENAME] 214s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 214s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 214s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 214s [--save-density-basename SAVE_DENSITY_BASENAME] 214s [--processes PROCESSES] 214s [--corrected-group CORRECTED_GROUP] 214s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 214s [--quiet] [--help] 214s 214s Required Arguments: 214s --alternate-model-filename ALTERNATE_MODEL_FILENAME 214s Tombo model for alternative likelihood ratio 214s significance testing. 214s --alternate-model-name ALTERNATE_MODEL_NAME 214s A short name to associate with this alternate model 214s (e.g. 5mC, 6mA, etc.). This text will be included in 214s output filenames when this model is used for testing. 214s --alternate-model-base {A,C,G,T} 214s Non-standard base is an alternative to this base. 214s 214s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 214s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 214s Directories containing fast5 files. 214s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 214s Set of directories containing fast5 files for control 214s reads, containing only canonical nucleotides. 214s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 214s File containing k-mer level kernel density estimates 214s for the alternative sample saved using --save-density- 214s basename. 214s --control-density-filename CONTROL_DENSITY_FILENAME 214s File containing k-mer level kernel density estimates 214s for the control sample saved using --save-density- 214s basename. 214s 214s Standard Model Arguments: 214s --dna Explicitly select canonical DNA model. Default: 214s Automatically determine from FAST5s 214s --rna Explicitly select canonical RNA model. Default: 214s Automatically determine from FAST5s 214s --tombo-model-filename TOMBO_MODEL_FILENAME 214s Tombo model filename. If no file is provided, the 214s default DNA or RNA Tombo model will be used. 214s 214s Model Fitting Arguments: 214s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 214s When esitmating the alternative base incorporation 214s rate, this percent of k-mers are assumed to have 214s significantly shifted signal so the alternative 214s distribution minimally overlaps the standard base 214s distribution. Default: 5.000000 214s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 214s Bandwidth applied when performing Gaussian kernal 214s density esitmation on standard and alternative base 214s signal distributions. Default: 0.050000 214s 214s Filtering Argument: 214s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 214s Number of each k-mer observations required in order to 214s produce a reference (genomic locations for standard 214s reference and per-read for alternative reference). 214s Default: 1000 214s 214s Output Argument: 214s --save-density-basename SAVE_DENSITY_BASENAME 214s Basename to save alternative model estimation density 214s estimation information. See scripts/debug_est_alt.R 214s for info use example. Default: Don't save. 214s 214s Multiprocessing Arguments: 214s --processes PROCESSES 214s Number of processes. Default: 1 214s 214s FAST5 Data Arguments: 214s --corrected-group CORRECTED_GROUP 214s FAST5 group created by resquiggle command. Default: 214s RawGenomeCorrected_000 214s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 214s FAST5 subgroup(s) (under /Analyses/[--basecall- 214s group]/) containing basecalls and created within 214s [--corrected-group] containing re-squiggle results. 214s Default: ['BaseCalled_template'] 214s 214s Miscellaneous Arguments: 214s --quiet, -q Don't print status information. 214s --help, -h Print this help message and exit 214s This test only tests the help system 214s There is an extensive test in 214s 214s tombo/tests/shell_tests.sh 214s 214s but this requires to download larger data 214s sets which is not done for the moment. 215s autopkgtest [10:43:14]: test run-unit-test: -----------------------] 218s run-unit-test PASS 218s autopkgtest [10:43:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 222s autopkgtest [10:43:21]: @@@@@@@@@@@@@@@@@@@@ summary 222s run-unit-test PASS